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This document provides an overview and specifications for several chemical structure file formats used by MDL, including Connection Table files (CTAB), Molfiles, Reaction files (Rxnfiles), and more. It describes the basic components and blocks within each file type, such as the header, atom and bond blocks in CTAB files, and molecule and reaction blocks in Rxnfiles. The document also covers enhancements to CTAB files like handling large molecules.

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CTFile Formats June 2005
June 2005 Copyright ©1995 - 2005 by MDL Information Systems, Inc (“Elsevier MDL”). All rights reserved. No part of this document may be copied for any means except as permitted in writing by Elsevier MDL, 14600 Catalina Street, San Leandro, CA 94577. MDL is a registered trademark in the U.S. and/or other countries, and ISIS is a trademark of Elsevier MDL. All other product and company names may be trademarks or registered trademarks of their respective holders in the U.S. and/or other countries. U.S. GOVERNMENT RESTRICTED RIGHTS If USER is a unit or agency of the U.S. Government or acquiring the Software with Governmental funds; (i) the Programs supplied to the U.S. Department of Defense (“DOD”) shall be subject to MDL’s standard commercial license and (ii) all Programs supplied to any unit or agency of the U.S. Government other than the DOD, shall be governed by clause 52.227-19(c) of the FAR (or any successor regulations) or, in the case of NASA, clause 48 1827.405(a) (or any successor regulations) and, in any such case, the U.S. Government acquires only “restricted rights” in the Programs. Contractor/Manufacturer is: Elsevier MDL, 14600 Catalina St., San Leandro, CA 94577
3 Contents Chapter 1: Introduction Change Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Extended Molfile Format (V3000). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Standard CTfiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Chapter 2: The Connection Table [CTAB] (V2000) Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 The Counts Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 The Atom Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 The Bond Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 The Atom List Block [Query] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 The Stext Block [MDL ISIS/Desktop] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 The Properties Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 The Properties Block for 3D Features [3D] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Chapter 3: Atom Limit Enhancements Phantom Extra Atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Superatom Attachment Point. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Superatom Class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Large REGNO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Sgroup Bracket Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Chapter 4: Molfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 The Header Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Chapter 5: RGfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Chapter 6: SDfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 SDfile after a CFS search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Chapter 7: Rxnfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4 CTFile Formats Header Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Reactants/Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Molfile Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Chapter 8: RDfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . RDfile Header . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Molecule and Reaction Identifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data-field Identifier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 49 49 50 50 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data Formatting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Hierarchy of Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Alphabetic List of Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XDfile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . DataSource. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ProgramSource. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CreatorName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CreateDate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CreateTime. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Copyright . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ParentDef . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . FieldDef . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Parent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 54 55 57 58 60 61 62 63 64 65 66 67 68 69 70 71 75 76 77 78 Chapter 9: XDfiles Chapter 10: The Extended Connection Table (V3000) Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Specifications For Atom and Bond Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . The Extended Connection Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . The Extended Rgroup Query Molfile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Automatic V3000 output. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 80 81 96 98 Chapter 11: The Extended Reaction File Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Appendix A: Stereo Notes Index
Chapter 1: Introduction Elsevier MDL supports a number of file formats for representation and communication of chemical information. This document describes the formats for Elsevier MDL’s CTfiles (chemical table files): • Chapters 2 and 3 describe the Connection Table (V2000) format. • Chapters 4 through 9 describe the standard CTfile formats. • Chapter 10 describes the V3000 extended molfile format. All extended molfiles can be easily identified by the “V3000” version stamp in the header portion of the file. You are most likely to find the extended molfile format in CTfiles written from MDL ISIS/Host or MDL ISIS/Desktop version 2.0 or higher. • Chapter 11 describes the V3000 extended rxnfile format. Change Log The following are the changes in this document: Change Page(s) June 2005 Product and company rebranding changes Fixed example in 3D feature type -5 in "The Connection Table [CTAB] (V2000)" 25 Added "Automatic V3000 Output" section in "The Extended Connection Table (V3000)" 98 October 2003 Added new chapter on XDfile format 51 Added XDfile in this Introduction 7 August 2002 Deleted chapter on moving CTfiles on/off the Clipboard Minor corrections 6, 8, 9, 13, 32, 40 Added new information on enhanced stereochemistry features 56 Added new chapter on Extended Reaction File format 62 May, 2001 Added section describing advantages of V3000 file format Added section on V3000 Collection Block Minor corrections December, 1999 Updated entries in “Atom List” December, 1998 Updated “Example of an SDfile” August, 1998 Added STBOX field
CTFile Formats June, 1997 Added Atom Attachment Order Added new ATTCHORD field October, 1996 Minor corrections Enhanced description of connection table properties block Added Sgroup bracket style Extended Molfile Format (V3000) The Extended Molfile format (V3000) molfile format offers a number of advantages over the V2000 format: • Consolidates property information for chemical objects • Provides better support for new chemical properties or objects • Removes fixed field widths to support large structures • Uses free format and tagging of information for easier parsing • Provides better support for backward compatibility through BEGIN/END blocks Current Elsevier MDL products support reading and writing of both molfile formats. These products will also preferentially write V2000 molfiles to maximize interoperability with third party applications. However, the fixed limits and distributed property information in the V2000 format make it harder to add new planned representational enhancements. The V3000 format is intended to be the primary means for communication of future enhancements to MDL chemical representation features. Note: There are situations when the V3000 format will automatically be written instead of the V2000 format. See “Automatic V3000 output” on page 98. Your code for writing molfiles should be able to export structure information in the V3000 format if any structural features are present which cannot be defined in the V2000 format. 6
Chapter 1: Introduction Standard CTfiles The following figure illustrates the relationship between the various file formats described below: molfiles Molecule files: Each molfile describes a single molecular structure which can contain disjoint fragments. RGfiles Rgroup files: An RGfile describes a single molecular query with Rgroups. Each RGfile is a combination of Ctabs defining the root molecule and each member of each Rgroup in the query. rxnfiles Reaction files: Each rxnfile contains the structural information for the reactants and products of a single reaction. Elsevier MDL currently supports only the REACCS type of rxnfile. The CPSS type of rxnfile written by CPSS programs is no longer supported and is not described in this document. SDfiles Structure-data files: An SDfile contains structures and data for any number of molecules. Together with RDfiles, SDfiles are the primary format for large-scale data transfer between MDL databases. RDfiles Reaction-data files: Similar to SDfiles in concept, the RDfile is a more general format that can include reactions as well as molecules, together with their associated data. Although RDfiles are used primarily by ISIS and REACCS, MACCS-II can also read and write RDfiles except for the reaction structure information (indicated by the square brackets in the MDL Program table). XDfiles XML-data files: XML-based data format for transferring recordsets of structure or reaction information with associated data. An XDfile can contain structures or reactions that use any of the CTfile formats, Chime strings, or SMILES strings. (Chime is an encrypted format that is used to render structures and reactions on a Web page. SMILES is a line notation format that uses character strings and SMILES, Simplified Molecule Input Line Entry System, syntax to represent a structure.) 7
CTFile Formats The following figure illustrates three examples of XDfiles: XDfile with molfile structures and associated data XDfile with rxnfile reactions and associated data XDfile with Chime strings and associated data Metadata Metadata Metadata Data Data Data Record Record Record Chime molfile rxnfile libraryID molname rxnregno dose molweight response This table shows which CTfiles MDL programs can read and write. Figure 1 MDL Programs CTfile Type MACCS-II REACCS ISIS Core Interface molfiles + + + + RGfiles + + + + + + + + + rxnfiles + SDfiles + RDfiles [+] + XDfiles + Some of the structural and query properties described in this document are generic in their applicability, while others are peculiar to certain CTfile types. The applicability of each property is identified in subsequent chapters by the bracketed terms shown in the following table. Figure 2 Properties applicable to various CTfile types Property molfile RGfile SDfile rxnfile RDfile XDfile [Generic] + + + + + + (mol/rxn) [Sgroup] + + + [+] [Rgroup] + + + + (mol) [3D] + + + + (mol) [Reaction] 8 + + (mol/[rxn]) + + (rxn)
Chapter 1: Introduction Figure 2 [Query] Properties applicable to various CTfile types + + + + (mol/rxn) Note: The XDfile inherits the functionality of the format of the embedded structure or reaction. In addition to the molfile and rxnfile formats, the XDfile supports Chime and SMILES strings. 9
CTFile Formats 10
Chapter 2: The Connection Table [CTAB] (V2000) Overview A connection table (Ctab) contains information describing the structural relationships and properties of a collection of atoms. The atoms may be wholly or partially connected by bonds. Such collections may, for example, describe molecules, molecular fragments, substructures, substituent groups, polymers, alloys, formulations, mixtures, and unconnected atoms. The connection table is fundamental to all of Elsevier MDL’s file formats. The following figure shows the connection table of a simple molecule (alanine) with the various data blocks identified. The connection table corresponds to the following alanine molecule. The atom numbers on the structure correspond to atom numbers in the Ctab. An atom number is assigned according to the order of the atom in the Atom Block. Figure 3 Connection table organization illustrated using alanine L-Alanine C hial r 13 C 3 N + 2 1 O 6 4 O 5 6 5 0 -0.6622 0.6622 -0.7207 -1.8622 0.6220 1.9464 1 2 1 1 3 1 1 4 1 2 5 2 2 6 1 M CHG 2 M ISO 1 M END 0 1 0 0.5342 -0.3000 2.0817 -0.3695 -1.8037 0.4244 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 1 6 3 13 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 3 V2000 C 0 0 C 0 0 C 1 0 N 0 3 O 0 0 O 0 5 Counts Line 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom Block Connection Table (Ctab) Bond Block -1 Blocks not used in this Ctab: Atom List, Stext Properties Block The format for a Ctab block is: Counts line: Important specifications here relate to the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version. Atom block: Specifies the atomic symbol and any mass difference, charge, stereochemistry, and associated hydrogens for each atom. Bond block: Specifies the two atoms connected by the bond, the bond type, and any bond stereochemistry and topology (chain or ring properties) for each bond. Atom list block: Identifies the atom (number) of the list and the atoms in the list. Stext (structural text descriptor) block: Used by MDL ISIS/Desktop programs. Properties block: Provides for future expandability of Ctab features, while maintaining compatibility with earlier Ctab configurations.
CTFile Formats The detailed format for each block outlined above follows: Note: A blank numerical entry on any line should be read as “0” (zero). Spaces are significant and correspond to one or more of the following: • Absence of an entry • Empty character positions within an entry • Spaces between entries; single unless specifically noted otherwise The FORTRAN f m atf coor nat i or aton i t V 2000 CTfl f m ati t caly or or di e nf m i n he ie or s ypi l F10.4. The Counts Line aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv Where:: aaa = number of atoms (current max 255)* [Generic] bbb = number of bonds (current max 255)* [Generic] lll = number of atom lists (max 30)* [Query] fff = (obsolete) ccc = chiral flag: 0=not chiral, 1=chiral [Generic] sss = number of stext entries [MDL ISIS/Desktop] xxx = (obsolete) rrr = (obsolete) ppp = (obsolete) iii = (obsolete) mmm = number of lines of additional properties, including the M END line. No longer supported, the default is set to 999. [Generic] * These limits apply to MACCS-II, REACCS, and the MDL ISIS/Host Reaction Gateway, but not to the MDL ISIS/Host Molecule Gateway or MDL ISIS/Desktop. For example, the counts line in the Ctab shown in the previous figure shows six atoms, five bonds, the CHIRAL flag on, and three lines in the properties block: 6 5 0 0 1 0 3 V2000 The Atom Block The Atom Block is made up of atom lines, one line per atom with the following format: xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee w her t val ar des i i t f l i t e: e he ues e crbed n he olow ng abl 12
Chapter 2: The Connection Table [CTAB] (V2000) Figure 4 Meaning of values in the atom block Field Meaning Values Notes xyz atom coordinates aaa atom symbol entry in periodic table or L for atom list, A, Q, * for unspecified atom, and LP for lone pair, or R# for Rgroup label [Generic, Query, 3D, Rgroup] dd mass difference -3, -2, -1, 0, 1, 2, 3, 4 (0 if value beyond these limits) [Generic] Difference from mass in periodic table. Wider range of values allowed by M ISO line, below. Retained for compatibility with older Ctabs, M ISO takes precedence. ccc charge 0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 = -3 [Generic] Wider range of values in M CHG and M RAD lines below. Retained for compatibility with older Ctabs, M CHG and M RAD lines take precedence. sss atom stereo parity 0 = not stereo, 1 = odd, 2 = even, 3 = either or unmarked stereo center [Generic] Ignored when read. hhh hydrogen count + 1 1 = H0, 2 = H1, 3 = H2, 4 = H3, 5 = H4 [Query] H0 means no H atoms allowed unless explicitly drawn. Hn means atom must have n or more H’s in excess of explicit H’s. bbb stereo care box 0 = ignore stereo configuration of this double bond atom, 1 = stereo configuration of double bond atom must match [Query] Double bond stereochemistry is considered during SSS only if both ends of the bond are marked with stereo care boxes. vvv valence 0 = no marking (default) (1 to 14) = (1 to 14) 15 = zero valence [Generic] Shows number of bonds to this atom, including bonds to implied H’s. HHH H0 designator 0 = not specified, 1 = no H atoms allowed [MDL ISIS/Desktop] Redundant with hydrogen count information. May be unsupported in future releases of Elsevier MDL software. rrr Not used iii Not used mmm atom-atom mapping number 1 - number of atoms [Reaction] nnn inversion/retention flag 0 = property not applied 1 = configuration is inverted, 2 = configuration is retained, [Reaction] eee exact change flag 0 = property not applied, 1 = change on atom must be exactly as shown [Reaction, Query] [Generic] 13
CTFile Formats W ih Ct ver i V 2000,t dd and ccc fel have been s t ab s on he i ds uper eded by t M ISO,M s he CHG,and M RAD lnesi t pr i n he operi bl tes ock,des i bel .Forcom patbiiy,al r eas crbed ow i lt l el es s nce M A CCS- I2. REA CCS 8. and M D L I S 1. i I 0, 1, SI 0: • Write appropriate values in both places if the values are in the old range. • Use the atom block fields if there are no M ISO, M CHG, or M RAD lines in the properties block. Support for these atom block fields may be removed in future releases of Elsevier MDL software. The Bond Block The Bond Block is made up of bond lines, one line per bond, with the following format: 111222tttsssxxxrrrccc where the values are described in the following table: Figure 5 Meaning of values in the bond block Field Meaning Values Notes 111 first atom number 1 - number of atoms [Generic] 222 second atom number 1 - number of atoms [Generic] ttt bond type 1 = Single, 2 = Double, 3 = Triple, 4 = Aromatic, 5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any [Query] Values 4 through 8 are for SSS queries only. sss bond stereo Single bonds: 0 = not stereo, 1 = Up, 4 = Either, 6 = Down, Double bonds: 0 = Use x-, y-, z-coords from atom block to determine cis or trans, 3 = Cis or trans (either) double bond [Generic] The wedge (pointed) end of the stereo bond is at the first atom (Field 111 above) xxx not used rrr bond topology 0 = Either, 1 = Ring, 2 = Chain [Query] SSS queries only. ccc reacting center status 0 = unmarked, 1 = a center, -1 = not a center, Additional: 2 = no change, 4 = bond made/broken, 8 = bond order changes 12 = 4+8 (both made/broken and changes); 5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) are also possible [Reaction, Query] The Atom List Block [Query] Note: Newer programs use the M ALS item in the properties block in place of the atom list block. The atom list block is retained for compatibility, but information in an M ALS item supersedes atom list block information. Made up of atom list lines, one line per list, with the following format: aaa kSSSSn 111 222 333 444 555 14
Chapter 2: The Connection Table [CTAB] (V2000) where: Field Meaning aaa = number of atom (L) where list is attached k = T = [NOT] list, = F = normal list n = number of entries in list; maximum is 5 111...555 = atomic number of each atom on the list S = space The Stext Block [MDL ISIS/Desktop] The Stext Block is made up of two-line entries with the following format: xxxxx.xxxxyyyyy.yyyy TTTT... where: Field Meaning xy = stext coordinate T = stext text The Properties Block The Properties Block is made up of mmm lines of additional properties, where mmm is the number in the counts line described above. If a version stamp is present, mmm is ignored and the file is read until an "M END" line is encountered. Currently mmm is no longer supported and is set to 999 as the default. Most lines in the properties block are identified by a prefix of the form M spaces separate the M and XXX. Exceptions are: XXX where two • A aaa, V aaa vvvvvv,and G aaappp, which indicate the following ISIS/Desktop properties: atom alias, atom value, and group abbreviation (called residue in ISIS), respectively. • S SKPnnn which causes the next nnn lines to be ignored. The prefix: M END terminates the properties block. Variables in the formats can change properties but keep the same letter designation. For example, on the Charge, Radical, or Isotope lines, the “uniformity” of the vvv designates a general property identifier. On Sgroup property lines, the sss uniformity is used as an Sgroup index identifier. All lines that are not understood by the program are ignored. The descriptions below use the following conventions for values in field widths of 3: n15 nn8 nn6 nn4 nn2 nn1 aaa number of entries on line; value = 1 to 15 number of entries on line; value = 1 to 8 number of entries on line; value = 1 to 6 number of entries on line; value = 1 to 4 number of entries on line; value = 1 or 2 number of entries on line; value = 1 atom number; value = (1 to number of atoms) 15
CTFile Formats The format for the properties included in this block follows. The format shows one entry; ellipses (. . .) indicate additional entries. Atom Alias [MDL ISIS/Desktop] A aaa x... aaa: Atom number x: Alias text Atom Value [MDL ISIS/Desktop] V aaa v... aaa: Atom number v: Value text Group Abbreviation [MDL ISIS/Desktop] G aaappp x... aaa: Atom number ppp: Atom number x: Abbreviation label Abbreviation is required for compatibility with previous versions of MDL ISIS/Desktop which allowed abbreviations with only one attachment. The attachment is denoted by two atom numbers, aaa and ppp. All of the atoms on the aaa side of the bond formed by aaa-ppp are abbreviated. The coordinates of the abbreviation are the coordinates of aaa. The text of the abbreviation is on the following line (x...). In current versions of ISIS, abbreviations can have any number of attachments and are written out using the Sgroup appendixes. However, any ISIS abbreviations that do have one attachment are also written out in the old style, again for compatibility with older ISIS versions, but this behavior might not be supported in future versions. Charge [Generic] M CHGnn8 aaa vvv ... vvv: -15 to +15. Default of 0 = uncharged atom. When present, this property supersedes all charge and radical values in the atom block, forcing a 0 charge on all atoms not listed in an M CHG or M RAD line. Radical [Generic] M RADnn8 aaa vvv ... vvv: 16 Default of 0 = no radical, 1 = singlet (:), 2 = doublet ( . or ^), 3 = triplet (^^). When present, this property supersedes all charge and radical values in the atom block, forcing a 0 (zero) charge and radical on all atoms not listed in an M CHG or M RAD line.
Chapter 2: The Connection Table [CTAB] (V2000) Isotope [Generic] M ISOnn8 aaa vvv ... vvv: Absolute mass of the atom isotope as a positive integer. When present, this property supersedes all isotope values in the atom block. Default (no entry) means natural abundance. The difference between this absolute mass value and the natural abundance value specified in the PTABLE.DAT file must be within the range of -18 to +12. Ring Bond Count [Query] M RBCnn8 aaa vvv ... vvv: Number of ring bonds allowed: default of 0 = off, -1 = no ring bonds (r0),-2 = as drawn (r*); 2 = (r2), 3 = (r3), 4 or more = (r4). Substitution Count [Query] M SUBnn8 aaa vvv ... vvv: Number of substitutions allowed: default of 0 = off, -1 = no substitution (s0),-2 = as drawn (s*); 1, 2, 3, 4, 5 = (s1) through (s5), 6 or more = (s6). Unsaturated Atom [Query] M UNSnn8 aaa vvv ... vvv: At least one multiple bond: default of 0 = off, 1 = on. Link Atom [Query] M LINnn4 aaa vvv bbb ccc vvv,bbb,ccc: Link atom (aaa) and its substituents, other than bbb and ccc, may be repeated 1 to vvv times, (vvv > = 2). The bbb and ccc parameters can be 0 (zero) for link nodes on atoms with attachment point information. Atom List [Query] M ALS aaannn e 11112222333344445555... aaa: Atom number, value nnn: Number of entries on line (16 maximum) e: Exclusion, value is T if a ’NOT’ list, F if a normal list. 1111: Atom symbol of list entry in field of width 4 Note: This line contains the atom symbol rather than the atom number used in the atom list block. Any data found in this item supersedes data from the atom list block. The number of entries can exceed the fixed limit of *5* in the atom list block entry. Attachment Point [Rgroup] M APOnn2 aaa vvv ... vvv: Indicates whether atom aaa of the Rgroup member is the first attachment point (vvv = 1), second attachment point (vvv = 2), both attachment points (vvv = 3); default of 0 = no attachment. 17
CTFile Formats Atom Attachment Order [Rgroup] M AAL aaann2 111 v1v 222 v2v ... aaa: Atom index of the Rgroup usage atom nn2: Number of pairs of entries that follow on the line 111: Atom index of a neighbor of aaa v1v Attachment order for the aaa-111 bond 222 Atom index of a neighbor of aaa v2v Attachment order for the aaa-222 bond Note: v1v and v2v are either 1 or 2 for the simple doubly attached Rgroup member. This appendix provides explicit attachment list order information for R# atoms. The appendix contains atom neighbor index and atom neighbor value pairs. The atom neighbor value information identifies the atom neighbor index as the nth attachment. The implied ordering in V2000 molfiles is by atom index order for the neighbors of Rgroup usage atoms. If atom index order conflicts with the desired neighbor ordering at the R# atom, this appendix allows you to override to this default order. If v1v=1 and v2v=2, MDL ISIS/Host only writes this appendix if 111 is greater than 222. Note, however, that the attachment values can be written in any order. Rgroup Label Location [Rgroup] M RGPnn8 aaa rrr ... rrr: Rgroup number, value from 1 to 32 *, labels position of Rgroup on root. * MACCS-II and ISIS/Desktop limit Rgroup Logic, Unsatisfied Sites, Range of Occurrence [Rgroup] M LOGnn1 rrr iii hhh ooo... rrr: Rgroup number, value from 1 to 32 * iii: Number of another Rgroup which must only be satisfied if rrr is satisfied (IF rrr THEN iii) hhh: RestH property of Rgroup rrr; default is 0 = off, 1 = on. If this property is applied (on), sites labeled with Rgroup rrr may only be substituted with a member of the Rgroup or with H ooo Range of Rgroup occurrence required: n = exactly n, n - m = n through m,> n = greater than n, < n = fewer than n, default (blank) is > 0. Any non-contradictory combination of the preceding values is also allowed; for example: 1, 3-7, 9, >11. * MACCS-II and ISIS/Desktop limit 18
Chapter 2: The Connection Table [CTAB] (V2000) Sgroup Type [Sgroup] M STYnn8 sss ttt ... sss: Sgroup number ttt: Sgroup type: SUP = superatom, MUL = multiple group, SRU = SRU type, MON = monomer, MER = Mer type, COP = copolymer, CRO = crosslink, MOD = modification, GRA = graft, COM = component, MIX = mixture, FOR = formulation, DAT = data Sgroup, ANY = any polymer, GEN = generic. Note: For a given Sgroup, an STY line giving its type must appear before any other line that supplies information about it. For a data Sgroup, an SDT line must describe the data field before the SCD and SED lines that contain the data (see Data Sgroup Data below). When a data Sgroup is linked to another Sgroup, the Sgroup must already have been defined. Sgroups can be in any order on the Sgroup Type line. Brackets are drawn around Sgroups with the M SDI lines defining the coordinates. 19
CTFile Formats Sgroup Subtype [Sgroup] M SSTnn8 sss ttt ... Polymer Sgroup subtypes: ALT = alternating, RAN = random, BLO = block ttt: Figure 6 Ctab organization of an Sgroup structure Polymer ht * 7 ht 5 6 2 n * n 1 3 ran Cl 4 GSMACCS-II10179110412D 1 7 M M M M M M M M M M M M M M M M 6 0 2.9463 1.6126 0.2789 0.2789 -1.0548 -2.3885 -3.9246 1 2 1 2 3 1 3 4 1 5 6 1 5 3 1 7 6 1 STY 3 SST 1 SLB 3 SCN 2 SAL 1 SBL 1 SDI 1 SDI 1 SAL 2 SBL 2 SDI 2 SDI 2 SAL 3 SDI 3 SDI 3 END 0.00374 0.00000 Header block (see Chapter 4 ) 0 0 0 16 V2000 0.3489 0.0000 * 0 0 0 0 0 0 1.1189 0.0000 C 0 0 0 0 0 0 0.3489 0.0000 C 0 0 3 0 0 0 -1.1911 0.0000 Cl 0 0 0 0 0 0 1.1190 0.0000 C 0 0 0 0 0 0 0.3490 0.0000 C 0 0 0 0 0 0 1.1470 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 Number of entries on line 0 0 0 0 0 0 0 0 0 0 0 0 1 SRU 2 SRU 3 COP Type Subtype 3 RAN 1 5 2 6 3 7 Label Connectivity 1 HT 2 HT 2 5 6 2 5 6 4 -0.6103 1.2969 -0.6103 0.1710 4 -3.1565 0.1850 -3.1565 1.3110 3 2 3 4 2 1 5 4 2.2794 1.2969 2.2794 0.1709 4 -0.1657 0.1710 -0.1657 1.2969 7 1 2 3 4 5 6 7 4 3.6382 1.6391 3.6382 -1.7685 4 -4.7070 -1.7685 -4.7070 1.6391 Counts line 0 Atom block Bond block General Sgroup Info Sgroup 1 Atom list block Stext block Sgroup properties Sgroup 2 Sgroup 3 Sgroup Labels [Sgroup] M SLBnn8 sss vvv ... vvv: 20 Unique Sgroup identifier (for MACCS-II only, the integer label is from 1-512) Ctab block
Chapter 2: The Connection Table [CTAB] (V2000) Sgroup Connectivity [Sgroup] M SCNnn8 sss ttt ... ttt: HH = head-to-head, HT = head-to-tail, EU = either unknown. Left justified. Sgroup Expansion [Sgroup] M SDS EXPn15 sss ... sss: Sgroup index of expanded superatoms Sgroup Atom List [Sgroup] M SAL sssn15 aaa ... aaa: Atoms in Sgroup sss Sgroup Bond List [Sgroup] M SBL sssn15 bbb ... bbb: Bonds in Sgroup sss. (For data Sgroups, bbb’s are the containment bonds, for all other Sgroup types, bbb’s are crossing bonds.) Multiple Group Parent Atom List [Sgroup] M SPA sssn15 aaa ... aaa: Atoms in paradigmatic repeating unit of multiple group sss Note: To ensure that all current molfile readers consistently interpret chemical structures, multiple groups are written in their fully expanded state to the molfile. The M SPA atom list is a subset of the full atom list that is defined by the Sgroup Atom List M SAL entry. Sgroup Subscript [Sgroup] M SMT sss m... m...: Text of subscript Sgroup sss. (For multiple groups, m... is the text representation of the multiple group multiplier. For superatoms, m... is the text of the superatom label.) Sgroup Correspondence [Sgroup] M CRS sssnn6 bb1 bb2 bb3 bb1, bb2: Crossing bonds that share a common bracket bb3: Crossing bond in repeating unit that connect to bond bb1 Sgroup Display Information [Sgroup] M SDI sssnn4 x1 y1 x2 y2 x1,y1, x2,y2: Coordinates of bracket endpoints 21
CTFile Formats Superatom Bond and Vector Information [Sgroup] M SBV sss bb1 x1 y1 bb1: Bond connecting to contracted superatom x1,y1: Vector for bond bb1 connecting to contracted superatom sss Data Sgroup Field Description [Sgroup] M SDT sss fff...fffgghhh...hhhiijjj... sss: Index of data Sgroup fff...fff: 30 character field name (in MACCS-II no blanks, commas, or hyphens) gg: Field type (in MACCS-II F = formatted, N = numeric, T = text) hhh...hhh 20-character field units or format ii: Nonblank if data line is a query rather than Sgroup data, MQ = MACCS-II query, IQ = ISIS query, PQ = program name code query jjj...: Data query operator (blank for MACCS-II) Data Sgroup Display Information [Sgroup] M SDD sss xxxxx.xxxxyyyyy.yyyy eeefgh i jjjkkk ll m sss: Index of data Sgroup x,y: Coordinates (2F10.4) eee: (Reserved for future use) f: Data display, A = attached, D = detached g: Absolute, relative placement, A = absolute, R = relative h: Display units, blank = no units displayed, U = display units i: (Reserved for future use) jjj: Number of characters to display (1...999 or ALL) kkk: Number of lines to display (unused, always 1) ll: (Reserved for future use) m: Tag character for tagged detached display (if non-blank) n: Data display DASP position (1...9). (MACCS-II only) oo: noo (Reserved for future use) Data Sgroup Data [Sgroup] M M SCD sss d... SED sss d... d...: Line of data for data Sgroup sss (69 chars per line, columns 12-80) Note: A line of data is entered as text in 69-character substrings. Each SCD line adds 69 characters to a text buffer (starting with successive SCDs at character positions 1, 70, and 139). Following zero or more SCDs must be an SED, which may supply a final 69 characters. The SED initiates processing of the buffered line of text: trailing blanks are removed and right truncation to 200 characters is performed, numeric and formatted data are validated, and the line of data is added to data Sgroup sss. Left justification is not performed. 22
Chapter 2: The Connection Table [CTAB] (V2000) A data Sgroup may have more than one line of data, so more than one set of SCD and SED lines can be present for the same data Sgroup. The lines are added in the same order that they are encountered. If 69 or fewer characters are to be entered on a line, they may be entered with a single SED not preceded by an SCD. On the other hand, if desired a line may be entered to a maximum of 3 SCDs followed by a blank SED that terminates the line. The set of SCD and SED lines describing one line of data for a given data Sgroup must appear together, with no intervening lines for other data Sgroups’ data. Sgroup Hierarchy Information [Sgroup] M SPLnn8 ccc ppp ... ccc: Sgroup index of the child Sgroup) ppp: Sgroup index of the parent Sgroup (ccc and ppp must already be defined via an STY line prior to encountering this line) Sgroup Component Numbers [Sgroup] M SNCnn8 sss ooo ... sss: Index of component Sgroup ooo: Integer component order (1...256). This limit applies only to MACCS-II 3D Feature Properties [3D] M $3Dnnn M $3D...: See below for information on the properties block of a 3D molfile. These lines must all be contiguous End of Block M END This entry goes at the end of the properties block and is required for molfiles which contain a version stamp in the counts line. The Properties Block for 3D Features [3D] For each 3D feature, the properties block includes: • One 3D features count line • One or more 3D features detail lines The characters M $3D appear at the beginning of each line describing a 3D feature. The information for 3D features starts in column 7. 23
CTFile Formats Figure 7 Ctab organization of a 3D query Normal 3D Query Exclusion sphere Point Angle Centroid o Plane 75-105 4.4-5.7 Benzene ring N Distance Nitrogen atom 3D Query MACCS-II10179109553D 1 8 M M M M M M M M M M M M M M M M M M 7 0 0 1.0252 -0.4562 -1.4813 -1.0252 0.4562 1.4813 4.1401 4.6453 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 1 2 0 7 8 1 0 $3D 7 $3D -7 6 $3D 3 $3D 6 4 $3D -5 13 $3D 6 $3D 1 2 $3D -8 7 $3D 9 10 $3D -3 6 $3D 9 11 $3D-16 12 $3D 12 1 $3D-12 10 $3D 12 9 $3D -9 3 $3D 7 9 END 0 0 0.2892 0.6578 0.3687 -0.2892 -0.6578 -0.3687 -0.1989 0.5081 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.00000 1.1122 1.3156 0.2033 -1.1122 -1.3156 -0.2033 1.3456 1.7417 18 V2000 C 0 0 C 0 0 C 0 0 C 0 0 C 0 0 C 0 0 N 0 0 C 0 0 0.00000 0 Header block (see Chapter 4) Counts line 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom block Bond block 3D Features Count Atom list block Stext block Ctab block Centroid 2 0.0000 3 4 5 Plane 6 Normal to Plane Point -2.0000 0 75.0000 Exclusion sphere 1.5000 7 4.4000 Properties block 105.0000 5.7000 Angle Distance 3D features count line The first line in the properties block is the 3D features count line and has the following format: M $3Dnnn where nnn is the number of 3D features on a model. 3D features detail lines The lines following the 3D features count line describe each 3D feature on a model. Each 3D feature description consists of an identification line and one or more data lines: 24
Chapter 2: The Connection Table [CTAB] (V2000) The identification line is the first line and contains the 3D feature’s type identifier, color, and name. Each data line describes the construction of the 3D feature. Identification line The 3D feature identification line has the following format: M $3Dfffccc aaa...aaa ttt...ttt where the variables represent: fff: 3D feature type ccc: Color number (an internal MDL number which is terminal dependent) aaa...aaa: 3D feature name (up to 32 characters) ttt...ttt: Text comments (up to 32 characters) used by MDL programs (see 3D data constraints later in this chapter) Figure 8 3D feature type identifiers Identifier Meaning -1 Point defined by two points and a distance (in Angstroms) -2 Point defined by two points and a percentage -3 Point defined by a point, a normal line, and a distance -4 Line defined by two or more points (a best fit line if more than two points) -5 Plane defined by three or more points (a best fit plane if more than three points) -6 Plane defined by a point and a line -7 Centroid defined by points -8 Normal line defined by a point and a plane -9 Distance defined by two points and a range (in Angstroms) -10 Distance defined by a point, line, and a range (in Angstroms) -11 Distance defined by a point, plane, and a range (in Angstroms) -12 Angle defined by three points and a range (in degrees) -13 Angle defined by two intersecting lines and a range (in degrees) -14 Angle defined by two intersecting planes and a range (in degrees) -15 Dihedral angle defined by 4 points and a range (in degrees) -16 Exclusion sphere defined by a point and a distance (in Angstroms) -17 Fixed atoms in the model nnn A positive integer indicates atom or atom-pair data constraints 25
CTFile Formats Data line The 3D feature defines the data line format. Each 3D object is treated as a pseudoatom and identified in the connection table by a number. The 3D object numbers are assigned sequentially, starting with the next number greater than the number of atoms. The data line formats for the 3D feature types are: Figure 9 3D feature type identifiers Type Description of Data Line -1 The data line for a point defined by two points and a distance (Å) has the following format: M $3Diiijjjddddd.dddd where the variables represent: iii: ID number of a point jjj: ID number of a second point ddddd.dddd Distance from first point in direction of second point (Å), 0 if not used The following example shows POINT_1 created from the atoms 1 and 3 with a constraint distance of 2Å. The first line is the identification line. The second line is the data line. M M -2 $3D -1 $3D 1 4 POINT_1 3 2.0000 The data line for a point defined by two points and a percentage has the format: M $3Diiijjjddddd.ddddd where the variables represent: iii jjj ID number of a second point ddddd.dddd -3 ID number of a point Distance (fractional) relative to distance between first and second points, 0 if not used The data line for a point defined by a point, a normal line, and a distance (Å) has the format: M $3Diiilllddddd.dddd where the variables represent: iii ID number of a point lll ID number of a normal line ddddd.dddd Distance (Å), 0 if not used Note: For chiral models, the distance value is signed to specify the same or opposite direction of the normal. 26
Chapter 2: The Connection Table [CTAB] (V2000) -4 The data lines for a best fit line defined by two or more points have the following format: M M $3Dpppttttt.tttt $3Diiijjj...zzz . . . where the variables represent: ppp Number of points defining the line ttttt.tttt Deviation (Å), 0 if not used. iii Each iii, jjj, and zzz is the ID number jjj of an item in the model that defines the line jjj ... (to maximum of 20 items per data line) zzz The following line is defined by the four points 1, 14, 15, and 19 and has a deviation of 1.2Å. The first line is the identification line. The second and third lines are the data lines. M M M -5 $3D -4 2 N_TO_AROM $3D 4 1.2000 $3D 1 14 15 19 The data lines for a plane defined by three or more points (a best fit plane if more than three points) have the following format: M $3Dpppttttt.tttt M $3Diiijjj...zzz ... where the variables represent: ppp Number of points defining the line ttttt.tttt Deviation (Å), 0 if not used. iii Each iii, jjj, and zzz is the ID number jjj of an item in the model that defines the plane jjj ... (to maximum of 20 items per data line) zzz The following plane is defined by the three points 1, 5, and 14. The first line is the identification line. The second and third lines are the data lines. M M M -6 $3D -5 4 PLANE_2 $3D 3 0.0000 $3D 1 5 14 The data line for a plane defined by a point and a line has the following format: M $3Diiilll where the variables represent: iii ID number of a point lll ID number of a line The following plane is defined by the point 1 and the plane 16. The first line is the identification line. The second line is the data line. M M $3D -6 3 PLANE_1 $3D 1 16 27
CTFile Formats -7 The data lines of a centroid defined by points have the following format: M M $3Dppp $3Diiijjj...zzz ... where the variables represent: ppp Number of points defining the centroid iii Each iii, jjj, and zzz is the ID number jjj of an item in the model that defines the centroid jjj ... (maximum of 20 items per data line). zzz The following centroid, ARO_CENTER, is defined by 3 items: 6, 8, and 10. The first line is the identification line. The second and third lines are the data lines. M M M -8 $3D -7 $3D 3 $3D 6 1 ARO_CENTER 8 10 The data line for a normal line defined by a point and a plane has the following format: M $3Diiijjj where the variables represent: iii ID number of a point jjj ID number of a plane The following normal line, ARO_NORMAL, is defined by the point 14 and the plane 15. The first line is the identification line. The second line is the data line. M M -9 $3D -8 1 ARO_NORMAL $3D 14 15 The data line for a distance defined by two points and a range (Å) has the following format: M $3Diiijjjddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a point jjj ID number of a second point ddddd.dddd Minimum distance (Å) zzzzz.zzzz Maximum distance (Å) The following distance, L, is between items 1 and 14 and has a minimum distance of 4.9Å and a maximum distance of 6.0Å. The first line is the identification line. The second line is the data line. M M -10 $3D -9 6 L $3D 1 14 4.9000 6.0000 The data line for a distance defined by a point, line, and a range (Å) has the format: M $3Diiilllddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a line ddddd.dddd Minimum distance (Å) zzzzz.zzzz 28 ID number of a point lll Maximum distance (Å)
Chapter 2: The Connection Table [CTAB] (V2000) -11 The data line for a distance defined by a point, plane, and a range (Å) has the format: M $3Diiijjjddddd.ddddzzzzz.zzzz where the variables represent: iii jjj ID number of a plane ddddd.dddd Minimum distance (Å) zzzzz.zzzz -12 ID number of a point Maximum distance (Å) The data line for an angle defined by three points and a range (in degrees) has the following format: M $3Diiijjjkkkddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a point jjj ID number of a second point kkk ID number of a third point ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees The following angle, THETA1, is defined by the three points: 5, 17, and 16. The minimum angle is 80° and the maximum is 105°. The first line is the identification line. The second line is the data line. M M -13 $3D-12 5 THETA1 $3D 5 17 16 80.0000 105.0000 The data line for an angle defined by two lines and a range (in degrees) has the following format: M $3Dlllmmmddddd.ddddzzzzz.zzzz where the variables represent: lll ID number of a line, mmm ID number of a second line ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees THETA2 is defined by the lines 27 and 26 with maximum and minimum angles of 45° and 80°. The first line is the identification line. The second line is the data line. M M -14 $3D-13 5 THETA2 $3D 27 26 45.0000 80.0000 The data line for an angle defined by two planes and a range (in degrees) has the following format: M $3Diiijjjddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a plane jjj ID numbers of a second plane ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees 29
CTFile Formats -15 The data line for a dihedral angle defined by four points and a range (in degrees) has the following format: M $3Diiijjjkkklllddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a point jjj ID number of a second point kkk ID number of a third point lll ID number of a fourth point ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees DIHED1 is defined by the items 7, 6, 4, and 8 with minimum and maximum angles of 45° and 80°, respectively. The first line is the identification line. The second line is the data line. M M -16 $3D-15 $3D 7 5 DIHED1 6 4 8 45.0000 80.0000 The data lines for an exclusion sphere defined by a point and a distance (Å) have the following format: M M $3Diiiuuuaaaddddd.dddd $3Dbbbccc...zzz ... where the variables represent: iii ID number of the center of the sphere uuu 1 or 0. 1 means unconnected atoms are ignored within the exclusion sphere during a search; 0 otherwise aaa Number of allowed atoms ddddd.dddd Radius of sphere (Å) bbb Each bbb, ccc, and zzz is an ID number of an allowed atom ccc ... (to maximum of 20 items per data line) zzz The following exclusion sphere is centered on point 24, has a radius of 5, and allows atom 9 within the sphere. The first line is the identification line. The second and third lines are the data lines. M M M -17 $3D-16 $3D 24 $3D 9 7 EXCL_SPHERE 0 1 5.0000 The data lines of the fixed atoms have the following format: M M $3Dppp $3Diiijjj...zzz ... where the variables represent: ppp Number of fixed points Each iii, jjj, and zzz is an ID number of a fixed atom iii jjj (to maximum of 20 items per data line) zzz The following examples shows 4 fixed atoms. The first line is the identification line. The second and third lines are the data lines. M M M 30 $3D-17 $3D 4 $3D 3 7 12 29
Chapter 2: The Connection Table [CTAB] (V2000) 3D data constraints [3D, Query] A positive integer is used as a type identifier to indicate an atom or atom-pair data constraint. Two lines are used to describe a data constraint. The lines have the following format: M M $3Dnnncccaaa...aaabbbbbbbbpppppppppsss...sss $3Diiijjjddd...ddd where the variables represent: nnn: Database-field number ccc: Color aaa...aaa: Database-field name (up to 30 characters) bbbbbbbb: /BOX = box-number (source of data) (up to 8 characters) ppppppppp: /DASP = n1, n2 where n1 and n2 are digits from 1-9 (data size and position) (up to 9 characters) sss...sss: /DISP = 3DN (name), 3DV (value), 3DQ (query), NOT (no text). First three in any combination to maximum total of 15 characters iii: ID number of an atom jjj: ID number of a second atom for atom-pair data, 0 if data is atom data ddd...ddd: Data constraint (based on format from database) (up to 64 characters) ISIS 3D data query syntax and MACCS-II 3D data query syntax are not identical. The ISIS data query requires a search operator, a blank space, then one or more operands. For more information on ISIS data query syntax, see the ISIS Help system entries on SBF (Search By Form) or QB (Query Builder) for entering text in a query. For information on MACCS-II data searches, see the MACCS-II Command Language Reference. Note: For MACCS-II, the atom number 999 stands for all atoms. The MACCS-II wild card character (@) can be used in the data constraints. The following example shows a numeric data constraint for the field CNDO.CHARGE on atom 12. The first line is the identification line. The second line is the data line. M M $3D 7 $3D 12 0 CNDO.CHARGE 0 -0.3300 -0.1300 The following example shows a numeric data constraint for the field BOND.LENGTH on the atom pair 1 and 4. The first line is the identification line. The second line is the data line. M M $3D $3D 9 1 0 BOND.LENGTH 4 2.0500 1.8200 The following example shows a data constraint allowing any charge value for the field CHARGE on all the atoms. The first line is the identification line. The second line is the data line. M M $3D 12 $3D999 0 CHARGE 0 @ 31
CTFile Formats 32
Chapter 3: Atom Limit Enhancements The formats presented in this chapter were added to support the chemical representation enhancements of MDL ISIS Desktop 2.0. Phantom Extra Atom The format for phantom extra atom information is as follows: M PXA aaaxxxxx.xxxxyyyyy.yyyyzzzzz.zzzz H e... where: aaa: Index of (real) atom for attachment xyz: Coordinates for the added atom H: Atom symbol e...: Additional text string (for example, the superatom label) The bond to the added phantom atom is added as a crossing bond to the outermost Sgroup that contains atom aaa. Note this appendix supplies coordinates and up to 35 characters of ‘label’ that can be used for the ISIS/Desktop superatom conversion mechanism. ISIS/Desktop uses this appendix to register hydrogen-only superatoms, which are often used as superatom leaving groups on the desktop, but which cannot be directly registered into ISIS/Host databases. The hydrogen-only leaving groups are converted to PXA appendices for registration, and converted back when ISIS/Desktop reads the structure. The following are limitations on phantom extra atom: • Superatom nesting cases • No bonded phantom atom-phantom atom support Superatom Attachment Point The format for superatom attachment point is as follows: M SAP sssnn6 iii ooo cc where: sss: Index of superatom Sgroup nn6: Number of iii,ooo,cc entries on the line (6 maximum) iii: Index of the attachment point atom ooo: Index of atom in sss that leaves when iii is substituted cc: 2 character attachment identifier (for example, H or T for head/tail). No validation of any kind is performed, and ‘ ’ is allowed. ISIS/Desktop uses the first character as the ID of the leaving group to attach if the bond between ooo and iii is deleted, and uses the second character to indicate the sequence polarity: l for left, r for right, and x for none (a crosslink).
CTFile Formats The bond iii-ooo is either a sequence bond, a sequence crosslink bond, or a bond to a leaving group that terminates a sequence or caps a crosslink bond. In some cases, this bond may have been deleted by the user, probably to perform a substructure search. In this case, ooo will be 0. If the leaving group attached to iii consists of only a hydrogen, the leaving group will be replaced by a Phantom Extra Atom, as previously described. In this case, iii is set equal to ooo as a signal to ISIS/Desktop that a hydrogen-only leaving group must be reattached to iii. An attachment point entry is one iii,ooo,cc triad. Multiple M SAP lines are permitted for each superatom Sgroup to the maximum of the atom attachment limit. The order of the attachment entries is significant because the first iii,ooo,c becomes the first connection made when drawing to the collapsed superatom, and so forth. Superatom Class The format for superatom class is as follows: M SCL sss d... where: sss: Index of superatom Sgroup d...: Text string (for example, PEPTIDE, ...) 69 characters maximum This appendix identifies the class of the superatom Sgroup. It distinguishes, for example, peptide groups from nucleotides. Large REGNO The format for the regno appendix is as follows: M REG r... where: rrr: Free format integer regno This appendix supports overflow of the I6 regno field in the molfile header. If this appendix is present, the value of the regno in the molfile header is superceded. Sgroup Bracket Style The format for the Sgroup bracket style is as follows: M SBTnn8 sss ttt ... where: sss: Index of Sgroup ttt: Bracket display style: 0 = default, 1 = curved (parenthetic) brackets This appendix supports altering the display style of the Sgroup brackets. 34
Chapter 4: Molfiles Overview A molfile consists of a header block and a connection table. The following shows a molfile for alanine corresponding to the following structure: Figure 10 Molfile organization illustrated using alanine L-Alanine C hial r 13 C 3 N + 2 O 1 6 4 O 5 L-Alanine (13C) GSMACCS-II10169115362D 1 6 5 0 -0.6622 0.6622 -0.7207 -1.8622 0.6220 1.9464 1 2 1 1 3 1 1 4 1 2 5 2 2 6 1 M CHG 2 M ISO 1 M END 1 0 0.5342 -0.3000 2.0817 -0.3695 -1.8037 0.4244 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 1 6 3 13 0.00366 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.00000 3 V2000 C 0 0 C 0 0 C 1 0 N 0 3 O 0 0 O 0 5 0 Header Block Counts Line 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom Block Connection Table (Ctab) Bond Block -1 Properties Block The format for a molfile is: Header Block: Identifies the molfile: molecule name, user's name, program, date, and other miscellaneous information and comments Ctab Block: Connection table (described in Chapter 2) The detailed format for the header block follows.
CTFile Formats The Header Block Line 1: Molecule name. This line is unformatted, but like all other lines in a molfile may not extend beyond column 80. If no name is available, a blank line must be present. Caution: This line must not contain any of the reserved tags that identify any of the other CTAB file types such as $MDL (RGfile), $$$$ (SDfile record separator), $RXN (rxnfile), or $RDFILE (RDfile headers). Line 2: This line has the format: (FORTRAN: IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> ) User's first and last initials (l), program name (P), date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s), energy (E) if modeling program input, internal registry number (R) if input through MDL form. A blank line can be substituted for line 2. If the internal registry number is more than 6 digits long, it is stored in an M Chapter 3). Line 3: 36 A line for comments. If no comment is entered, a blank line must be present. REG line (described in
Chapter 5: RGfiles Overview The format of an RGfile (Rgroup query file) is shown below. Lines beginning with $ define the overall structure of the Rgroup query; the molfile header block is embedded in the Rgroup header block. In addition to the primary connection table (Ctab block) for the root structure, a Ctab block defines each member (*m) within each Rgroup (*r). *r *m $MDL REV 1 date/time $MOL $HDR [Molfile Header Block (see Chapter 4) = name, pgm info, comment] $END HDR $CTAB [Ctab Block (see Chapter 2) = count + atoms + bonds + lists + props] $END CTAB $RGP rrr [where rrr = Rgroup number] $CTAB [Ctab Block] $END CTAB $END RGP $END MOL where: *r (Rgroup) is repeated. MACCS-II and ISIS/Desktop have an internal limit of 32 Rgroups. *m (member) is repeated. MACCS-II has a maximum internal limit of 255 total atoms and bonds per Rgroup.
CTFile Formats Example of an RGfile (Rgroup query file) Figure 11 $MDL $MOL $HDR REV 1 16OCT91 15:40 GSMACCS-II10169115402D 1 $END HDR $CTAB 9 9 0 1.3337 . 1.3337 0.0000 2.6674 -2.6674 1 2 1 . 3 9 1 M RGP 3 M LOG 1 M LOG 1 M END $END CTAB $RGP 1 $CTAB 1 0 0 12.2100 M APO 1 M END $END CTAB $END RGP $RGP 2 $CTAB 2 1 0 -1.4969 0.0431 1 2 2 M APO 1 M END $END CTAB $CTAB 1 0 0 12.2100 M APO 1 M END $END CTAB $END RGP $END MOL 38 0 0 0 0.7700 -0.7700 3.0800 1.5400 1.5400 0 0 0 . 0 0 0 7 1 8 1 2 0 2 0 0 0.00353 0.0000 . 0.0000 0.0000 0.0000 0.0000 C 0.00000 4 V2000 0 0 C R# R# R# 0 0 0 0 0 0 0 0 0 Molfile header block Counts line 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom block of root Number of entries on line Bond block of root Atom list block Stext block Properties block of root Rgroup label location and Rgroup number 2 9 RGfile header block 2 0 Ctab for Rgroup root If/then, RestH, and Occurrence 0 0 0 14.3903 1 1 0 0 0.0508 0.0508 0 0 0 1 1 2 V2000 0.0000 C 0 0 0 0 0 0 2 V2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14.3903 1 1 0.0000 C 0.0000 O Ctab for Rgroup 1 member 1 Block for Rgroup R1 Ctab for Rgroup 2 member 1 Block for Rgroup R2 0.0000 N 2 V2000 0 0 0 0 0 0 Ctab for Rgroup 2 member 2
Chapter 5: RGfiles The RGfile shown in Figure 11 on page 38 cor es r ponds t t f l i Rgr quer o he olow ng oup y: R1 IF R1 THEN R2 R2 * R2 R1 = R1 > 0 C * * R2 = R2 = 0 C O N 39
CTFile Formats 40
Chapter 6: SDfiles Overview An SDfile (structure-data file) contains the structural information and associated data items for one or more compounds.The f m ati : or s *c *d [Molfile (see Chapter 4)] [Data Header] *l [Data] [Blank line] $$$$ where: *l is repeated for each line of data *d is repeated for each data item *c is repeated for each compound A [Molfile] block has the molfile format described in Chapter 4. A [Data Header] (one line) precedes each item of data, starts with a greater than (>) sign, and contains at least one of the following: • The field name enclosed in angle brackets. For example: <melting.point> • The field number, DTn , where n represents the number assigned to the field in a MACCS-II database Optional information for the data header includes: • The compound’s external and internal registry numbers. External registry numbers must be enclosed in parentheses. • Any combination of information The following are examples of valid data headers: > > > > <MELTING.POINT> 55 (MD-08974) <BOILING.POINT> DT12 DT12 55 (MD-0894) <BOILING.POINT> FROM ARCHIVES
CTFile Formats Figure 12 Example of an SDfile 1,2 CYCLO-C6 DI-COOH TRANS,L MACCS-II06039016292D 1 0.00339 12 12 0 0 1 0 -0.0238 -0.7702 . 2.6974 0.7634 1 2 1 0 0 0 . . 7 10 1 0 0 0 M END > 25 <MELTING.POINT> 179.0 - 183.0 0.0000 C 0.00000 1 V2000 0 0 25 1 0 0 0 0 0 0 0 Header block Molfile . 0.0000 O 0 0 Connection table Data header Data Blank line Data item Compound > 25 <DESCRIPTION> PW(W) > 25 <ALTERNATE.NAMES> 1,2 CYCLOHEXANE-DICARBOXYLIC ACID TRANS,L HEXAHYDROPHTHALIC ACID TRANS,L Data items > 25 <DATE> 01-10-1980 Nonstructural data > 25 <CRC.NUMBER> C-0710Dat $$$$ 2-METHYL FURAN MACCS-II06039016302D 1 6 0 0 0 0 0.5343 0.3006 . -2.0038 0.2857 1 2 2 0 0 0 . . 5 6 2 0 0 0 M END > 29 <DENSITY> 0.9132 - 20.0 Delimiter 0.00186 6 > 29 <BOILING.POINT> 63.0 (737 MM) 79.0 (42 MM) 0.0000 C 0.00000 1 V2000 0 0 29 0 0 0 0 0 0 0 0 0 Connection table 0 . 0.0000 C Header block Molfile Compound Data header Data Data items Nonstructural data Blank line > 29 <ALTERNATE.NAMES> SYLVAN > 29 <DATE> 09-23-1980 > 29 <CRC.NUMBER> F-0213 $$$$ Delimiter A [Data] value may extend over multiple lines containing up to 200 characters each. A blank line terminates each data item. A line beginning with four dollar signs ($$$$) terminates each complete data block describing a compound. 42
Chapter 6: SDfiles A datfile (data file) is effectively an SDfile with no [Molfile] descriptions or $$$$ delimiters. The [Data Header] in a datfile must include either an external or internal registry number in addition to a field name or number. Notes about using blank lines • Only one blank line should terminate a data item. • There should only be one blank line between the last data item and the $$$$ delimiter line. • If the SDfile only contains structures, there can be no blank line between the last "M END" and the $$$$ delimiter line. SDfile after a CFS search After a conformationally flexible substructure (CFS) search, the following format information is appended by MDL ISIS/Base PL to your SDfile after the connection table: • Query information (M $3D appendix lines added to embedded molfile) • CFS generated data (*DATA) • MAPPED ATOMS and BONDS This information describes, for example, how query atoms are mapped, the atom coordinates in models, and what is fitted during a CFS search. Figure 13 Example of SDfile with appended CFS query information M CHG 2 14 -1 16 M $3D 5 M $3D -9 3 M $3D 13 18 6.3000 M $3D -9 3 M $3D 18 9 3.1000 M $3D -9 3 M $3D 18 4 2.4000 M $3D -9 3 M $3D 13 9 2.8000 M $3D -9 3 M $3D 13 4 3.1000 M END > 31 <*DATA> Method = Derivative 1 8.3000 5.1000 3D Query Fields 4.4000 4.8000 5.1000 > 31 <MAPPED ATOMS AND BONDS> (8 13 14 3 9 4 18) (12 13 7 8) CFS-Generated Data Mapping Atoms and Bonds $$$$ 43
CTFile Formats 44
Chapter 7: Rxnfiles Overview Rxnfiles contain structural data for the reactants and products of a reaction. To see a sample rxnfile go to Figure 14 on page 46.The f m ati : or s [Rxnfile Header] rrrppp $MOL [Molfile of reactant] $MOL [Molfile of product] *r *p where: *r is repeated for each reactant *p is repeated for each product Header Block Line 1: $RXN in the first position on this line identifies the file as a reaction file. Line 2: A line for the reaction name. If no name is available, a blank line must be present. Line 3: User’s initials (I), program name and version (P), date/time (M/D/Y,H:m), and reaction registry number (R). This line has the format: (FORTRAN: IIIIIIPPPPPPPPPMMDDYYYYHHmmRRRRRRR <-A6-><---A9--><---A12----><--I7-> ) A blank line can be substituted for line 3. If the internal registry number is more than 7 digits long, it is stored in an “M line (described in Chapter 3). REG” Note: In rxnfiles produced by earlier versions of MDL ISIS/Host, the year occupied two digits instead of four. There are corresponding minor changes in the adjacent fields. The format of the line is: (FORTRAN: Line 4 IIIIIIPPPPPPPPPPMMDDYYHHmmRRRRRRRR <-A6-><---A10--><---A10--><--I8--> ) A line for comments. If no comment is entered, a blank line must be present.
CTFile Formats Figure 14 Rxnfile for the acylation of benzene $RXN Header block REACCS81 1017911041 7439 #Reactants and #Products 2 1 $MOL REACCS8110179110412D 1 4 3 0 0.3929 -1.0590 0.3929 1.6503 1 2 1 1 3 2 1 4 1 M END $MOL 0 0 -0.2577 -0.7710 1.2823 -1.1468 0 0 0 2 0 0 0 2 0 0 0 4 0 6 0 1.3335 1.3335 0.0000 0.0000 -1.3335 -1.3335 1 2 1 1 3 2 2 4 2 3 5 1 4 6 1 5 6 2 M END $MOL 0 0 0 0 0 0 0 0 0 -0.7689 0.7689 -1.5415 1.5415 -0.7689 0.7689 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 9 0 -0.5311 -1.8626 -0.5311 0.8191 -3.2278 -1.8813 2.1282 0.8191 -3.2278 1 2 1 1 3 2 1 4 1 2 5 2 3 6 1 4 7 1 4 8 2 5 9 1 6 9 2 M END 46 1 V2000 C 0 0 C 0 0 O 0 0 Cl 0 0 0 0 0 0 0 0 0 0 315 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 0 0 0 0 0 0 0 0 0 Molfile for first reactant 0.00371 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 C C C C C C 1 V2000 0 0 0 0 0 0 0 0 0 0 0 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 6 0 7 0 8 0 9 0 10 0 0 0 0 0 0 0 0 0 0 0 0 Molfile for second reactant Molfile delimiter REACCS8110179110412D 1 9 0.0000 0.0000 0.0000 0.0000 0.00000 Molfile delimiter REACCS8110179110412D 1 6 0.00380 Molfile delimiter 0 0 0 0 0 0 0 0 0 0 0 0 -0.1384 0.6321 -1.6943 0.6284 -0.1346 -2.4723 -0.1085 2.2292 -1.6831 0 0 2 0 0 2 0 0 4 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 0.00374 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 C C C C C C C O C 1 V2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 255 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 6 0 7 0 1 0 8 0 9 0 2 0 3 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Molfile for product
Chapter 7: Rxnfiles Reactants/Products A line identifying the number of reactants and products, in that order. The format is: rrrppp where the variables represent: rrr Number of reactants* ppp Number of products* * MDL ISIS/Host has a limit of 8 reactants and 8 products. MDL Direct does not impose any limits. Molfile Blocks A series of blocks, each starting with $MOL as a delimiter, giving the molfile for each reactant and product in turn. The molfile blocks are always in the same order as the molecules in the reaction; reactants first and products second. The rxnfile in Figure 14 on page 46 corresponds to the following reaction: O O + CH3 Cl 47
CTFile Formats 48
Chapter 8: RDfiles Overview An RDfile (reaction-data file) consists of a set of editable “records.” Each record defines a molecule or reaction, and its associated data. An example RDfile incorporating the rxnfile described in Chapter 7 is shown later in this chapter (see Figure 15 on page 51).The f m atf or or an RD fl i : ie s [RDfile Header] [Molecule or Reaction Identifier] *d [Data-field Identifier] [Data] *r where: *d is repeated for each data item *r is repeated for each reaction or molecule Each logical line in an RDfile starts with a keyword in column 1 of a physical line. One or more blanks separate the first argument (if any) from the keyword. The blanks are ignored when the line is read. After the first argument, blanks are significant. An argument longer than 80 characters breaks at column 80 and continues in column 1 of the next line. (The argument may continue on additional lines up to the physical limits on text length imposed by the database.) The RDfile must not contain any blank lines except as part of embedded molfiles, rxnfiles, or data. An identifier separates records. RDfile Header Line 1: $RDFILE 1: The [RDfile Header] must occur at the beginning of the physical file and identifies the file as an RDfile. The version stamp “1” is intended for future expansion of the format. Line 2: $DATM: Date/time (M/D/Y, c) stamp. This line is treated as a comment and ignored when the program is read. Molecule and Reaction Identifiers A [Molecule or Reaction Identifier] defines the start of each complete record in an RDfile. The form of a molecule identifier must be one of the following: $MFMT [$MIREG internal-regno [$MEREG external-regno]] embedded molfile $MIREG internal-regno $MEREG external-regno where: • $MFMT defines a molecule by specifying its connection table as a molfile • $MIREG internal-regno is the internal registry number (sequence number in the database) of the molecule
CTFile Formats • $MEREG external-regno is the external registry number of the molecule (any uniquely identifying character string known to the database, for example, CAS number) • Square brackets ( [] ) enclose optional parameters • An embedded molfile (see Chapter 4) follows immediately after the $MFMT line The forms of a reaction identifier closely parallel that of a molecule: $RFMT [$RIREG internal-regno [$REREG external-regno]] embedded rxnfile $RIREG internal-regno $REREG external-regno where: • $RFMT defines a reaction by specifying its description as a rxnfile • $RIREG internal-regno is the internal registry number (sequence number in the database) of the reaction • $REREG external-regno is the external registry number of the reaction (any uniquely identifying character string known to the database) • Square brackets ( [] ) enclose optional parameters • An embedded rxnfile (see Chapter 7) follows immediately after the $RFMT line Data-field Identifier The [Data-field Identifier] specifies the name of a data field in the database. The format is: $DTYPE field name Data Data associated with a field follows the field name on the next line and has the form: $DATUM datum The format of datum depends upon the data type of the field as defined in the database. For example: integer, real number, real range, text, molecule regno. For fields whose data type is “molecule regno,” the datum must specify a molecule and, with the exception noted below, use one of the formats defined above for a molecular identifier. For example: $DATUM $MFMT embedded molfile $DATUM $MEREG external-regno $DATUM $MIREG internal-regno In addition, the following special format is accepted: $DATUM molecule-identifier Here, molecule-identifier acts in the same way as external-regno in that it can be any text string known to the database that uniquely identifies a molecule. (It is usually associated with a data field different from the external-regno.) 50
Chapter 8: RDfiles Figure 15 Example of a reaction RDfile $RDFILE 1 $DATM 10/17/91 10:41 $RFMT $RIREG 7439 $RXN REACCS81 RDfile header 1017911041 Rxnfile header 7439 #Reactants and #Products 2 1 $MOL REACCS8110179110412D 1 4 1 $MOL 3 . 4 0 1 0 . 0 0 0 0 . 0 0 0 5 $MOL 6 . 6 0 2 0 . 0 0 0 0 . 0 0 0 0.00000 315 0 Molfile for first reactant First Rxn record 4 REACCS8110179110412D 1 6 0.00380 0 0 0.00371 0 0 0.00000 8 Molfile for second reactant 0 2 REACCS8110179110412D 1 0.00374 0.00000 255 Molfile for product 9 9 0 0 0 0 0 0 0 0 0 . . . 6 9 2 0 0 0 2 $DTYPE rxn:VARIATION(1):rxnTEXT(1) $DATUM CrCl3 $DTYPE rxn:VARIATION(1):LITTEXT(1) $DATUM A G Repin, Y Y Makarov-Zemlyanskii, Zur Russ Fiz-Chim, 44, p.2360, 1974 . . . . . $DTYPE rxn:VARIATION(1):CATALYST(1):REGNO $DATUM $MFMT $MIREG 688 REACCS8110179110412D 1 0.00371 0.00000 Data block for reaction 0 4 3 0 0 0 0 0 0 0 0 0 . . . 1 4 1 0 0 0 0 $DTYPE rxn:VARIATION(1):PRODUCT(1):YIELD $DATUM 70.0 . . . $RFMT $RIREG 8410 $RXN REACCS81 1017911041 8410 Start of next Rxn record 2 1 $MOL ... 51
CTFile Formats 52
Chapter 9: XDfiles Overview An XDfile (XML-data file) uses a standard set of XML elements that represent records of data. The XDfile format also provides: • Metadata or information about the origin of the data. Unlike the other CTfile formats such as the SDfile or RDfile, the XDfile enables the consumer of the data to correctly interpret it. • The ability to handle generalized data models, such as multiple structures and nonstructure fields per record, multiple reactions per record, multiline data, and binary data. None of the other CTfile formats such as SDFiles or RDFiles have this ability. • Very few restrictions on data formatting within the actual content. Data formatting is based on XML, which does not have restrictions on line length or blank lines. See “Data Formatting” on page 54. • Fast and easy parsing by using any XML parser. The XML data can be validated by using a DTD (Document Type Definition) or an XML schema that defines primitive rules which the data must follow. You can download the DTD and XML schema from the CTFile Formats download page at the Elsevier MDL web site (www.mdl.com). From the Elsevier MDL web site, click Downloads > Download Products > Select a Product > MDL CTFile Formats no-fee > MDL CTFile Formats. Note: Due to limitations in the capabilities of DTDs and XML schemas, an XDfile that is validated by the DTD and XML schema is not guaranteed to be correct. For example, it is possible to create a record with duplicate field values. The DTD and XML schema only provide a low level of validation. Applications which process XDfiles must provide high level checks on the consistency of the data. • Flexibility in creating application-specific XML tags. Note, however, that it is the responsibility of the client application to interpret these custom tags. The Data Source Service of MDL® Core Interface can read an XDfile and load it into an XML data source. It also provides tools for converting SDfiles and RDfiles to XDfiles. For information about these tools, see the "Utilities" section in the "Data Source Service" chapter of MDL Core Interface Developer’s Guide. Note: Although it is possible to convert SDfiles and RDfiles to XDfiles, there are risks involved in converting an XDfile to the original format. This is because the backward conversion will lose the metadata which is not supported in the other CTfile formats. The rest of this chapter contains reference information about the XML elements in an XDfile. For the structure of an XDfile, see “Hierarchy of Elements” on page 55. For an alphabetic list of elements in an XDfile, see “Alphabetic List of Elements” on page 57.
CTFile Formats Data Formatting XML puts little or no restrictions on data formatting within the actual content. Data that is sensitive to white space, molfiles and rxnfiles in particular, must be enclosed in a CDATA section. You must set the xml:space attribute to "preserve". The following example is a Field element that contains a molfile: <Field name="Mol" xml:space="preserve"><![CDATA[ -ISIS- 03190310282D 1 0 0 0 0 0 0 -2.1000 -0.1208 M END ]]></Field> 0 0 0999 V2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 Note that for data outside a CDATA section, certain characters must be escaped as described in the following table: Character Representation in XML < &lt; > &gt; " &quot; ’ &apos; & &amp; For example, "mp < 100" becomes "mp &lt; 100". See also the XML specification for more details. 54
Chapter 9: XDfiles Hierarchy of Elements The following shows the hierarchy of elements within an XDfile. The attributes of the elements are not shown in order to more clearly show the structure of the XML: <XDfile> <Dataset> <Source> <DataSource /> <ProgramSource /> <CreatorName /> <CreateDate /> <CreateTime /> <Description /> <Copyright /> </Source> <Metadata> <FieldDef /> <ParentDef> <FieldDef /> </ParentDef> </Metadata> <Data> <Record> <Field> </Field <Parent> <Record> <Field> </Field> </Record> </Parent> </Record> </Data> </Dataset> </XDfile> 55
CTFile Formats The following XML schema diagram also illustrates the hierarchy of elements in an XDfile: 56
Chapter 9: XDfiles Alphabetic List of Elements Element Parent Brief Description Copyright Source A copyright notice for the data CreateDate Source The date the data was created CreateTime Source The time the data was created CreatorName Source The person who created the data Data Dataset Contains records of data Dataset XDfile Contains a collection of data DataSource Source The source of the data Description Source A description or comment about the data Field Record The value of a field in a record FieldDef Metadata The definition of a field in the data ParentDef The root element XDfile Metadata Dataset Contains definitions of fields in the data Parent Record Contains subrecords of data ParentDef Metadata The definition of a parent field in the data ProgramSource Source The program that created the data Record Data The unit of data; contains a set of field values Parent Source Dataset Contains information about the source of data 57
CTFile Formats XDfile The root element. XML data that uses the XDfile format must begin with <XDfile> and end with </XDfile>. It contains one or more Dataset elements. Attributes The data type of all attributes is CDATA. Attribute Required Description xmlns Yes The default namespace for elements in the XDfile. The default is http://www.mdl.com/XDfile/NS. version Yes The version number of the XDfile data. The default is 1.2. Parent Element None Child Elements Element Description Dataset 58 Required Yes A single collection of data
Chapter 9: XDfiles Example <?xml version="1.0"?> <XDfile xmlns="http://www.mdl.com/XDfile/NS"> <Dataset name="MySource"> <Source> <DataSource>ACD99.1 Hview</DataSource> <ProgramSource>GCS 1.0</ProgramSource> <CreatorName>John Doe</CreatorName> <CreateDate DATEFORMAT="M/D/Y">7/22/99</CreateDate> <CreateTime TIMEFORMAT="24">13:45</CreateTime> </Source> <Metadata> <FieldDef name="Molstructure" type="Structure" molFormat="Chime"/> <FieldDef name="Reaction Vessel ID" type="FixedText" maxLength="15"/> <FieldDef name="Library ID" type="FixedText" maxLength="8"/> <FieldDef name="Tag Id" type="fixedText" maxLength="3"/> <ParentDef name="XYZ Test Results"> <FieldDef name="Dose" type="Double"/> <FieldDef name="Response" type="Double"/> </ParentDef> </Metadata> <Data> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A02</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">yes</Field> <Parent name="XYZ Test Results" totalRecords="2"> <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> <Record> <Field name="Dose">2.0</Field> <Field name="Response">999.0</Field> </Record> </Parent> </Record> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A03</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">no</Field> </Record> </Data> </Dataset> </XDfile> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 59
CTFile Formats Dataset A self-contained, single collection of data. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes, if multiple datasets The name of the dataset. If XDfile contains only one dataset, name is optional. If XDfile contains multiple datasets, name is required in order to identify each dataset. Parent Element XDfile Child Elements Element Required Description Source No Describes the source of the data Metadata No Describes the individual fields in the actual data Data Yes The actual data Example <Dataset> <Metadata> <FieldDef name="CTAB" type="Structure" molFormat="Chime"/> <FieldDef name="Regno" type="Integer" isPrimaryKey="true"/> <FieldDef name="Molname" type="FixedText"/> <FieldDef name="Date" type="Date"/> <FieldDef name="DoubleValue" type="Double"/> </Metadata> <Data totalRecords="1"> <Record> <Field name="CTAB">40Aieg6Mprlczdb^fg37JiOh</Field> <Field name="Regno">1</Field> <Field name="Molname">Test Structure</Field> <Field name="Date">05/10/2002</Field> </Record> </Data> </Dataset> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 60
Chapter 9: XDfiles Source Contains information that describes the source of the data. Note that although each child element is optional, the order of the child elements is fixed. If a child element does not follow the order specified below, the element is discarded. Attributes None Parent Element Dataset Child Elements Element Required Description DataSource No The source of the data. ProgramSource No The program that created the data. CreatorName No The name of the person who created the data. CreateDate No The date the data was created. The default format is M-D-Y. CreateTime No The time the data was created. The default format is 24-hour. Description No A description or comments about the data. Copyright No A copyright notice for the data. Example <Source> <DataSource>ACD99.1 Hview</DataSource> <ProgramSource>Core Interface 1.1</ProgramSource> <CreatorName>John Doe</CreatorName> <CreateDate dateOrder="M/D/Y">7/22/99</CreateDate> <CreateTime timeFormat="24">13:45</CreateTime> </Source> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 61
CTFile Formats DataSource The source of the actual data. Attributes None Parent Element Source Child Elements None Example <DataSource>ACD99.1 Hview</DataSource> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 62
Chapter 9: XDfiles ProgramSource The program that created the actual data. Attributes None Parent Element Source Child Elements None Example <ProgramSource>MDL Core Interface 1.0</ProgramSource> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 63
CTFile Formats CreatorName The person who created the actual data. Attributes None Parent Element Source Child Elements None Example <CreatorName>John Doe</CreatorName> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 64
Chapter 9: XDfiles CreateDate The date the actual data was created. The default format is M-D-Y. Attributes The data type of all attributes is CDATA. Attribute Required Description dateOrder No The format for the date in <CreateDate>. The separator character is specified as part of the format. The valid formats are: M-D-Y D-M-Y Y-M-D Y-D-M The default format is M-D-Y. Parent Element Source Child Elements None Example <CreateDate dateOrder="M/D/Y">7/22/99</CreateDate> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 65
CTFile Formats CreateTime The time the actual data was created. The default format is 24-hour. Attributes The data type of all attributes is CDATA. Attribute Required Description timeFormat No The format for the time in <CreateTime>. The valid values are: 24 12 The default format is 24. Parent Element Source Child Elements None Example <CreateTime>24:15</CreateTime> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 66
Chapter 9: XDfiles Description A description or comment about the actual data. Attributes None Parent Element Source Child Elements None Example <Description>This is test data.</Description> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 67
CTFile Formats Copyright A copyright notice for the data. Attributes None Parent Element Source Child Elements None Example <Copyright>Copyright 2003 by Acme Corporation </Copyright> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 68
Chapter 9: XDfiles Metadata Contains information that describes the fields in the data. Applications can use this information to allow automatic creation of database tables or better formatting of data. The hierarchical structure of the Metadata element must match the data model contained in the Data element. Attributes None Parent Element Dataset Child Elements Element Required Description ParentDef No Contains information about a single parent within the data FieldDef No Contains information about a single field within the data Example <Metadata> <FieldDef name="Molstructure" type="Structure" molFormat="Chime"/> <FieldDef name="Reaction Vessel ID" type="FixedText" maxLength="15"/> <FieldDef name="Library ID" type="FixedText" maxLength="8"/> <FieldDef name="Tag Id" type="FixedText"/> <ParentDef name="XYZ Test Results"> <FieldDef name="Dose" type="Double"/> <FieldDef name="Response" type="Double"/> </ParentDef> </Metadata> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 69
CTFile Formats ParentDef Contains information about a single parent field within the data. Note: Do not create unnecessary parent fields at the root. Parent fields should only be used when there is an actual hierarchical structure to the data. For example, an SDFile would not have ParentDef elements, but would only have multiple FieldDef elements directly under the Metadata element. The actual data in the SDFile follows this format by having multiple Record elements directly under the Data element. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the parent field. This is a simple name because the context of the parent in the hierarchy is implied by the XML structure. Parent Element Metadata ParentDef Child Elements Element Required Description FieldDef Yes Contains information about a single field within the data ParentDef No Contains information about a single parent within the data. A parent within a parent creates a hierarchy. Example <ParentDef name="XYZ Test Results"> <FieldDef name="Dose" type="Double"/> <FieldDef name="Response" type="Double"/> </ParentDef> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 70
Chapter 9: XDfiles FieldDef Contains information about a single field within the data. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the field. This is a simple name because the context of the field in the hierarchy is implied by the XML structure. type Yes The type of data in the field. Applications can define their own type, but it will be the responsibility of client applications to interpret these. The valid values are: Reaction Structure Integer Double FixedText VariableText Date Time DateTime Binary isKey No “true” if the field is a key. The valid values are: true false The default value is false. isPrimaryKey No “true” if the field is a primary key. The valid values are: true false The default value is false. nativeName No The name of the field specific to the source from which it is derived. For example, a native name for an Oracle database is schema.table.column. encoding No The encoding set used by the data. Sample values are: binhex rot64 71
CTFile Formats Attribute Required Description charset No The character set used by the text. A sample value is ISO-8859-1. decimalSeparator No The decimal separator used for floating point numbers. The valid values are: Period Comma The default value is Period. maxLength No The maximum length of the data in this field. For binary fields in a relational data source (such as CLOB and BLOB fields), the maximum length varies depending on the version of the Oracle JDBC driver. molFormat No The format for the structure, if the field contains structures. The valid values are: Molfile Chime Smiles The default value is Molfile. rxnFormat No The format for the reaction, if the field contains reactions. The valid values are: Rxnfile Chime The default value is Rxnfile. molVersion No The version of the data format. molVersion is currently only applicable to structures. The absence of this attribute implies a pre-V2000 molfile. The valid values are: V2000 V3000 dateOrder No The order and format of a date field. The value specifies the separator character. Dates must be specified using numbers only; do not use month names. The valid orders are: M-D-Y D-M-Y Y-M-D Y-D-M The default value is M-D-Y. 72
Chapter 9: XDfiles Attribute Required Description timeOrder No The order of a date field. The value specifies the separator character. The valid orders are: h:m m:h The default value is h:m. timeFormat No The format of a time field. The valid values are: 24 12 The default value is 24. precision No The precision for a real number field. This is the total number of digits. scale No The scale for a real number field. This is the number of digits to the right of the decimal point. nullsAllowed No “true” if the field can contain nulls. The valid values are: true false The default value is false. isIndexed No “true” if the field is indexed. The valid values are: true false The default value is false. isHidden No “true” if the field is hidden. The valid values are: true false The default value is false. units No The units of measure associated with the field. javaFormat No The Java format to use when the field value is parsed. This is the Java output format used by the NumberFormat or DateFormat class. Parent Element Metadata, ParentDef Child Elements None 73
CTFile Formats Example <FieldDef name="Molstructure" type="Structure" molFormat="Chime"/> <FieldDef name="Reaction Vessel ID" type="FixedText" maxLength="15" /> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 74
Chapter 9: XDfiles Data Contains a collection of Record child elements that contain the actual data. Each Record element contains a collection of Parent and Field elements whose hierarchical structure must match the hierarchy in the Metadata element. The Data element can be empty if there is no data or only the metadata is to be transferred. Attributes The data type of all attributes is CDATA. Attribute Required Description totalRecords No The total number of root-level records in the data Parent Element Dataset Child Elements Element Required Description Record No A record of data Example <Data totalRecords="2"> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A02</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">yes</Field> <Parent name="XYZ Test Results" totalRecords="2"> <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> <Record> <Field name="Dose">2.0</Field> <Field name="Response">999.0</Field> </Record> </Parent> </Record> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A03</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">no</Field> </Record> </Data> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 75
CTFile Formats Parent Contains child records of data. A Parent can contain other Parent elements, thus, creating a sub-hierarchy of data. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the field. totalRecords No The total number of records under this parent Parent Element Record Child Elements Element Required Description Record No A record of data Example <Parent name="XYZ Test Results" ID="100"> <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> <Record> <Field name="Dose">2.0</Field> <Field name="Response">999.0</Field> </Record> </Parent> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 76
Chapter 9: XDfiles Record A record of data, and contains a set of Field elements. Attributes None Parent Element Data Parent Child Elements Element Required Description Field No A single field of data Parent No Contains subrecords of data. A parent within a record creates a hierarchy. Example <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 77
CTFile Formats Field Contains data for a single field in a record. Note that the molFormat, molVersion, and rxnFormat attributes can be used on individual Field elements to override the format specified in the Metadata element. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the parent field. molFormat No The format for the structure, if the field contains structures. This value overrides the molFormat specified in the Metadata element. The valid values are: Molfile Chime Smiles The default value is Molfile. rxnFormat No The format for the reaction, if the field contains reactions. This value overrides the rxnFormat specified in the Metadata element. The valid values are: Rxnfile Chime The default value is Rxnfile. molVersion No The version of the data format. molVersion is currently only applicable to structures. The absence of this attribute implies a pre-V2000 molfile. This value overrides the molVersion specified in the Metadata element. The valid values are: V2000 V3000 Parent Element Record Example <Field name="Dose">1.0</Field> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 78
Chapter 10: The Extended Connection Table (V3000) Overview The extended (V3000) molfile consists of a regular molfile “no structure” followed by a single molfile appendix that contains the body of the connection table (Ctab). The following figure shows both an alanine structure and the extended molfile corresponding to it. See Chapter 2 for the V2000 version of this same structure. Figure 16 Extended molfile organization illustrated using alanine L-Alanine C hial r 13 C 3 N + 2 1 O 6 4 O 5 L-Alanine GSMACCS-II07189510252D 1 0.00366 0.00000 0 Figure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 5 0 0 1 M V30 BEGIN ATOM M V30 1 C -0.6622 0.5342 0 0 CFG=2 M V30 2 C 0.6622 -0.3 0 0 M V30 3 C -0.7207 2.0817 0 0 MASS=13 M V30 4 N -1.8622 -0.3695 0 0 CHG=1 M V30 5 O 0.622 -1.8037 0 0 M V30 6 O 1.9464 0.4244 0 0 CHG=-1 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 3 CFG=1 M V30 3 1 1 4 M V30 4 2 2 5 Blocks not used in this Ctab: M V30 5 1 2 6 Sgroup block, Rgroup block, 3D block M V30 END BOND M V30 END CTAB M END Header Block Comment Line Counts Line Atom Block Connection Table (Ctab) Bond Block Note that the “no structure” is flagged with the “V3000” instead of the “V2000” version stamp. There are two other changes to the header in addition to the version: • The number of appendix lines is always written as 999, regardless of how many there actually are. (All current readers will disregard the count and stop at M END.) • The “dimensional code” is maintained more explicitly. Thus “3D” really means 3D, although “2D” will be interpreted as 3D if any non-zero Z-coordinates are found. Unlike the V2000 molfile, the V3000 extended Rgroup molfile has the same header format as a non-Rgroup molfile.
CTFile Formats Note: Do not create a molfile with a pre-V3000 Rgroup header ("$MDL", and so forth) but with V3000 Ctab blocks. This is not allowed. A pre-V3000 Rgroup molfile can only have embedded molfiles that are also pre-V3000 versions, for example, the version is either "V2000" or " ". Specifications For Atom and Bond Descriptions The general syntax of an entry is: M V30 key posval posval ... [keyword=value] [keyword=value] ... or M V30 BEGIN key [blockname] M V30 posval posval ... keyword=value keyword=value ... ... M V30 END key Each line must begin with "M V30 " with the two blank spaces after M and one blank space after 30. Following this is a list of zero or more required positional values (posval). Optional values may follow which use a ’KEYWORD=value’ format. Items are separated by white space. There can also be white space preceding the first item. Trailing white space is ignored. The value of a keyword can be a list containing two or more values: KEYWORD=(N val1 val2 ... valN) where N specifies the number of items that follow. Values (posval, value, or val1, and so forth) can be strings. Strings that contain blank spaces or start with left parenthesis or double quote, must be surrounded by double quotes. A double quote may be entered literally by doubling it. Each entry is one line of no more than 80 characters. To allow continuation when the 80-character line is too short, use a dash (-) as the last character. When read, the line is concatenated with the next line by removing the dash and stripping the initial "M V30" from the following line. For example: M M V30 10 20 30 “abcV30 def” is read as: M V30 10 20 30 "abc def" Generally, each section of the molfile is enclosed in a block that consists of lines such as: M V30 BEGIN key [blockname] ... M V30 END key The ‘key’ value defines the kind of block, for example, CTAB, ATOM, or BOND. Depending upon the type of block, there may or may not be values on the BEGIN line. 80
Chapter 10: The Extended Connection Table (V3000) Conventions The new format conventions used in this chapter are as follows: UPPERCASE Literal text, to be entered as shown. Only the position of "M V30 " is significant; white space may be added anywhere else to improve readability. Note that both lower- and uppercase characters, or any combination of them, are acceptable for literals. They are shown here in uppercase only for readability. lowercase A token, which is defined elsewhere. [] An optional item. Do not include the brackets. [ ]* An optional item, where there may be zero, one, two, or more of the item. | Separates two or more options, only one of which is valid. / Separates two or more items. Either or both may appear in any order. {} Braces are used for grouping. They indicate indefinite or definite repeat. The Extended Connection Table The features of the extended connection table are described in this section. CTAB Block A Ctab block defines the basic connection table, which is defined as: M V30 BEGIN CTAB [ctabname] counts-line atom-block [bond-block] [sgroup-block] [3d-block] [link-line]* M V30 END CTAB The atom block, like the counts line, is required. The Sgroup block, 3D block, and link lines may occur in any order after the atom and bond blocks. The counts line, atom block, and bond block must appear in the order indicated. 81
CTFile Formats Counts Line A counts line is required, and must be first. It specifies the number of atoms, bonds, 3D objects, and Sgroups. It also specifies whether or not the CHIRAL flag is set. Optionally, the counts line can specify molregno. This is only used when the regno exceeds 999999 (the limit of the format in the molfile header line). The format of the counts line is: M V30 COUNTS na nb nsg n3d chiral [REGNO=regno] where: na = number of atoms nb = number of bonds nsg = number of Sgroups n3d = number of 3D constraints chiral = 1 if molecule is chiral, 0 if not regno = molecule or model regno Atom Block An atom block specifies all node information for the connection table. It must precede the bond block. It has the following format: M V30 M V30 M V30 M V30 M V30 M V30 M V30 M V30 M V30 . . . M V30 BEGIN ATOM index type x y z aamap [CHG=val] [RAD=val] [CFG=val] [MASS=val] [VAL=val] [HCOUNT=val] [STBOX=val] [INVRET=val] [EXACHG=val] [SUBST=val] [UNSAT=val] [RBCNT=val] [ATTCHPT=val] [RGROUPS=(nvals val [val ...])] [ATTCHORD=(nvals nbr1 val1 [nbr2 val2 ...])] END ATOM The values are described in the following table. Figure 17 Meaning of values in the atom block Field Meaning Values Notes index Atom index Integer > 0 Identifies atoms. The actual value of the index does not matter as long as each index is unique to each atom. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Atom type Type = reserved atom or atom or [NOT] ‘[‘atom, atom,...’]’ A character string. If the string contains white space, it must be quoted. It can be a single atom or an atom list enclosed in square brackets with an optional preceding NOT. where reserved atom = R# = Rgroup A = “any” atom Q = any atom but C or H * = “star” atom Atom = character string (For example, ‘C’ or ‘Cl') xyz 82 Atom coordinates Angstroms
Chapter 10: The Extended Connection Table (V3000) aamap Atom-atom mapping 0 = no mapping Reaction property > 0 = mapped atom CHG Atom charge Integer Same range as V2000 0 = none (default) RAD Atom radical 0 = none (default) 1 = singlet 2 = doublet 3 = triplet CFG Stereo configuration 0 = none (default) 1 = odd parity 2 = even parity 3 = either parity MASS Atomic weight Default = natural abundance A specified value indicates the absolute atomic weight of the designated atom. VAL Valence Integer > 0 or Abnormal valence 0 = none (default) -1 = zero HCOUNT Query hydrogen count Integer > 0 or Same maximum value as V2000 0 = not specified (default) -1 = zero STBOX Stereo box 0 = ignore the configuration of this double bond atom (default) 1 = consider the stereo configuration of this double bond atom INVRET Configuration inversion 0 = none (default) Both atoms of a double bond must be marked to search double bond stereochemistry. Alternatively, the STBOX bond property can be used. Reaction property 1 = configuration inverts 2 = configuration retained EXACHG Exact change 0 = property not applied (default) Reaction property 1 = exact change as displayed in the reaction SUBST Query substitution count Integer > 0 or Same maximum value as V2000. 0 = not specified (default) -1 = none UNSAT RBCNT Query unsaturation flag 0 = not specified (default) Query ring bond count Integer > 0 or 1 = unsaturated Same maximum value as V2000. 0 = not specified (default) -1 = none 83
CTFile Formats ATTCHPT Rgroup member attachment points Attachment points on member: -1 = first and second site 1 = first site only When the Rgroup member atom has two attachment points, the atom with the lowest index number attaches to the first attachment point 2 = second site only RGROUPS Integer > 0 val is the Rgroup number. ATTCHORD nvals is the number of Rgroups that comprise this R# atom. Integer > 0 nvals is the number of values that follow on the ATTCHORD line Integer > 0 A list of atom neighbor index and atom neighbor value pairs that identify the attachment order information at the R# atom nbr1 is atom neighbor index #1, nbr2 is index #2 val1 is the attachment order for the nbr1 attachment. Bond block A bond block specifies all edge information for the connection table. It must precede the Sgroup or 3D blocks. Its format is: M V30 BEGIN BOND M V30 index type atom1 atom2 [CFG=val] [TOPO=val] [RXCTR=val] [STBOX=val] ... M V30 END BOND where the values are described in the following table: Figure 18 Meaning of values in the bond block Field Meaning Values Notes index Bond index Integer > 0 The actual value of the index does not matter as long as all are unique. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Bond type Integer: Types 4 through 8 are for queries only. 1 = single 2 = double 3 = triple 4 = aromatic 5 = single or double 6 = single or aromatic 7 = double or aromatic 8 = any 84
Chapter 10: The Extended Connection Table (V3000) atom1,ato m2 Atom indexes Integer > 0 CFG Bond configuration Atom1 and Atom2 are bond end points. 0 = none (default) 1 = up 2 = either 3 = down TOPO Query property 0 = not specified (default) 1 = ring 2 = chain RXCTR Reacting center status 0 = unmarked (default) -1 = not a reacting center 1 = generic reacting center Additional: 2 = no change 4 = bond made or broken 8 = bond order changes 12 =( 4 + 8) bond made or broken and changes 5 = (4 + 1), 9 = (8 + 1), and 13 =(12 + 1) are also possible STBOX Stereo box 0 = ignore the configuration of this double bond (default) A double bond must be marked to search double bond stereochemistry 1 = consider the stereo configuration of this double bond Link atom line There is one link atom line for each link atom in the Ctab. A link atom line has the format: M V30 LINKNODE minrep maxrep nbonds inatom outatom [inatom outatom...] 85
CTFile Formats Figure 19 Meaning of values in link lines Field Values Notes minrep Minimum number of group repetitions. 1 For future expansion. Not currently used. maxrep Maximum number of group repetitions. Integer > 0 nbonds Number of directed bonds defining the group. nbonds = # of pairs of inatom-outatom tuples inatom Atom index of atom in the repeating group. Integer > 0 outatom 86 Meaning Atom index of atom bonded to inatom, but outside of repeating group. Integer > 0 Number of tuples is usually two but may be one for link nodes with an attachment point.
Chapter 10: The Extended Connection Table (V3000) Sgroup block The Sgroup block contains general Sgroup information and information on each Sgroup structure as shown here. For the V2000 version of this Sgroup structure and connection table, see Chapter 2. Figure 20 Connection Table Organization of an Sgroup Structure Pol er ym 7 5 2 1 * 6 n 3 4C l n * r an Polymer GSMACCS-II07189510252D 1 0.00374 0.00000 0 Figure 5, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 6 3 0 0 M V30 BEGIN ATOM M V30 1 * 2.9463 0.3489 0 0 M V30 2 C 1.6126 1.1189 0 0 M V30 3 C 0.2789 0.3489 0 0 CFG=3 Blocks not used in this Ctab: M V30 4 Cl 0.2789 -1.1911 0 0 Rgroup block, 3D block M V30 5 C -1.0548 1.119 0 0 M V30 6 C -2.3885 0.349 0 0 M V30 7 * -3.9246 1.147 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 4 1 5 6 M V30 5 1 5 3 M V30 6 1 7 6 M V30 END BOND M V30 BEGIN SGROUP M V30 1 SRU 5 ATOMS=(2 5 6) XBONDS=(2 5 6) BRKXYZ=(9 -0.6103 1.2969 0 -0.6103 M V30 0.171 0 0 0 0) BRKXYZ=(9 -3.1565 0.185 0 -3.1565 1.311 0 0 0 0) M V30 CONNECT=HT M V30 2 SRU 6 ATOMS=(3 2 3 4) XBONDS=(2 1 5) BRKXYZ=(9 2.2794 1.2969 0 2.2794 M V30 0.1709 0 0 0 0) BRKXYZ=(9 -0.1657 0.171 0 -0.1657 1.2969 0 0 0 0) M V30 CONNECT=HT M V30 3 COP 7 ATOMS=(7 1 2 3 4 5 6 7) BRKXYZ=(9 3.6382 1.6391 0 3.6382 M V30 -1.7685 0 0 0 0) BRKXYZ=(9 -4.707 -1.7685 0 -4.707 1.6391 0 0 0 0) M V30 SUBTYPE=RAN M V30 END SGROUP M V30 END CTAB M END Header Block Comment Line Counts Line Atom Block Connection Table (Ctab) Bond Block Sgroup Block Sgroup 1 Properties Sgroup 2 Properties Sgroup 3 Properties 87
CTFile Formats An Sgroup block defines all Sgroups in the molecule, including superatoms. The format is as follows: M V30 BEGIN SGROUP [M V30 DEFAULT [CLASS=class] -] M V30 index type extindex M V30 [ATOMS=(natoms atom [atom ...])] M V30 [XBONDS=(nxbonds xbond [xbond ...])] M V30 [CBONDS=(ncbonds cbond [cbond ...])] M V30 [PATOMS=(npatoms patom [patom ...])] M V30 [SUBTYPE=subtype] [MULT=mult] M V30 [CONNECT=connect] [PARENT=parent] [COMPNO=compno] M V30 [XBHEAD=(nxbonds xbond [xbond ...])] M V30 [XBCORR=(nxbpairs xb1 xb2 [xb1 xb2 ...])] M V30 [LABEL=label] M V30 [BRKXYZ=(9 bx1 by1 bz1 bx2 by2 bz2 bx3 by3 bz3])* M V30 [ESTATE=estate] [CSTATE=(4 xbond cbvx cbvy cbvz)]* M V30 [FIELDNAME=fieldname] [FIELDINFO=fieldinfo] M V30 [FIELDDISP=fielddisp] M V30 [QUERYTYPE=querytype] [QUERYOP=queryop] M V30 [FIELDDATA=fielddata] ... M V30 [CLASS=class] M V30 [SAP=(3 aidx lvidx id)]* M V30 [BRKTYP=bracketType] ... M V30 END SGROUP The DEFAULT field provides a way to specify default values for keyword options. The same keyword options and values as defined in the following table. Figure 21 Meaning of values in the Sgroup block Field Meaning Values Notes index Sgroup index Integer > 0 The actual value of the index does not matter as long as all indexes are unique. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Sgroup type String. Only first 3 letters are significant: SUPeratom MULtiple SRU MONomer COPolymer CROsslink MODification GRAft COMponent MIXture FORmulation DATa ANY GENeric extindex Integer => 0: Use 0 to autogenerate a number. If 0, positive integer assigned 88 External index value This is the V2000 Sgroup label
Chapter 10: The Extended Connection Table (V3000) ATOMS natoms is the number of atoms that define the Sgroup. atom is the atom index. XBONDS Integer > 0 Integer > 0 Integer > 0 ncbonds is the number of containment bonds. Integer > 0 cbond is the containment-bond index PATOMS Integer > 0 xbond is the crossing-bond index. CBONDS nxbonds is the number of crossing bonds. Integer > 0 npatom is the number of paradigmatic repeating unit atoms. Integer > 0 Only used for Data Sgroups. This field is expected to become obsolete and is retained for compatibility with MACCS-II. The field is only used for multiple groups. patom is the atom index of an atom in the paradigmatic repeating unit for a multiple group. SUBTYPE subtype is the Sgroup subtype. String. Only the first 3 letters are significant: ALTernate RANdom BLOck MULT mult is the multiple group multiplier. Integer > 0 CONNECT connect is the connectivity. String values are as follows: EU (default) The default, if missing, is EU. The MDL V2000 writer never writes an EU entry. HH HT PARENT parent is the parent Sgroup index. Integer > 0 COMPNO compno is the component order number. Integer > 0 XBHEAD nxbonds is the number of crossing bonds that cross the “head” bracket. Integer > 0 xbond is the crossing-bond index. Integer > 0 If XBHEAD is missing, no bonds are paired as the head or tail of the repeating unit 89
CTFile Formats XBCORR nxbpairs 2 x the number of pairs of crossing-bond correspondence, that is, the number of values in list. xb1 - xb2 is the pairs of crossing-bond correspondence, that is, xb1 connects to xb2. Integer > 0 LABEL label is the display label for this Sgroup. String For example, superatom name BRKXYZ bx1 - bz3 are the double (X,Y,Z) display coordinates in each bracket. Angstroms By specifying 3 triples, the format allows a 3D display. estate is the expanded display state information for superatoms. String xbond is the crossing bond of the expanded superatom. Integer > 0 Display vector information for the contracted superatom. cbvx - cvbz is the vector to contracted superatom. Angstroms Only present for expanded superatoms. One CSTATE entry per crossing bond. FIELDNAME fieldname is the name of data field for Data Sgroup. String FIELDINFO fieldinfo is the program-specific field information. Free-format string Example: In MACCS-II this is: “<type> <units/format>” FIELDDISP fielddisp is the Data Sgroup field display information. Free-format string This string is interpreted by V3000 as identical to V2000 appendix for Data Sgroup display (‘M SDD’) except for the index value. QUERYTYPE querytype is the type of query or no query if missing. String ESTATE CSTATE However, only the first two (X, Y) coordinates are currently used. The Z value and last (X, Y) coordinates are currently ignored and should be set to zero. E = expanded superatom or multiple group Only superatoms and multiple groups (shortcuts) in an expanded internal state are supported. This field defines whether a superatom or multiple group is displayed as expanded or contracted. This field is expected to become obsolete. ‘ ’ = not a query (default) ‘MQ’ = MACCS-II query ‘IQ’ = ISIS query <p>Q’ = <program> query QUERYOP queryop is the query operator. String. Example: “=” or “LIKE” in ISIS ISIS: query operator MACCS-II: blank or missing FIELDDATA fielddata is the query or field data. Free-format string Only one entry per query, but can be more than one for actual data. The order of the entries is important. CLASS class is the character string for superatom class. String Example: PEPTIDE 90
Chapter 10: The Extended Connection Table (V3000) SAP aidx is the index of attachment point or potential attachment point atom. Integer > 0 lvidx is the index of leaving atom. Allowed integers are: 0 = none or implied H ‘aidx’ = atom index number of attachment point atom > 0 = atom index number of atom bonded to ‘aidx’ id is the attachment identifier. BRKTYP String (two chars in V2000) There must be multiple entries if superatom has more than one attachment point. The order of the entries defines the order of the attachment points. Note that SAP entries may or may not include the actual attachment points, depending on the particular superatom and its representation on MDL ISIS/Desktop. bracketType is the displayed bracket style. Allowed values for this string are: This information supports Sgroup enhancements on MDL ISIS/Desktop. BRACKET (default) PAREN Correspondence with existing V2000 appendices M M M M M M M M M M M M M M M M M M M M M STY SST SLB SCN SDS SAL SBL SPA SMT CRS SDI SBV SDT SDD SCD SED SPL SNC SAP SCL SBT = = = = = = = = = = = = = = = = = = = = = type SUBTYPE extindex CONNECT ESTATE ATOMS XBONDS or CBONDS PATOMS LABEL and MULT XBHEAD,XBCORR BRKXYZ CSTATE FIELDNAME, FIELDINFO, QUERYTYPE, QUERYOP FIELDDISP (not required) FIELDDATA PARENT COMPNO SAP CLASS BRKTYP 91
CTFile Formats Collection block A collection block specifies all collection information for objects in the current connection table context. Collection blocks must be provided after the blocks that define the objects included in the collection to minimize the amount of forward object references that must be maintained by the file reader. M V30 BEGIN COLLECTION [M V30 DEFAULT -]M V30 name/subname M V30 [ATOMS=(natoms atom [atom ...])] M V30 [BONDS=(nbonds bond [bond ...])] M V30 [SGROUPS=(nsgroups sgrp [sgrp ...])] M V30 [OBJ3DS=(nobj3ds obj3d [obj3d ...])] M V30 [MEMBERS=(nmembers member [member ...])] M V30 [RGROUPS=(nrgroups rgroup [rgroup ...])] ... M V30 END COLLECTION Figure 22 Meaning of values in the collection block Field Meaning Value name/subname Collection id Nonblank string ATOMS natoms is the number of atoms included in the collection Integer > 0 atom is the atom index Integer > 0 nbonds is the number of bonds included in the collection Integer > 0 bond is the bond index Integer > 0 nsgroups is the number of sgroups included in the collection Integer > 0 sgrp is the sgroup index Integer > 0 nobj3ds is the number of 3D features included in the collection Integer > 0 obj3d is the 3D feature index Integer > 0 nmembers is the number of members included in the collection Integer > 0 member is the member identifier ROOT or RrMm nrgroups is the number of rgroups included in the collection Integer > 0 rgroup is the rgroup identifier Rr BONDS SGROUPS OBJ3DS MEMBERS RGROUPS Notes r > 0, m > 0 r>0 • Collections can be named in a semi-arbitrary fashion. • A two part name is supported for collections on import and export. • The subname designation is required. • The name is the unique identifier for the collection contents. • All collections of the same name are presumed to indicate various pieces of the same collection, which may be provided in one or more COLLECTION block entries provided within various subblocks of the full connection table. • Collection names are not case sensitive, must contain only printable characters, and must begin with an alphanumeric character. 92
Chapter 10: The Extended Connection Table (V3000) • Collection objects are presumed to be unordered, and no preservation of input order is necessary or required on subsequent file writes. • Future enhancements to the collection block information will provide ordered collection support. The default delimiter for the collection name is the '/' character. If the name begins with a non-alphanumeric character, it is presumed to indicate an alternate delimiter character, thus a collection name that contains a '/' character might be designed as '|name|/subname/|', for example. In addition, if the first character is ‘”’,it is presumed that the collection name is being quoted due to the presence of spaces. The name MDLV30 is a reserved name used to designate internal collections. User specified collections may use any other arbitrary naming conventions. The default action for all MDL provided V3000 readers and writers is to preserve all user collection information for CTfile import/export operations. Internal collections may also be preserved if their contents have been validated as correct input for the specified internal representation. There is no implied validation for user collections other than requiring the collection to refer to valid objects. Collections may not contain other collections in their definition. The default action on registration is to strip user collection information without error, but possibly with status or warning messages being issued. The internal collection types are: MDLV30/HILITE Highlighting collection. Default action for renderers is to provide a "highlighted" display of the specified objects. All object types are allowed in this collection: atoms, bonds, Sgroups, 3Dfeatures, Rgroups, members, and components. MDLV30/STEABS Absolute stereochemistry collection. This collection defines the set of stereocenters in the structure that have absolute configurations. This is an atom collection. MDLV30/STERACn "Racemic" stereochemistry collection (n >0). This collection defines a set of stereogenic centers whose relative configuration is known. A mixture of the two enantiomeric relative configurations is present. This is an atom collection. MDLV30/STERELn Relative stereochemistry collection (n>0). This collection defines a set of stereogenic centers whose relative configuration is known. Only one of the two enantiomeric relative configurations is present. There is no assumption about which of the two configurations is present. This is an atom collection. 93
CTFile Formats 3D block The 3D block contains 3D information as shown below. For the V2000 version of this 3D query and its connection table, see Chapter 2.3D Block Normal 3D Query Exclusion sphere Point Angle Centroid Plane Benzene ring o 75-105 4.4-5.7 N Distance Nitrogen atom 3D Query MACCS-II07189510253D 1 1.00000 0.00000 0 Figure 6, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 7 0 7 0 M V30 BEGIN ATOM M V30 1 C 1.0252 0.2892 1.1122 0 M V30 2 C -0.4562 0.6578 1.3156 0 M V30 3 C -1.4813 0.3687 0.2033 0 M V30 4 C -1.0252 -0.2892 -1.1122 0 M V30 5 C 0.4562 -0.6578 -1.3156 0 M V30 6 C 1.4813 -0.3687 -0.2033 0 M V30 7 N 4.1401 -0.1989 1.3456 0 M V30 8 C 4.6453 0.5081 1.7417 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 2 3 M V30 3 1 3 4 Blocks not used in this Ctab: Sgroup block, M V30 4 2 4 5 Rgroup block M V30 5 1 5 6 M V30 6 2 6 1 M V30 7 1 7 8 M V30 END BOND M V30 BEGIN OBJ3D M V30 1 -7 6 "" 0 0 BASIS=(3 6 4 2) M V30 2 -5 13 "" 0 0 BASIS=(6 1 2 3 4 5 6) M V30 3 -8 7 "" 0 0 BASIS=(2 O3D.1 O3D.2) M V30 4 -3 6 "" -2 0 BASIS=(2 O3D.1 O3D.3) PNTDIR=1 M V30 5 -16 12 "" 1.5 0 BASIS=(1 O3D.4) UNCONNOK=1 M V30 6 -12 10 "" 75 105 BASIS=(3 O3D.4 O3D.1 7) M V30 7 -9 3 "" 4.4 5.7 BASIS=(2 7 O3D.1) M V30 END OBJ3D M V30 END CTAB M END Header Block Comment Line Counts Line Atom Block Connection Table (Ctab) Bond Block 3D object block A 3D block specifies information for all 3D objects in the connection table. It must follow the atom and bond blocks. As in V2000 molfiles, there can be only one fixed-atom constraint. 94
Chapter 10: The Extended Connection Table (V3000) The format of the 3D block is as follows: M V30 M V30 M V30 M V30 M V30 M V30 ... M V30 BEGIN OBJ3D index type color name value1 value2 BASIS=(nbvals bval [bval ...]) [ALLOW=(nvals val [val ...])] [PNTDIR=val] [ANGDIR=val] [UNCONNOK=val] [DATA=strval] [COMMENT=comment] END OBJ3D Figure 23 Meaning of values in the 3D block Field Meaning Values Notes index 3D object index Integer > 0 The actual value of the index does not matter as long as all indexes are unique. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Object type Integer < 0 for geometric constraints and for data constraints This format is the same as V2000. Integer > 0 are field IDs color Color value Integer > 0 name Object name or, for data query, the field name. String value1 Distance, radius, deviation, or minimum value. Floating point, value1 = 0 if constraint has no floating values value2 Maximum value for range constraints. Floating point, value2 = 0 if not a range constraint BASIS nbvals is the number of objects in basis. Integer > 0 bval is the atom number or 3D object index Integer or O3D.integer nvals is the number of atoms allowed in an exclusion sphere. Integer > 0 val is the atom number. Integer > 0 ALLOW PNTDIR For objects where order is important, for example, in an angle constructed from three points, the order must be the same as in V2000 molfiles. 0 = point has no direction 1 = point has direction ANGDIR 0 = dihedral angle has no direction MACCS-II uses ‘Chiral’. 1 = dihedral angle has direction UNCONNOK 0 = unconnected atoms are not OK 1 = unconnected atoms are OK DATA strval is the data query string String COMMENT string comment String. Normally uses the MACCS-II DASP, DISP, and BOX values Same as V2000 molfile 95
CTFile Formats The Extended Rgroup Query Molfile A single molecule or Rgroup molecule connection table. The header is contained in the normal header location, that is, in the first three lines of the file. The body of the new molecule is contained in new appendixes, organized as follows:A molecule block consists of a main Ctab, plus optionally one or more Rgroup definitions. ctab-block [rgroup-block]* Rgroup block The Rgroup file shown in the next figure corresponds to the following Rgroup query. For the V2000 version of the Rgroup query and its connection table, see Chapter 5 Figure 24 Connection table organization of an Rgroup query. I R 1 TH EN R 2 F R1 R2 * R2 R1 = R1 > 0 C * * R2 = R2 = 0 C 96 O N
Chapter 10: The Extended Connection Table (V3000) GSMACCS-II07189510252D 1 0 M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M 0 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 END 0.00353 0.00000 0 0 0 999 V3000 BEGIN CTAB COUNTS 9 9 0 0 0 BEGIN ATOM 1 C 1.3337 0.77 0 0 2 C 0 1.54 0 0 3 C -1.3337 0.77 0 0 4 C -1.3337 -0.77 0 0 5 C 0 -1.54 0 0 6 C 1.3337 -0.77 0 0 7 R# 0 3.08 0 0 RGROUPS=(1 1) 8 R# 2.6674 1.54 0 0 RGROUPS=(1 2) 9 R# -2.6674 1.54 0 0 RGROUPS=(1 2) END ATOM BEGIN BOND 1 1 1 2 2 2 2 3 3 1 3 4 4 2 4 5 5 1 5 6 6 2 6 1 7 1 1 8 8 1 2 7 9 1 3 9 END BOND END CTAB BEGIN RGROUP 1 RLOGIC 2 0 "" BEGIN CTAB COUNTS 1 0 0 0 0 BEGIN ATOM 1 C 12.21 14.3903 0 0 ATTCHPT=1 END ATOM END CTAB END RGROUP BEGIN RGROUP 2 RLOGIC 0 0 0 BEGIN CTAB COUNTS 2 1 0 0 0 BEGIN ATOM 1 C -1.4969 0.0508 0 0 ATTCHPT=1 2 O 0.0431 0.0508 0 0 END ATOM BEGIN BOND 1 2 1 2 END BOND END CTAB BEGIN CTAB COUNTS 1 0 0 0 0 BEGIN ATOM 1 N 12.21 14.3903 0 0 ATTCHPT=1 END ATOM END CTAB END RGROUP Header Block 0 Counts Line Atom Block for root Ctab for Rgroup root Bond Block for root Rgroup logic Line Counts Line Atom Block Ctab for Rgroup 1 Member 1 Block for Rgroup 1 Rgroup logic Line Counts Line Atom Block Ctab for Rgroup 2 Member 1 Bond Block Counts Line Atom Block Block for Rgroup 2 Ctab for Rgroup 2 Member 2 97
CTFile Formats An Rgroup block defines one Rgroup. Each Ctab block specifies one member. M V30 BEGIN RGROUP rgroup-number [rgroup-logic-line] ctab-block [ctab-block]* M V30 END RGROUP Figure 25 Meaning of values in the Rgroup block Field Meaning Values rgroup-number Index of this rgroup Notes Integer > 0 Rgroup logic lines There is zero or one Rgroup logic line for each Rgroup in the molecule. If present, the Rgroup logic line specifies if-then logic between Rgroups, the convention about unfilled valence sites, and the Rgroup occurrence information. Its format is: M V30 RLOGIC thenR RestH Occur Figure 26 Meaning of values in Rgroup logic line Field Meaning Values thenR Number of a “then” Rgroup 0 = none (default) RestH Attachment(s) at Rgroup position 0 = off, that is, any molecule fragment at any unsatisfied Rgroup location (default) 1 = only hydrogen or a member of Rgroup is allowed Occur String specifying number (range) of Rgroup occurrence sites that need to be satisfied. String ‘> 0’ = default Notes Similar to MACCS-II and ISIS: [N[,[N[,...]]]] Automatic V3000 output Current Elsevier MDL products support reading and writing of V2000 and V3000 formats. These products will preferentially write V2000 molfiles to maximize interoperability with third party applications. However, because of the limitations imposed by the V2000 format, there are situations when the V3000 format will be automatically used. The following are cases in which the V3000 format is automatically written instead of the V2000 format: • • 98 Structure highlighting - The V3000 format is required for molecule or collection highlighting. See the “Collection block” on page 92 which contains information about structure highlighting. Enhanced stereochemistry features - The V3000 format is required when using the enhanced stereochemical representations. See the “Collection block” on page 92 which contains information about the enhanced stereochemistry features.
Chapter 10: The Extended Connection Table (V3000) • The maximum length of a field with a fixed width is exceeded - If any of the fields with fixed widths for any connection table properties are exceeded, then the V3000 format will be used. For example, if the number of atoms (or bonds) exceeds 999, the V3000 format will be used. This is because the number of atoms (or bonds) on the V2000 counts line cannot exceed 3 columns (see “The Counts Line” on page 12). For more details about the fixed field widths in the V2000 format, see “Chapter 2: The Connection Table [CTAB] (V2000)” on page 11. 99
CTFile Formats 100
Chapter 11: The Extended Reaction File Overview Rxnfiles contain structural data for the reactants and products of a reaction. For the V2000 version of this reaction file, see Chapter 7. The first line of the file begins with $RXN to identify the file as a reaction file. The V3000 version follows the $RXN token to indicate the extended version of the reaction file. There are two new block types introduced: REACTANT and PRODUCT.
CTFile Formats Figure 27 V3000 Rxnfile for the acylation of benzene $RXN V3000 0503021738 M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M 102 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 END Header Block 7439 COUNTS 2 1 BEGIN REACTANT BEGIN CTAB COUNTS 4 3 0 0 0 BEGIN ATOM 1 C 0.323 -0.2377 0 1 2 C -1.0362 -0.9618 0 2 3 O 0.323 1.4154 0 3 4 Cl 1.6423 -1.0307 0 0 END ATOM BEGIN BOND 1 1 1 2 RXCTR=2 2 2 1 3 RXCTR=2 3 1 1 4 RXCTR=4 END BOND END CTAB BEGIN CTAB COUNTS 6 6 0 0 0 BEGIN ATOM 1 C 1.3331 -0.7694 0 5 2 C 1.3331 0.7694 0 6 3 C 0 -1.5417 0 7 4 C 0 1.5417 0 8 5 C -1.3331 -0.7694 0 9 6 C -1.3331 0.7694 0 10 END ATOM BEGIN BOND 1 1 1 2 RXCTR=2 2 2 1 3 RXCTR=2 3 2 2 4 RXCTR=2 4 1 3 5 RXCTR=2 5 1 4 6 RXCTR=2 6 2 5 6 RXCTR=2 END BOND END CTAB END REACTANT BEGIN PRODUCT BEGIN CTAB COUNTS 9 9 0 0 0 BEGIN ATOM 1 C -0.5331 -0.1358 0 5 2 C -1.8606 0.633 0 6 3 C -0.5331 -1.6992 0 7 4 C 0.8201 0.6305 0 1 5 C -3.2189 -0.1358 0 8 6 C -1.8811 -2.4731 0 9 7 C 2.1297 -0.1128 0 2 8 O 0.8534 2.2297 0 3 9 C -3.2292 -1.6863 0 10 END ATOM BEGIN BOND 1 1 1 2 RXCTR=2 2 2 1 3 RXCTR=2 3 1 1 4 RXCTR=4 4 2 2 5 RXCTR=2 5 1 3 6 RXCTR=2 6 1 4 7 RXCTR=2 7 2 4 8 RXCTR=2 8 1 5 9 RXCTR=2 9 2 6 9 RXCTR=2 END BOND END CTAB END PRODUCT Counts Line Counts Line Atom Block Ctab for first reactant Bond Block Counts Line Reactant block Atom Block Ctab for second reactant Bond Block Counts Line Atom Block Ctab for product Bond Block Product block
Appendix A: Stereo Notes Parity is illustrated as follows: Mark a bond attached at a stereo center Up or Down to define the configuration Number the atoms surrounding the stereo center with 1, 2, 3, and 4 in order of increasing atom number (position in the atom block) (a hydrogen atom should be considered the highest numbered atom, in this case atom 4). View the center from a position such that the bond connecting the highest-numbered atom (4) projects behind the plane formed by atoms 1, 2, and 3. Note: In the figure, atoms 1, 2, and 4 are all in the plane of the paper, and atom 3 is above the plane. 3 4 C 2 1 Sighting towards atom number 4 through the plane (123), you see that the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order. 1 3 2 3 Part = 2 iy Part = 1 iy 2 1 The Ctab lists a parity value of 1 for a clockwise arrangement at the stereo center and 2 for counterclockwise. A center with an Either bond has a parity value of 3. An unmarked stereo center is also assigned a value of 3. The first example above has a parity value of 2.
CTFile Formats 104
105 Index Numbers 3D block (V3000 molfiles) 94 3D features (ctab) count line 24 data constraints 31 data line 26 detail lines 24 identification line 25 properties block 23 type identifiers 25 A atom alias (ctab) 16 atom attachment order (ctab) 18 atom block (ctab) 12 atom block (V3000 molfiles) 82 atom descriptions (V3000 molfiles) 80 atom limit enhancements 33 atom list (ctab) 17 atom list block (query) 14 atom value (ctab) 16 atom, phantom extra 33 attachment point (ctab) 17 attachment point, superatom 33 B blank lines in SDfiles 43 bond block (ctab) 14 bond block (V3000 molfiles) 84 bond descriptions (V3000 molfiles) 80 bracket style, Sgroup 34 C charge (ctab) 16 collection block (V3000 molfiles) 92 connection table 11 Copyright (XDfile) 68 correspondence, Sgroup 21 counts line (ctab) 12 counts line (V3000 molfiles) 82 CreateDate (XDfile) 65 CreateTime (XDfile) 66 CreatorName (XDfile) 64 ctab atom block 12 atom list block (query) 14 bond block 14 counts line 12 end of block 23 extended connection table (V3000 molfiles) 81 overview 11 properties block 15 stext block 15 ctab block (V3000 molfiles) 81 3D block 94 atom block 82 bond block 84 collection block 92 counts line 82 link atom line 85 Sgroup block 87 ctab properties 3D data constraints 31 3D features count line 24 3D features detail lines 24 3D properties block 23 atom alias 16 atom attachment order 18 atom list 17 atom value 16 attachment point 17 charge 16 data Sgroup data 22 data Sgroup display information 22 data Sgroup field description 22 group abbreviation 16 isotope 17 large REGNO 34 link atom 17 multiple group parent atom list 21 phantom extra atom 33 radical 16 range of occurence 18 Rgroup label location 18 Rgroup logic 18 ring bond count 17 Sgroup atom list 21 Sgroup bond list 21 Sgroup bracket style 34 Sgroup component numbers 23 Sgroup connectivity 21 Sgroup correspondence 21
106 CTFile Formats Sgroup display information 21 Sgroup expansion 21 Sgroup hierarchy information 23 Sgroup labels 20 Sgroup subscript 21 Sgroup subtype 20 Sgroup type 19 substitution count 17 superatom attachment point 33 superatom bond and vector 22 superatom class 34 unsatisfied sites 18 unsaturated atoms 17 CTfile formats 7 D Data (XDfile) 75 data line (3D) 26 data Sgroup data (ctab) 22 data Sgroup display information (ctab) 22 data Sgroup field description (ctab) 22 Dataset (XDfile) 60 DataSource (XDfile) 62 Description (XDfile) 67 E end of block (ctab) 23 escaped characters (XDfile) 54 extended connection table (V3000 molfiles) 81 extended molfiles 79 extended Rgroup query molecule (V3000 molfiles) 96 extended rxnfiles 101 extra atom, phantom 33 F Field (XDfile) 78 FieldDef (XDfile) 71 I isotope (ctab) 17 L large REGNO 34 link atom (ctab) 17 link atom line (V3000 molfiles) 85 list of elements, XDfile 57 M MDLV30, reserved name (V3000) 93 Metadata (XDfile) 69 molfile blocks (Rxnfiles) 47 molfiles 35 extended 79 header block 36 multiple group parent atom list (ctab) 21 P Parent (XDfile) 76 ParentDef (XDfile) 70 parity 103 phantom extra atom 33 preserve CDATA (XDfile) 54 products (Rxnfiles) 47 ProgramSource (XDfile) 63 properties block - 3D (ctab) 23 properties block (ctab) 15 Q query properties 3D data constraints 31 atom list 17 link atoms 17 ring bond count 17 substitution count 17 unsaturated atoms 17 G group abbreviation (ctab) 16 H header (RDfiles) 49 header block (molfiles) 36 header block (Rxnfiles) 45 hierarchy of elements, XDfile 55 R radical (ctab) 16 range of occurence (ctab) 18 RDfiles header 49 reactants (Rxnfiles) 47 Record (XDfile) 77 REGNO, large 34 RGfiles 37 Rgroup block (V3000 molfiles) 96 Rgroup label location (ctab) 18 Rgroup logic (ctab) 18
Index Rgroup logic lines (V3000 molfiles) 98 Rgroup properties (ctab) atom attachment order 18 attachment point 17 range of occurence 18 Rgroup label location 18 Rgroup logic 18 unsatisfied sites 18 ring bond count (ctab) 17 Rxnfiles 45 header block 45 molfile blocks 47 reactants and products 47 V3000 101 V V2000 11 V3000 molfiles 79 atoms 80 bonds 80 compared with V2000 6 correspondence with existing V2000 appendices 91 ctab block 81 extended connection table 81 extended Rgroup query molecule 96 V3000 Rxnfiles 101 X S SDfiles 41 after a CFS search 43 blank lines 43 Sgroup block (V3000 molfiles) 87 Sgroup bracket style 34 Sgroup properties (ctab) data Sgroup data 22 data Sgroup display information 22 data Sgroup field description 22 multiple group parent atom list 21 phantom extra atom 33 Sgroup atom list 21 Sgroup bond list 21 Sgroup bracket style 34 Sgroup component numbers 23 Sgroup connectivity 21 Sgroup correspondence 21 Sgroup display information 21 Sgroup expansion 21 Sgroup hierarchy information 23 Sgroup labels 20 Sgroup subscript 21 Sgroup subtype 20 Sgroup type 19 superatom attachment point 33 superatom bond and vector 22 superatom class 34 Source (XDfile) 61 stereo parity 103 stext block 15 substitution count (ctab) 17 superatom attachment point 33 superatom bond and vector (ctab) 22 superatom class 34 U unsatisfied sites (ctab) 18 unsaturated atoms (ctab) 17 107 XDfile data formatting 54 example 59 hierarchy of elements 55 list of elements 57 overview 53 preserve CDATA 54 root element 58
108 CTFile Formats

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Ctfile

  • 2. June 2005 Copyright ©1995 - 2005 by MDL Information Systems, Inc (“Elsevier MDL”). All rights reserved. No part of this document may be copied for any means except as permitted in writing by Elsevier MDL, 14600 Catalina Street, San Leandro, CA 94577. MDL is a registered trademark in the U.S. and/or other countries, and ISIS is a trademark of Elsevier MDL. All other product and company names may be trademarks or registered trademarks of their respective holders in the U.S. and/or other countries. U.S. GOVERNMENT RESTRICTED RIGHTS If USER is a unit or agency of the U.S. Government or acquiring the Software with Governmental funds; (i) the Programs supplied to the U.S. Department of Defense (“DOD”) shall be subject to MDL’s standard commercial license and (ii) all Programs supplied to any unit or agency of the U.S. Government other than the DOD, shall be governed by clause 52.227-19(c) of the FAR (or any successor regulations) or, in the case of NASA, clause 48 1827.405(a) (or any successor regulations) and, in any such case, the U.S. Government acquires only “restricted rights” in the Programs. Contractor/Manufacturer is: Elsevier MDL, 14600 Catalina St., San Leandro, CA 94577
  • 3. 3 Contents Chapter 1: Introduction Change Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Extended Molfile Format (V3000). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Standard CTfiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Chapter 2: The Connection Table [CTAB] (V2000) Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 The Counts Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 The Atom Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 The Bond Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 The Atom List Block [Query] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 The Stext Block [MDL ISIS/Desktop] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 The Properties Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 The Properties Block for 3D Features [3D] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Chapter 3: Atom Limit Enhancements Phantom Extra Atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Superatom Attachment Point. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Superatom Class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Large REGNO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Sgroup Bracket Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Chapter 4: Molfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 The Header Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Chapter 5: RGfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Chapter 6: SDfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 SDfile after a CFS search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Chapter 7: Rxnfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
  • 4. 4 CTFile Formats Header Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Reactants/Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Molfile Blocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Chapter 8: RDfiles Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . RDfile Header . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Molecule and Reaction Identifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data-field Identifier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 49 49 50 50 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data Formatting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Hierarchy of Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Alphabetic List of Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XDfile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . DataSource. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ProgramSource. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CreatorName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CreateDate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CreateTime. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Copyright . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ParentDef . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . FieldDef . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Parent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 54 55 57 58 60 61 62 63 64 65 66 67 68 69 70 71 75 76 77 78 Chapter 9: XDfiles Chapter 10: The Extended Connection Table (V3000) Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Specifications For Atom and Bond Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . The Extended Connection Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . The Extended Rgroup Query Molfile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Automatic V3000 output. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 80 81 96 98 Chapter 11: The Extended Reaction File Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Appendix A: Stereo Notes Index
  • 5. Chapter 1: Introduction Elsevier MDL supports a number of file formats for representation and communication of chemical information. This document describes the formats for Elsevier MDL’s CTfiles (chemical table files): • Chapters 2 and 3 describe the Connection Table (V2000) format. • Chapters 4 through 9 describe the standard CTfile formats. • Chapter 10 describes the V3000 extended molfile format. All extended molfiles can be easily identified by the “V3000” version stamp in the header portion of the file. You are most likely to find the extended molfile format in CTfiles written from MDL ISIS/Host or MDL ISIS/Desktop version 2.0 or higher. • Chapter 11 describes the V3000 extended rxnfile format. Change Log The following are the changes in this document: Change Page(s) June 2005 Product and company rebranding changes Fixed example in 3D feature type -5 in "The Connection Table [CTAB] (V2000)" 25 Added "Automatic V3000 Output" section in "The Extended Connection Table (V3000)" 98 October 2003 Added new chapter on XDfile format 51 Added XDfile in this Introduction 7 August 2002 Deleted chapter on moving CTfiles on/off the Clipboard Minor corrections 6, 8, 9, 13, 32, 40 Added new information on enhanced stereochemistry features 56 Added new chapter on Extended Reaction File format 62 May, 2001 Added section describing advantages of V3000 file format Added section on V3000 Collection Block Minor corrections December, 1999 Updated entries in “Atom List” December, 1998 Updated “Example of an SDfile” August, 1998 Added STBOX field
  • 6. CTFile Formats June, 1997 Added Atom Attachment Order Added new ATTCHORD field October, 1996 Minor corrections Enhanced description of connection table properties block Added Sgroup bracket style Extended Molfile Format (V3000) The Extended Molfile format (V3000) molfile format offers a number of advantages over the V2000 format: • Consolidates property information for chemical objects • Provides better support for new chemical properties or objects • Removes fixed field widths to support large structures • Uses free format and tagging of information for easier parsing • Provides better support for backward compatibility through BEGIN/END blocks Current Elsevier MDL products support reading and writing of both molfile formats. These products will also preferentially write V2000 molfiles to maximize interoperability with third party applications. However, the fixed limits and distributed property information in the V2000 format make it harder to add new planned representational enhancements. The V3000 format is intended to be the primary means for communication of future enhancements to MDL chemical representation features. Note: There are situations when the V3000 format will automatically be written instead of the V2000 format. See “Automatic V3000 output” on page 98. Your code for writing molfiles should be able to export structure information in the V3000 format if any structural features are present which cannot be defined in the V2000 format. 6
  • 7. Chapter 1: Introduction Standard CTfiles The following figure illustrates the relationship between the various file formats described below: molfiles Molecule files: Each molfile describes a single molecular structure which can contain disjoint fragments. RGfiles Rgroup files: An RGfile describes a single molecular query with Rgroups. Each RGfile is a combination of Ctabs defining the root molecule and each member of each Rgroup in the query. rxnfiles Reaction files: Each rxnfile contains the structural information for the reactants and products of a single reaction. Elsevier MDL currently supports only the REACCS type of rxnfile. The CPSS type of rxnfile written by CPSS programs is no longer supported and is not described in this document. SDfiles Structure-data files: An SDfile contains structures and data for any number of molecules. Together with RDfiles, SDfiles are the primary format for large-scale data transfer between MDL databases. RDfiles Reaction-data files: Similar to SDfiles in concept, the RDfile is a more general format that can include reactions as well as molecules, together with their associated data. Although RDfiles are used primarily by ISIS and REACCS, MACCS-II can also read and write RDfiles except for the reaction structure information (indicated by the square brackets in the MDL Program table). XDfiles XML-data files: XML-based data format for transferring recordsets of structure or reaction information with associated data. An XDfile can contain structures or reactions that use any of the CTfile formats, Chime strings, or SMILES strings. (Chime is an encrypted format that is used to render structures and reactions on a Web page. SMILES is a line notation format that uses character strings and SMILES, Simplified Molecule Input Line Entry System, syntax to represent a structure.) 7
  • 8. CTFile Formats The following figure illustrates three examples of XDfiles: XDfile with molfile structures and associated data XDfile with rxnfile reactions and associated data XDfile with Chime strings and associated data Metadata Metadata Metadata Data Data Data Record Record Record Chime molfile rxnfile libraryID molname rxnregno dose molweight response This table shows which CTfiles MDL programs can read and write. Figure 1 MDL Programs CTfile Type MACCS-II REACCS ISIS Core Interface molfiles + + + + RGfiles + + + + + + + + + rxnfiles + SDfiles + RDfiles [+] + XDfiles + Some of the structural and query properties described in this document are generic in their applicability, while others are peculiar to certain CTfile types. The applicability of each property is identified in subsequent chapters by the bracketed terms shown in the following table. Figure 2 Properties applicable to various CTfile types Property molfile RGfile SDfile rxnfile RDfile XDfile [Generic] + + + + + + (mol/rxn) [Sgroup] + + + [+] [Rgroup] + + + + (mol) [3D] + + + + (mol) [Reaction] 8 + + (mol/[rxn]) + + (rxn)
  • 9. Chapter 1: Introduction Figure 2 [Query] Properties applicable to various CTfile types + + + + (mol/rxn) Note: The XDfile inherits the functionality of the format of the embedded structure or reaction. In addition to the molfile and rxnfile formats, the XDfile supports Chime and SMILES strings. 9
  • 11. Chapter 2: The Connection Table [CTAB] (V2000) Overview A connection table (Ctab) contains information describing the structural relationships and properties of a collection of atoms. The atoms may be wholly or partially connected by bonds. Such collections may, for example, describe molecules, molecular fragments, substructures, substituent groups, polymers, alloys, formulations, mixtures, and unconnected atoms. The connection table is fundamental to all of Elsevier MDL’s file formats. The following figure shows the connection table of a simple molecule (alanine) with the various data blocks identified. The connection table corresponds to the following alanine molecule. The atom numbers on the structure correspond to atom numbers in the Ctab. An atom number is assigned according to the order of the atom in the Atom Block. Figure 3 Connection table organization illustrated using alanine L-Alanine C hial r 13 C 3 N + 2 1 O 6 4 O 5 6 5 0 -0.6622 0.6622 -0.7207 -1.8622 0.6220 1.9464 1 2 1 1 3 1 1 4 1 2 5 2 2 6 1 M CHG 2 M ISO 1 M END 0 1 0 0.5342 -0.3000 2.0817 -0.3695 -1.8037 0.4244 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 1 6 3 13 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 3 V2000 C 0 0 C 0 0 C 1 0 N 0 3 O 0 0 O 0 5 Counts Line 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom Block Connection Table (Ctab) Bond Block -1 Blocks not used in this Ctab: Atom List, Stext Properties Block The format for a Ctab block is: Counts line: Important specifications here relate to the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version. Atom block: Specifies the atomic symbol and any mass difference, charge, stereochemistry, and associated hydrogens for each atom. Bond block: Specifies the two atoms connected by the bond, the bond type, and any bond stereochemistry and topology (chain or ring properties) for each bond. Atom list block: Identifies the atom (number) of the list and the atoms in the list. Stext (structural text descriptor) block: Used by MDL ISIS/Desktop programs. Properties block: Provides for future expandability of Ctab features, while maintaining compatibility with earlier Ctab configurations.
  • 12. CTFile Formats The detailed format for each block outlined above follows: Note: A blank numerical entry on any line should be read as “0” (zero). Spaces are significant and correspond to one or more of the following: • Absence of an entry • Empty character positions within an entry • Spaces between entries; single unless specifically noted otherwise The FORTRAN f m atf coor nat i or aton i t V 2000 CTfl f m ati t caly or or di e nf m i n he ie or s ypi l F10.4. The Counts Line aaabbblllfffcccsssxxxrrrpppiiimmmvvvvvv Where:: aaa = number of atoms (current max 255)* [Generic] bbb = number of bonds (current max 255)* [Generic] lll = number of atom lists (max 30)* [Query] fff = (obsolete) ccc = chiral flag: 0=not chiral, 1=chiral [Generic] sss = number of stext entries [MDL ISIS/Desktop] xxx = (obsolete) rrr = (obsolete) ppp = (obsolete) iii = (obsolete) mmm = number of lines of additional properties, including the M END line. No longer supported, the default is set to 999. [Generic] * These limits apply to MACCS-II, REACCS, and the MDL ISIS/Host Reaction Gateway, but not to the MDL ISIS/Host Molecule Gateway or MDL ISIS/Desktop. For example, the counts line in the Ctab shown in the previous figure shows six atoms, five bonds, the CHIRAL flag on, and three lines in the properties block: 6 5 0 0 1 0 3 V2000 The Atom Block The Atom Block is made up of atom lines, one line per atom with the following format: xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee w her t val ar des i i t f l i t e: e he ues e crbed n he olow ng abl 12
  • 13. Chapter 2: The Connection Table [CTAB] (V2000) Figure 4 Meaning of values in the atom block Field Meaning Values Notes xyz atom coordinates aaa atom symbol entry in periodic table or L for atom list, A, Q, * for unspecified atom, and LP for lone pair, or R# for Rgroup label [Generic, Query, 3D, Rgroup] dd mass difference -3, -2, -1, 0, 1, 2, 3, 4 (0 if value beyond these limits) [Generic] Difference from mass in periodic table. Wider range of values allowed by M ISO line, below. Retained for compatibility with older Ctabs, M ISO takes precedence. ccc charge 0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 = -3 [Generic] Wider range of values in M CHG and M RAD lines below. Retained for compatibility with older Ctabs, M CHG and M RAD lines take precedence. sss atom stereo parity 0 = not stereo, 1 = odd, 2 = even, 3 = either or unmarked stereo center [Generic] Ignored when read. hhh hydrogen count + 1 1 = H0, 2 = H1, 3 = H2, 4 = H3, 5 = H4 [Query] H0 means no H atoms allowed unless explicitly drawn. Hn means atom must have n or more H’s in excess of explicit H’s. bbb stereo care box 0 = ignore stereo configuration of this double bond atom, 1 = stereo configuration of double bond atom must match [Query] Double bond stereochemistry is considered during SSS only if both ends of the bond are marked with stereo care boxes. vvv valence 0 = no marking (default) (1 to 14) = (1 to 14) 15 = zero valence [Generic] Shows number of bonds to this atom, including bonds to implied H’s. HHH H0 designator 0 = not specified, 1 = no H atoms allowed [MDL ISIS/Desktop] Redundant with hydrogen count information. May be unsupported in future releases of Elsevier MDL software. rrr Not used iii Not used mmm atom-atom mapping number 1 - number of atoms [Reaction] nnn inversion/retention flag 0 = property not applied 1 = configuration is inverted, 2 = configuration is retained, [Reaction] eee exact change flag 0 = property not applied, 1 = change on atom must be exactly as shown [Reaction, Query] [Generic] 13
  • 14. CTFile Formats W ih Ct ver i V 2000,t dd and ccc fel have been s t ab s on he i ds uper eded by t M ISO,M s he CHG,and M RAD lnesi t pr i n he operi bl tes ock,des i bel .Forcom patbiiy,al r eas crbed ow i lt l el es s nce M A CCS- I2. REA CCS 8. and M D L I S 1. i I 0, 1, SI 0: • Write appropriate values in both places if the values are in the old range. • Use the atom block fields if there are no M ISO, M CHG, or M RAD lines in the properties block. Support for these atom block fields may be removed in future releases of Elsevier MDL software. The Bond Block The Bond Block is made up of bond lines, one line per bond, with the following format: 111222tttsssxxxrrrccc where the values are described in the following table: Figure 5 Meaning of values in the bond block Field Meaning Values Notes 111 first atom number 1 - number of atoms [Generic] 222 second atom number 1 - number of atoms [Generic] ttt bond type 1 = Single, 2 = Double, 3 = Triple, 4 = Aromatic, 5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any [Query] Values 4 through 8 are for SSS queries only. sss bond stereo Single bonds: 0 = not stereo, 1 = Up, 4 = Either, 6 = Down, Double bonds: 0 = Use x-, y-, z-coords from atom block to determine cis or trans, 3 = Cis or trans (either) double bond [Generic] The wedge (pointed) end of the stereo bond is at the first atom (Field 111 above) xxx not used rrr bond topology 0 = Either, 1 = Ring, 2 = Chain [Query] SSS queries only. ccc reacting center status 0 = unmarked, 1 = a center, -1 = not a center, Additional: 2 = no change, 4 = bond made/broken, 8 = bond order changes 12 = 4+8 (both made/broken and changes); 5 = (4 + 1), 9 = (8 + 1), and 13 = (12 + 1) are also possible [Reaction, Query] The Atom List Block [Query] Note: Newer programs use the M ALS item in the properties block in place of the atom list block. The atom list block is retained for compatibility, but information in an M ALS item supersedes atom list block information. Made up of atom list lines, one line per list, with the following format: aaa kSSSSn 111 222 333 444 555 14
  • 15. Chapter 2: The Connection Table [CTAB] (V2000) where: Field Meaning aaa = number of atom (L) where list is attached k = T = [NOT] list, = F = normal list n = number of entries in list; maximum is 5 111...555 = atomic number of each atom on the list S = space The Stext Block [MDL ISIS/Desktop] The Stext Block is made up of two-line entries with the following format: xxxxx.xxxxyyyyy.yyyy TTTT... where: Field Meaning xy = stext coordinate T = stext text The Properties Block The Properties Block is made up of mmm lines of additional properties, where mmm is the number in the counts line described above. If a version stamp is present, mmm is ignored and the file is read until an "M END" line is encountered. Currently mmm is no longer supported and is set to 999 as the default. Most lines in the properties block are identified by a prefix of the form M spaces separate the M and XXX. Exceptions are: XXX where two • A aaa, V aaa vvvvvv,and G aaappp, which indicate the following ISIS/Desktop properties: atom alias, atom value, and group abbreviation (called residue in ISIS), respectively. • S SKPnnn which causes the next nnn lines to be ignored. The prefix: M END terminates the properties block. Variables in the formats can change properties but keep the same letter designation. For example, on the Charge, Radical, or Isotope lines, the “uniformity” of the vvv designates a general property identifier. On Sgroup property lines, the sss uniformity is used as an Sgroup index identifier. All lines that are not understood by the program are ignored. The descriptions below use the following conventions for values in field widths of 3: n15 nn8 nn6 nn4 nn2 nn1 aaa number of entries on line; value = 1 to 15 number of entries on line; value = 1 to 8 number of entries on line; value = 1 to 6 number of entries on line; value = 1 to 4 number of entries on line; value = 1 or 2 number of entries on line; value = 1 atom number; value = (1 to number of atoms) 15
  • 16. CTFile Formats The format for the properties included in this block follows. The format shows one entry; ellipses (. . .) indicate additional entries. Atom Alias [MDL ISIS/Desktop] A aaa x... aaa: Atom number x: Alias text Atom Value [MDL ISIS/Desktop] V aaa v... aaa: Atom number v: Value text Group Abbreviation [MDL ISIS/Desktop] G aaappp x... aaa: Atom number ppp: Atom number x: Abbreviation label Abbreviation is required for compatibility with previous versions of MDL ISIS/Desktop which allowed abbreviations with only one attachment. The attachment is denoted by two atom numbers, aaa and ppp. All of the atoms on the aaa side of the bond formed by aaa-ppp are abbreviated. The coordinates of the abbreviation are the coordinates of aaa. The text of the abbreviation is on the following line (x...). In current versions of ISIS, abbreviations can have any number of attachments and are written out using the Sgroup appendixes. However, any ISIS abbreviations that do have one attachment are also written out in the old style, again for compatibility with older ISIS versions, but this behavior might not be supported in future versions. Charge [Generic] M CHGnn8 aaa vvv ... vvv: -15 to +15. Default of 0 = uncharged atom. When present, this property supersedes all charge and radical values in the atom block, forcing a 0 charge on all atoms not listed in an M CHG or M RAD line. Radical [Generic] M RADnn8 aaa vvv ... vvv: 16 Default of 0 = no radical, 1 = singlet (:), 2 = doublet ( . or ^), 3 = triplet (^^). When present, this property supersedes all charge and radical values in the atom block, forcing a 0 (zero) charge and radical on all atoms not listed in an M CHG or M RAD line.
  • 17. Chapter 2: The Connection Table [CTAB] (V2000) Isotope [Generic] M ISOnn8 aaa vvv ... vvv: Absolute mass of the atom isotope as a positive integer. When present, this property supersedes all isotope values in the atom block. Default (no entry) means natural abundance. The difference between this absolute mass value and the natural abundance value specified in the PTABLE.DAT file must be within the range of -18 to +12. Ring Bond Count [Query] M RBCnn8 aaa vvv ... vvv: Number of ring bonds allowed: default of 0 = off, -1 = no ring bonds (r0),-2 = as drawn (r*); 2 = (r2), 3 = (r3), 4 or more = (r4). Substitution Count [Query] M SUBnn8 aaa vvv ... vvv: Number of substitutions allowed: default of 0 = off, -1 = no substitution (s0),-2 = as drawn (s*); 1, 2, 3, 4, 5 = (s1) through (s5), 6 or more = (s6). Unsaturated Atom [Query] M UNSnn8 aaa vvv ... vvv: At least one multiple bond: default of 0 = off, 1 = on. Link Atom [Query] M LINnn4 aaa vvv bbb ccc vvv,bbb,ccc: Link atom (aaa) and its substituents, other than bbb and ccc, may be repeated 1 to vvv times, (vvv > = 2). The bbb and ccc parameters can be 0 (zero) for link nodes on atoms with attachment point information. Atom List [Query] M ALS aaannn e 11112222333344445555... aaa: Atom number, value nnn: Number of entries on line (16 maximum) e: Exclusion, value is T if a ’NOT’ list, F if a normal list. 1111: Atom symbol of list entry in field of width 4 Note: This line contains the atom symbol rather than the atom number used in the atom list block. Any data found in this item supersedes data from the atom list block. The number of entries can exceed the fixed limit of *5* in the atom list block entry. Attachment Point [Rgroup] M APOnn2 aaa vvv ... vvv: Indicates whether atom aaa of the Rgroup member is the first attachment point (vvv = 1), second attachment point (vvv = 2), both attachment points (vvv = 3); default of 0 = no attachment. 17
  • 18. CTFile Formats Atom Attachment Order [Rgroup] M AAL aaann2 111 v1v 222 v2v ... aaa: Atom index of the Rgroup usage atom nn2: Number of pairs of entries that follow on the line 111: Atom index of a neighbor of aaa v1v Attachment order for the aaa-111 bond 222 Atom index of a neighbor of aaa v2v Attachment order for the aaa-222 bond Note: v1v and v2v are either 1 or 2 for the simple doubly attached Rgroup member. This appendix provides explicit attachment list order information for R# atoms. The appendix contains atom neighbor index and atom neighbor value pairs. The atom neighbor value information identifies the atom neighbor index as the nth attachment. The implied ordering in V2000 molfiles is by atom index order for the neighbors of Rgroup usage atoms. If atom index order conflicts with the desired neighbor ordering at the R# atom, this appendix allows you to override to this default order. If v1v=1 and v2v=2, MDL ISIS/Host only writes this appendix if 111 is greater than 222. Note, however, that the attachment values can be written in any order. Rgroup Label Location [Rgroup] M RGPnn8 aaa rrr ... rrr: Rgroup number, value from 1 to 32 *, labels position of Rgroup on root. * MACCS-II and ISIS/Desktop limit Rgroup Logic, Unsatisfied Sites, Range of Occurrence [Rgroup] M LOGnn1 rrr iii hhh ooo... rrr: Rgroup number, value from 1 to 32 * iii: Number of another Rgroup which must only be satisfied if rrr is satisfied (IF rrr THEN iii) hhh: RestH property of Rgroup rrr; default is 0 = off, 1 = on. If this property is applied (on), sites labeled with Rgroup rrr may only be substituted with a member of the Rgroup or with H ooo Range of Rgroup occurrence required: n = exactly n, n - m = n through m,> n = greater than n, < n = fewer than n, default (blank) is > 0. Any non-contradictory combination of the preceding values is also allowed; for example: 1, 3-7, 9, >11. * MACCS-II and ISIS/Desktop limit 18
  • 19. Chapter 2: The Connection Table [CTAB] (V2000) Sgroup Type [Sgroup] M STYnn8 sss ttt ... sss: Sgroup number ttt: Sgroup type: SUP = superatom, MUL = multiple group, SRU = SRU type, MON = monomer, MER = Mer type, COP = copolymer, CRO = crosslink, MOD = modification, GRA = graft, COM = component, MIX = mixture, FOR = formulation, DAT = data Sgroup, ANY = any polymer, GEN = generic. Note: For a given Sgroup, an STY line giving its type must appear before any other line that supplies information about it. For a data Sgroup, an SDT line must describe the data field before the SCD and SED lines that contain the data (see Data Sgroup Data below). When a data Sgroup is linked to another Sgroup, the Sgroup must already have been defined. Sgroups can be in any order on the Sgroup Type line. Brackets are drawn around Sgroups with the M SDI lines defining the coordinates. 19
  • 20. CTFile Formats Sgroup Subtype [Sgroup] M SSTnn8 sss ttt ... Polymer Sgroup subtypes: ALT = alternating, RAN = random, BLO = block ttt: Figure 6 Ctab organization of an Sgroup structure Polymer ht * 7 ht 5 6 2 n * n 1 3 ran Cl 4 GSMACCS-II10179110412D 1 7 M M M M M M M M M M M M M M M M 6 0 2.9463 1.6126 0.2789 0.2789 -1.0548 -2.3885 -3.9246 1 2 1 2 3 1 3 4 1 5 6 1 5 3 1 7 6 1 STY 3 SST 1 SLB 3 SCN 2 SAL 1 SBL 1 SDI 1 SDI 1 SAL 2 SBL 2 SDI 2 SDI 2 SAL 3 SDI 3 SDI 3 END 0.00374 0.00000 Header block (see Chapter 4 ) 0 0 0 16 V2000 0.3489 0.0000 * 0 0 0 0 0 0 1.1189 0.0000 C 0 0 0 0 0 0 0.3489 0.0000 C 0 0 3 0 0 0 -1.1911 0.0000 Cl 0 0 0 0 0 0 1.1190 0.0000 C 0 0 0 0 0 0 0.3490 0.0000 C 0 0 0 0 0 0 1.1470 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 Number of entries on line 0 0 0 0 0 0 0 0 0 0 0 0 1 SRU 2 SRU 3 COP Type Subtype 3 RAN 1 5 2 6 3 7 Label Connectivity 1 HT 2 HT 2 5 6 2 5 6 4 -0.6103 1.2969 -0.6103 0.1710 4 -3.1565 0.1850 -3.1565 1.3110 3 2 3 4 2 1 5 4 2.2794 1.2969 2.2794 0.1709 4 -0.1657 0.1710 -0.1657 1.2969 7 1 2 3 4 5 6 7 4 3.6382 1.6391 3.6382 -1.7685 4 -4.7070 -1.7685 -4.7070 1.6391 Counts line 0 Atom block Bond block General Sgroup Info Sgroup 1 Atom list block Stext block Sgroup properties Sgroup 2 Sgroup 3 Sgroup Labels [Sgroup] M SLBnn8 sss vvv ... vvv: 20 Unique Sgroup identifier (for MACCS-II only, the integer label is from 1-512) Ctab block
  • 21. Chapter 2: The Connection Table [CTAB] (V2000) Sgroup Connectivity [Sgroup] M SCNnn8 sss ttt ... ttt: HH = head-to-head, HT = head-to-tail, EU = either unknown. Left justified. Sgroup Expansion [Sgroup] M SDS EXPn15 sss ... sss: Sgroup index of expanded superatoms Sgroup Atom List [Sgroup] M SAL sssn15 aaa ... aaa: Atoms in Sgroup sss Sgroup Bond List [Sgroup] M SBL sssn15 bbb ... bbb: Bonds in Sgroup sss. (For data Sgroups, bbb’s are the containment bonds, for all other Sgroup types, bbb’s are crossing bonds.) Multiple Group Parent Atom List [Sgroup] M SPA sssn15 aaa ... aaa: Atoms in paradigmatic repeating unit of multiple group sss Note: To ensure that all current molfile readers consistently interpret chemical structures, multiple groups are written in their fully expanded state to the molfile. The M SPA atom list is a subset of the full atom list that is defined by the Sgroup Atom List M SAL entry. Sgroup Subscript [Sgroup] M SMT sss m... m...: Text of subscript Sgroup sss. (For multiple groups, m... is the text representation of the multiple group multiplier. For superatoms, m... is the text of the superatom label.) Sgroup Correspondence [Sgroup] M CRS sssnn6 bb1 bb2 bb3 bb1, bb2: Crossing bonds that share a common bracket bb3: Crossing bond in repeating unit that connect to bond bb1 Sgroup Display Information [Sgroup] M SDI sssnn4 x1 y1 x2 y2 x1,y1, x2,y2: Coordinates of bracket endpoints 21
  • 22. CTFile Formats Superatom Bond and Vector Information [Sgroup] M SBV sss bb1 x1 y1 bb1: Bond connecting to contracted superatom x1,y1: Vector for bond bb1 connecting to contracted superatom sss Data Sgroup Field Description [Sgroup] M SDT sss fff...fffgghhh...hhhiijjj... sss: Index of data Sgroup fff...fff: 30 character field name (in MACCS-II no blanks, commas, or hyphens) gg: Field type (in MACCS-II F = formatted, N = numeric, T = text) hhh...hhh 20-character field units or format ii: Nonblank if data line is a query rather than Sgroup data, MQ = MACCS-II query, IQ = ISIS query, PQ = program name code query jjj...: Data query operator (blank for MACCS-II) Data Sgroup Display Information [Sgroup] M SDD sss xxxxx.xxxxyyyyy.yyyy eeefgh i jjjkkk ll m sss: Index of data Sgroup x,y: Coordinates (2F10.4) eee: (Reserved for future use) f: Data display, A = attached, D = detached g: Absolute, relative placement, A = absolute, R = relative h: Display units, blank = no units displayed, U = display units i: (Reserved for future use) jjj: Number of characters to display (1...999 or ALL) kkk: Number of lines to display (unused, always 1) ll: (Reserved for future use) m: Tag character for tagged detached display (if non-blank) n: Data display DASP position (1...9). (MACCS-II only) oo: noo (Reserved for future use) Data Sgroup Data [Sgroup] M M SCD sss d... SED sss d... d...: Line of data for data Sgroup sss (69 chars per line, columns 12-80) Note: A line of data is entered as text in 69-character substrings. Each SCD line adds 69 characters to a text buffer (starting with successive SCDs at character positions 1, 70, and 139). Following zero or more SCDs must be an SED, which may supply a final 69 characters. The SED initiates processing of the buffered line of text: trailing blanks are removed and right truncation to 200 characters is performed, numeric and formatted data are validated, and the line of data is added to data Sgroup sss. Left justification is not performed. 22
  • 23. Chapter 2: The Connection Table [CTAB] (V2000) A data Sgroup may have more than one line of data, so more than one set of SCD and SED lines can be present for the same data Sgroup. The lines are added in the same order that they are encountered. If 69 or fewer characters are to be entered on a line, they may be entered with a single SED not preceded by an SCD. On the other hand, if desired a line may be entered to a maximum of 3 SCDs followed by a blank SED that terminates the line. The set of SCD and SED lines describing one line of data for a given data Sgroup must appear together, with no intervening lines for other data Sgroups’ data. Sgroup Hierarchy Information [Sgroup] M SPLnn8 ccc ppp ... ccc: Sgroup index of the child Sgroup) ppp: Sgroup index of the parent Sgroup (ccc and ppp must already be defined via an STY line prior to encountering this line) Sgroup Component Numbers [Sgroup] M SNCnn8 sss ooo ... sss: Index of component Sgroup ooo: Integer component order (1...256). This limit applies only to MACCS-II 3D Feature Properties [3D] M $3Dnnn M $3D...: See below for information on the properties block of a 3D molfile. These lines must all be contiguous End of Block M END This entry goes at the end of the properties block and is required for molfiles which contain a version stamp in the counts line. The Properties Block for 3D Features [3D] For each 3D feature, the properties block includes: • One 3D features count line • One or more 3D features detail lines The characters M $3D appear at the beginning of each line describing a 3D feature. The information for 3D features starts in column 7. 23
  • 24. CTFile Formats Figure 7 Ctab organization of a 3D query Normal 3D Query Exclusion sphere Point Angle Centroid o Plane 75-105 4.4-5.7 Benzene ring N Distance Nitrogen atom 3D Query MACCS-II10179109553D 1 8 M M M M M M M M M M M M M M M M M M 7 0 0 1.0252 -0.4562 -1.4813 -1.0252 0.4562 1.4813 4.1401 4.6453 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 1 2 0 7 8 1 0 $3D 7 $3D -7 6 $3D 3 $3D 6 4 $3D -5 13 $3D 6 $3D 1 2 $3D -8 7 $3D 9 10 $3D -3 6 $3D 9 11 $3D-16 12 $3D 12 1 $3D-12 10 $3D 12 9 $3D -9 3 $3D 7 9 END 0 0 0.2892 0.6578 0.3687 -0.2892 -0.6578 -0.3687 -0.1989 0.5081 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.00000 1.1122 1.3156 0.2033 -1.1122 -1.3156 -0.2033 1.3456 1.7417 18 V2000 C 0 0 C 0 0 C 0 0 C 0 0 C 0 0 C 0 0 N 0 0 C 0 0 0.00000 0 Header block (see Chapter 4) Counts line 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom block Bond block 3D Features Count Atom list block Stext block Ctab block Centroid 2 0.0000 3 4 5 Plane 6 Normal to Plane Point -2.0000 0 75.0000 Exclusion sphere 1.5000 7 4.4000 Properties block 105.0000 5.7000 Angle Distance 3D features count line The first line in the properties block is the 3D features count line and has the following format: M $3Dnnn where nnn is the number of 3D features on a model. 3D features detail lines The lines following the 3D features count line describe each 3D feature on a model. Each 3D feature description consists of an identification line and one or more data lines: 24
  • 25. Chapter 2: The Connection Table [CTAB] (V2000) The identification line is the first line and contains the 3D feature’s type identifier, color, and name. Each data line describes the construction of the 3D feature. Identification line The 3D feature identification line has the following format: M $3Dfffccc aaa...aaa ttt...ttt where the variables represent: fff: 3D feature type ccc: Color number (an internal MDL number which is terminal dependent) aaa...aaa: 3D feature name (up to 32 characters) ttt...ttt: Text comments (up to 32 characters) used by MDL programs (see 3D data constraints later in this chapter) Figure 8 3D feature type identifiers Identifier Meaning -1 Point defined by two points and a distance (in Angstroms) -2 Point defined by two points and a percentage -3 Point defined by a point, a normal line, and a distance -4 Line defined by two or more points (a best fit line if more than two points) -5 Plane defined by three or more points (a best fit plane if more than three points) -6 Plane defined by a point and a line -7 Centroid defined by points -8 Normal line defined by a point and a plane -9 Distance defined by two points and a range (in Angstroms) -10 Distance defined by a point, line, and a range (in Angstroms) -11 Distance defined by a point, plane, and a range (in Angstroms) -12 Angle defined by three points and a range (in degrees) -13 Angle defined by two intersecting lines and a range (in degrees) -14 Angle defined by two intersecting planes and a range (in degrees) -15 Dihedral angle defined by 4 points and a range (in degrees) -16 Exclusion sphere defined by a point and a distance (in Angstroms) -17 Fixed atoms in the model nnn A positive integer indicates atom or atom-pair data constraints 25
  • 26. CTFile Formats Data line The 3D feature defines the data line format. Each 3D object is treated as a pseudoatom and identified in the connection table by a number. The 3D object numbers are assigned sequentially, starting with the next number greater than the number of atoms. The data line formats for the 3D feature types are: Figure 9 3D feature type identifiers Type Description of Data Line -1 The data line for a point defined by two points and a distance (Å) has the following format: M $3Diiijjjddddd.dddd where the variables represent: iii: ID number of a point jjj: ID number of a second point ddddd.dddd Distance from first point in direction of second point (Å), 0 if not used The following example shows POINT_1 created from the atoms 1 and 3 with a constraint distance of 2Å. The first line is the identification line. The second line is the data line. M M -2 $3D -1 $3D 1 4 POINT_1 3 2.0000 The data line for a point defined by two points and a percentage has the format: M $3Diiijjjddddd.ddddd where the variables represent: iii jjj ID number of a second point ddddd.dddd -3 ID number of a point Distance (fractional) relative to distance between first and second points, 0 if not used The data line for a point defined by a point, a normal line, and a distance (Å) has the format: M $3Diiilllddddd.dddd where the variables represent: iii ID number of a point lll ID number of a normal line ddddd.dddd Distance (Å), 0 if not used Note: For chiral models, the distance value is signed to specify the same or opposite direction of the normal. 26
  • 27. Chapter 2: The Connection Table [CTAB] (V2000) -4 The data lines for a best fit line defined by two or more points have the following format: M M $3Dpppttttt.tttt $3Diiijjj...zzz . . . where the variables represent: ppp Number of points defining the line ttttt.tttt Deviation (Å), 0 if not used. iii Each iii, jjj, and zzz is the ID number jjj of an item in the model that defines the line jjj ... (to maximum of 20 items per data line) zzz The following line is defined by the four points 1, 14, 15, and 19 and has a deviation of 1.2Å. The first line is the identification line. The second and third lines are the data lines. M M M -5 $3D -4 2 N_TO_AROM $3D 4 1.2000 $3D 1 14 15 19 The data lines for a plane defined by three or more points (a best fit plane if more than three points) have the following format: M $3Dpppttttt.tttt M $3Diiijjj...zzz ... where the variables represent: ppp Number of points defining the line ttttt.tttt Deviation (Å), 0 if not used. iii Each iii, jjj, and zzz is the ID number jjj of an item in the model that defines the plane jjj ... (to maximum of 20 items per data line) zzz The following plane is defined by the three points 1, 5, and 14. The first line is the identification line. The second and third lines are the data lines. M M M -6 $3D -5 4 PLANE_2 $3D 3 0.0000 $3D 1 5 14 The data line for a plane defined by a point and a line has the following format: M $3Diiilll where the variables represent: iii ID number of a point lll ID number of a line The following plane is defined by the point 1 and the plane 16. The first line is the identification line. The second line is the data line. M M $3D -6 3 PLANE_1 $3D 1 16 27
  • 28. CTFile Formats -7 The data lines of a centroid defined by points have the following format: M M $3Dppp $3Diiijjj...zzz ... where the variables represent: ppp Number of points defining the centroid iii Each iii, jjj, and zzz is the ID number jjj of an item in the model that defines the centroid jjj ... (maximum of 20 items per data line). zzz The following centroid, ARO_CENTER, is defined by 3 items: 6, 8, and 10. The first line is the identification line. The second and third lines are the data lines. M M M -8 $3D -7 $3D 3 $3D 6 1 ARO_CENTER 8 10 The data line for a normal line defined by a point and a plane has the following format: M $3Diiijjj where the variables represent: iii ID number of a point jjj ID number of a plane The following normal line, ARO_NORMAL, is defined by the point 14 and the plane 15. The first line is the identification line. The second line is the data line. M M -9 $3D -8 1 ARO_NORMAL $3D 14 15 The data line for a distance defined by two points and a range (Å) has the following format: M $3Diiijjjddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a point jjj ID number of a second point ddddd.dddd Minimum distance (Å) zzzzz.zzzz Maximum distance (Å) The following distance, L, is between items 1 and 14 and has a minimum distance of 4.9Å and a maximum distance of 6.0Å. The first line is the identification line. The second line is the data line. M M -10 $3D -9 6 L $3D 1 14 4.9000 6.0000 The data line for a distance defined by a point, line, and a range (Å) has the format: M $3Diiilllddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a line ddddd.dddd Minimum distance (Å) zzzzz.zzzz 28 ID number of a point lll Maximum distance (Å)
  • 29. Chapter 2: The Connection Table [CTAB] (V2000) -11 The data line for a distance defined by a point, plane, and a range (Å) has the format: M $3Diiijjjddddd.ddddzzzzz.zzzz where the variables represent: iii jjj ID number of a plane ddddd.dddd Minimum distance (Å) zzzzz.zzzz -12 ID number of a point Maximum distance (Å) The data line for an angle defined by three points and a range (in degrees) has the following format: M $3Diiijjjkkkddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a point jjj ID number of a second point kkk ID number of a third point ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees The following angle, THETA1, is defined by the three points: 5, 17, and 16. The minimum angle is 80° and the maximum is 105°. The first line is the identification line. The second line is the data line. M M -13 $3D-12 5 THETA1 $3D 5 17 16 80.0000 105.0000 The data line for an angle defined by two lines and a range (in degrees) has the following format: M $3Dlllmmmddddd.ddddzzzzz.zzzz where the variables represent: lll ID number of a line, mmm ID number of a second line ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees THETA2 is defined by the lines 27 and 26 with maximum and minimum angles of 45° and 80°. The first line is the identification line. The second line is the data line. M M -14 $3D-13 5 THETA2 $3D 27 26 45.0000 80.0000 The data line for an angle defined by two planes and a range (in degrees) has the following format: M $3Diiijjjddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a plane jjj ID numbers of a second plane ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees 29
  • 30. CTFile Formats -15 The data line for a dihedral angle defined by four points and a range (in degrees) has the following format: M $3Diiijjjkkklllddddd.ddddzzzzz.zzzz where the variables represent: iii ID number of a point jjj ID number of a second point kkk ID number of a third point lll ID number of a fourth point ddddd.dddd Minimum degrees zzzzz.zzzz Maximum degrees DIHED1 is defined by the items 7, 6, 4, and 8 with minimum and maximum angles of 45° and 80°, respectively. The first line is the identification line. The second line is the data line. M M -16 $3D-15 $3D 7 5 DIHED1 6 4 8 45.0000 80.0000 The data lines for an exclusion sphere defined by a point and a distance (Å) have the following format: M M $3Diiiuuuaaaddddd.dddd $3Dbbbccc...zzz ... where the variables represent: iii ID number of the center of the sphere uuu 1 or 0. 1 means unconnected atoms are ignored within the exclusion sphere during a search; 0 otherwise aaa Number of allowed atoms ddddd.dddd Radius of sphere (Å) bbb Each bbb, ccc, and zzz is an ID number of an allowed atom ccc ... (to maximum of 20 items per data line) zzz The following exclusion sphere is centered on point 24, has a radius of 5, and allows atom 9 within the sphere. The first line is the identification line. The second and third lines are the data lines. M M M -17 $3D-16 $3D 24 $3D 9 7 EXCL_SPHERE 0 1 5.0000 The data lines of the fixed atoms have the following format: M M $3Dppp $3Diiijjj...zzz ... where the variables represent: ppp Number of fixed points Each iii, jjj, and zzz is an ID number of a fixed atom iii jjj (to maximum of 20 items per data line) zzz The following examples shows 4 fixed atoms. The first line is the identification line. The second and third lines are the data lines. M M M 30 $3D-17 $3D 4 $3D 3 7 12 29
  • 31. Chapter 2: The Connection Table [CTAB] (V2000) 3D data constraints [3D, Query] A positive integer is used as a type identifier to indicate an atom or atom-pair data constraint. Two lines are used to describe a data constraint. The lines have the following format: M M $3Dnnncccaaa...aaabbbbbbbbpppppppppsss...sss $3Diiijjjddd...ddd where the variables represent: nnn: Database-field number ccc: Color aaa...aaa: Database-field name (up to 30 characters) bbbbbbbb: /BOX = box-number (source of data) (up to 8 characters) ppppppppp: /DASP = n1, n2 where n1 and n2 are digits from 1-9 (data size and position) (up to 9 characters) sss...sss: /DISP = 3DN (name), 3DV (value), 3DQ (query), NOT (no text). First three in any combination to maximum total of 15 characters iii: ID number of an atom jjj: ID number of a second atom for atom-pair data, 0 if data is atom data ddd...ddd: Data constraint (based on format from database) (up to 64 characters) ISIS 3D data query syntax and MACCS-II 3D data query syntax are not identical. The ISIS data query requires a search operator, a blank space, then one or more operands. For more information on ISIS data query syntax, see the ISIS Help system entries on SBF (Search By Form) or QB (Query Builder) for entering text in a query. For information on MACCS-II data searches, see the MACCS-II Command Language Reference. Note: For MACCS-II, the atom number 999 stands for all atoms. The MACCS-II wild card character (@) can be used in the data constraints. The following example shows a numeric data constraint for the field CNDO.CHARGE on atom 12. The first line is the identification line. The second line is the data line. M M $3D 7 $3D 12 0 CNDO.CHARGE 0 -0.3300 -0.1300 The following example shows a numeric data constraint for the field BOND.LENGTH on the atom pair 1 and 4. The first line is the identification line. The second line is the data line. M M $3D $3D 9 1 0 BOND.LENGTH 4 2.0500 1.8200 The following example shows a data constraint allowing any charge value for the field CHARGE on all the atoms. The first line is the identification line. The second line is the data line. M M $3D 12 $3D999 0 CHARGE 0 @ 31
  • 33. Chapter 3: Atom Limit Enhancements The formats presented in this chapter were added to support the chemical representation enhancements of MDL ISIS Desktop 2.0. Phantom Extra Atom The format for phantom extra atom information is as follows: M PXA aaaxxxxx.xxxxyyyyy.yyyyzzzzz.zzzz H e... where: aaa: Index of (real) atom for attachment xyz: Coordinates for the added atom H: Atom symbol e...: Additional text string (for example, the superatom label) The bond to the added phantom atom is added as a crossing bond to the outermost Sgroup that contains atom aaa. Note this appendix supplies coordinates and up to 35 characters of ‘label’ that can be used for the ISIS/Desktop superatom conversion mechanism. ISIS/Desktop uses this appendix to register hydrogen-only superatoms, which are often used as superatom leaving groups on the desktop, but which cannot be directly registered into ISIS/Host databases. The hydrogen-only leaving groups are converted to PXA appendices for registration, and converted back when ISIS/Desktop reads the structure. The following are limitations on phantom extra atom: • Superatom nesting cases • No bonded phantom atom-phantom atom support Superatom Attachment Point The format for superatom attachment point is as follows: M SAP sssnn6 iii ooo cc where: sss: Index of superatom Sgroup nn6: Number of iii,ooo,cc entries on the line (6 maximum) iii: Index of the attachment point atom ooo: Index of atom in sss that leaves when iii is substituted cc: 2 character attachment identifier (for example, H or T for head/tail). No validation of any kind is performed, and ‘ ’ is allowed. ISIS/Desktop uses the first character as the ID of the leaving group to attach if the bond between ooo and iii is deleted, and uses the second character to indicate the sequence polarity: l for left, r for right, and x for none (a crosslink).
  • 34. CTFile Formats The bond iii-ooo is either a sequence bond, a sequence crosslink bond, or a bond to a leaving group that terminates a sequence or caps a crosslink bond. In some cases, this bond may have been deleted by the user, probably to perform a substructure search. In this case, ooo will be 0. If the leaving group attached to iii consists of only a hydrogen, the leaving group will be replaced by a Phantom Extra Atom, as previously described. In this case, iii is set equal to ooo as a signal to ISIS/Desktop that a hydrogen-only leaving group must be reattached to iii. An attachment point entry is one iii,ooo,cc triad. Multiple M SAP lines are permitted for each superatom Sgroup to the maximum of the atom attachment limit. The order of the attachment entries is significant because the first iii,ooo,c becomes the first connection made when drawing to the collapsed superatom, and so forth. Superatom Class The format for superatom class is as follows: M SCL sss d... where: sss: Index of superatom Sgroup d...: Text string (for example, PEPTIDE, ...) 69 characters maximum This appendix identifies the class of the superatom Sgroup. It distinguishes, for example, peptide groups from nucleotides. Large REGNO The format for the regno appendix is as follows: M REG r... where: rrr: Free format integer regno This appendix supports overflow of the I6 regno field in the molfile header. If this appendix is present, the value of the regno in the molfile header is superceded. Sgroup Bracket Style The format for the Sgroup bracket style is as follows: M SBTnn8 sss ttt ... where: sss: Index of Sgroup ttt: Bracket display style: 0 = default, 1 = curved (parenthetic) brackets This appendix supports altering the display style of the Sgroup brackets. 34
  • 35. Chapter 4: Molfiles Overview A molfile consists of a header block and a connection table. The following shows a molfile for alanine corresponding to the following structure: Figure 10 Molfile organization illustrated using alanine L-Alanine C hial r 13 C 3 N + 2 O 1 6 4 O 5 L-Alanine (13C) GSMACCS-II10169115362D 1 6 5 0 -0.6622 0.6622 -0.7207 -1.8622 0.6220 1.9464 1 2 1 1 3 1 1 4 1 2 5 2 2 6 1 M CHG 2 M ISO 1 M END 1 0 0.5342 -0.3000 2.0817 -0.3695 -1.8037 0.4244 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 4 1 6 3 13 0.00366 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.00000 3 V2000 C 0 0 C 0 0 C 1 0 N 0 3 O 0 0 O 0 5 0 Header Block Counts Line 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom Block Connection Table (Ctab) Bond Block -1 Properties Block The format for a molfile is: Header Block: Identifies the molfile: molecule name, user's name, program, date, and other miscellaneous information and comments Ctab Block: Connection table (described in Chapter 2) The detailed format for the header block follows.
  • 36. CTFile Formats The Header Block Line 1: Molecule name. This line is unformatted, but like all other lines in a molfile may not extend beyond column 80. If no name is available, a blank line must be present. Caution: This line must not contain any of the reserved tags that identify any of the other CTAB file types such as $MDL (RGfile), $$$$ (SDfile record separator), $RXN (rxnfile), or $RDFILE (RDfile headers). Line 2: This line has the format: (FORTRAN: IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> ) User's first and last initials (l), program name (P), date/time (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s), energy (E) if modeling program input, internal registry number (R) if input through MDL form. A blank line can be substituted for line 2. If the internal registry number is more than 6 digits long, it is stored in an M Chapter 3). Line 3: 36 A line for comments. If no comment is entered, a blank line must be present. REG line (described in
  • 37. Chapter 5: RGfiles Overview The format of an RGfile (Rgroup query file) is shown below. Lines beginning with $ define the overall structure of the Rgroup query; the molfile header block is embedded in the Rgroup header block. In addition to the primary connection table (Ctab block) for the root structure, a Ctab block defines each member (*m) within each Rgroup (*r). *r *m $MDL REV 1 date/time $MOL $HDR [Molfile Header Block (see Chapter 4) = name, pgm info, comment] $END HDR $CTAB [Ctab Block (see Chapter 2) = count + atoms + bonds + lists + props] $END CTAB $RGP rrr [where rrr = Rgroup number] $CTAB [Ctab Block] $END CTAB $END RGP $END MOL where: *r (Rgroup) is repeated. MACCS-II and ISIS/Desktop have an internal limit of 32 Rgroups. *m (member) is repeated. MACCS-II has a maximum internal limit of 255 total atoms and bonds per Rgroup.
  • 38. CTFile Formats Example of an RGfile (Rgroup query file) Figure 11 $MDL $MOL $HDR REV 1 16OCT91 15:40 GSMACCS-II10169115402D 1 $END HDR $CTAB 9 9 0 1.3337 . 1.3337 0.0000 2.6674 -2.6674 1 2 1 . 3 9 1 M RGP 3 M LOG 1 M LOG 1 M END $END CTAB $RGP 1 $CTAB 1 0 0 12.2100 M APO 1 M END $END CTAB $END RGP $RGP 2 $CTAB 2 1 0 -1.4969 0.0431 1 2 2 M APO 1 M END $END CTAB $CTAB 1 0 0 12.2100 M APO 1 M END $END CTAB $END RGP $END MOL 38 0 0 0 0.7700 -0.7700 3.0800 1.5400 1.5400 0 0 0 . 0 0 0 7 1 8 1 2 0 2 0 0 0.00353 0.0000 . 0.0000 0.0000 0.0000 0.0000 C 0.00000 4 V2000 0 0 C R# R# R# 0 0 0 0 0 0 0 0 0 Molfile header block Counts line 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Atom block of root Number of entries on line Bond block of root Atom list block Stext block Properties block of root Rgroup label location and Rgroup number 2 9 RGfile header block 2 0 Ctab for Rgroup root If/then, RestH, and Occurrence 0 0 0 14.3903 1 1 0 0 0.0508 0.0508 0 0 0 1 1 2 V2000 0.0000 C 0 0 0 0 0 0 2 V2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14.3903 1 1 0.0000 C 0.0000 O Ctab for Rgroup 1 member 1 Block for Rgroup R1 Ctab for Rgroup 2 member 1 Block for Rgroup R2 0.0000 N 2 V2000 0 0 0 0 0 0 Ctab for Rgroup 2 member 2
  • 39. Chapter 5: RGfiles The RGfile shown in Figure 11 on page 38 cor es r ponds t t f l i Rgr quer o he olow ng oup y: R1 IF R1 THEN R2 R2 * R2 R1 = R1 > 0 C * * R2 = R2 = 0 C O N 39
  • 41. Chapter 6: SDfiles Overview An SDfile (structure-data file) contains the structural information and associated data items for one or more compounds.The f m ati : or s *c *d [Molfile (see Chapter 4)] [Data Header] *l [Data] [Blank line] $$$$ where: *l is repeated for each line of data *d is repeated for each data item *c is repeated for each compound A [Molfile] block has the molfile format described in Chapter 4. A [Data Header] (one line) precedes each item of data, starts with a greater than (>) sign, and contains at least one of the following: • The field name enclosed in angle brackets. For example: <melting.point> • The field number, DTn , where n represents the number assigned to the field in a MACCS-II database Optional information for the data header includes: • The compound’s external and internal registry numbers. External registry numbers must be enclosed in parentheses. • Any combination of information The following are examples of valid data headers: > > > > <MELTING.POINT> 55 (MD-08974) <BOILING.POINT> DT12 DT12 55 (MD-0894) <BOILING.POINT> FROM ARCHIVES
  • 42. CTFile Formats Figure 12 Example of an SDfile 1,2 CYCLO-C6 DI-COOH TRANS,L MACCS-II06039016292D 1 0.00339 12 12 0 0 1 0 -0.0238 -0.7702 . 2.6974 0.7634 1 2 1 0 0 0 . . 7 10 1 0 0 0 M END > 25 <MELTING.POINT> 179.0 - 183.0 0.0000 C 0.00000 1 V2000 0 0 25 1 0 0 0 0 0 0 0 Header block Molfile . 0.0000 O 0 0 Connection table Data header Data Blank line Data item Compound > 25 <DESCRIPTION> PW(W) > 25 <ALTERNATE.NAMES> 1,2 CYCLOHEXANE-DICARBOXYLIC ACID TRANS,L HEXAHYDROPHTHALIC ACID TRANS,L Data items > 25 <DATE> 01-10-1980 Nonstructural data > 25 <CRC.NUMBER> C-0710Dat $$$$ 2-METHYL FURAN MACCS-II06039016302D 1 6 0 0 0 0 0.5343 0.3006 . -2.0038 0.2857 1 2 2 0 0 0 . . 5 6 2 0 0 0 M END > 29 <DENSITY> 0.9132 - 20.0 Delimiter 0.00186 6 > 29 <BOILING.POINT> 63.0 (737 MM) 79.0 (42 MM) 0.0000 C 0.00000 1 V2000 0 0 29 0 0 0 0 0 0 0 0 0 Connection table 0 . 0.0000 C Header block Molfile Compound Data header Data Data items Nonstructural data Blank line > 29 <ALTERNATE.NAMES> SYLVAN > 29 <DATE> 09-23-1980 > 29 <CRC.NUMBER> F-0213 $$$$ Delimiter A [Data] value may extend over multiple lines containing up to 200 characters each. A blank line terminates each data item. A line beginning with four dollar signs ($$$$) terminates each complete data block describing a compound. 42
  • 43. Chapter 6: SDfiles A datfile (data file) is effectively an SDfile with no [Molfile] descriptions or $$$$ delimiters. The [Data Header] in a datfile must include either an external or internal registry number in addition to a field name or number. Notes about using blank lines • Only one blank line should terminate a data item. • There should only be one blank line between the last data item and the $$$$ delimiter line. • If the SDfile only contains structures, there can be no blank line between the last "M END" and the $$$$ delimiter line. SDfile after a CFS search After a conformationally flexible substructure (CFS) search, the following format information is appended by MDL ISIS/Base PL to your SDfile after the connection table: • Query information (M $3D appendix lines added to embedded molfile) • CFS generated data (*DATA) • MAPPED ATOMS and BONDS This information describes, for example, how query atoms are mapped, the atom coordinates in models, and what is fitted during a CFS search. Figure 13 Example of SDfile with appended CFS query information M CHG 2 14 -1 16 M $3D 5 M $3D -9 3 M $3D 13 18 6.3000 M $3D -9 3 M $3D 18 9 3.1000 M $3D -9 3 M $3D 18 4 2.4000 M $3D -9 3 M $3D 13 9 2.8000 M $3D -9 3 M $3D 13 4 3.1000 M END > 31 <*DATA> Method = Derivative 1 8.3000 5.1000 3D Query Fields 4.4000 4.8000 5.1000 > 31 <MAPPED ATOMS AND BONDS> (8 13 14 3 9 4 18) (12 13 7 8) CFS-Generated Data Mapping Atoms and Bonds $$$$ 43
  • 45. Chapter 7: Rxnfiles Overview Rxnfiles contain structural data for the reactants and products of a reaction. To see a sample rxnfile go to Figure 14 on page 46.The f m ati : or s [Rxnfile Header] rrrppp $MOL [Molfile of reactant] $MOL [Molfile of product] *r *p where: *r is repeated for each reactant *p is repeated for each product Header Block Line 1: $RXN in the first position on this line identifies the file as a reaction file. Line 2: A line for the reaction name. If no name is available, a blank line must be present. Line 3: User’s initials (I), program name and version (P), date/time (M/D/Y,H:m), and reaction registry number (R). This line has the format: (FORTRAN: IIIIIIPPPPPPPPPMMDDYYYYHHmmRRRRRRR <-A6-><---A9--><---A12----><--I7-> ) A blank line can be substituted for line 3. If the internal registry number is more than 7 digits long, it is stored in an “M line (described in Chapter 3). REG” Note: In rxnfiles produced by earlier versions of MDL ISIS/Host, the year occupied two digits instead of four. There are corresponding minor changes in the adjacent fields. The format of the line is: (FORTRAN: Line 4 IIIIIIPPPPPPPPPPMMDDYYHHmmRRRRRRRR <-A6-><---A10--><---A10--><--I8--> ) A line for comments. If no comment is entered, a blank line must be present.
  • 46. CTFile Formats Figure 14 Rxnfile for the acylation of benzene $RXN Header block REACCS81 1017911041 7439 #Reactants and #Products 2 1 $MOL REACCS8110179110412D 1 4 3 0 0.3929 -1.0590 0.3929 1.6503 1 2 1 1 3 2 1 4 1 M END $MOL 0 0 -0.2577 -0.7710 1.2823 -1.1468 0 0 0 2 0 0 0 2 0 0 0 4 0 6 0 1.3335 1.3335 0.0000 0.0000 -1.3335 -1.3335 1 2 1 1 3 2 2 4 2 3 5 1 4 6 1 5 6 2 M END $MOL 0 0 0 0 0 0 0 0 0 -0.7689 0.7689 -1.5415 1.5415 -0.7689 0.7689 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 9 0 -0.5311 -1.8626 -0.5311 0.8191 -3.2278 -1.8813 2.1282 0.8191 -3.2278 1 2 1 1 3 2 1 4 1 2 5 2 3 6 1 4 7 1 4 8 2 5 9 1 6 9 2 M END 46 1 V2000 C 0 0 C 0 0 O 0 0 Cl 0 0 0 0 0 0 0 0 0 0 315 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 0 0 0 0 0 0 0 0 0 Molfile for first reactant 0.00371 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 C C C C C C 1 V2000 0 0 0 0 0 0 0 0 0 0 0 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 6 0 7 0 8 0 9 0 10 0 0 0 0 0 0 0 0 0 0 0 0 Molfile for second reactant Molfile delimiter REACCS8110179110412D 1 9 0.0000 0.0000 0.0000 0.0000 0.00000 Molfile delimiter REACCS8110179110412D 1 6 0.00380 Molfile delimiter 0 0 0 0 0 0 0 0 0 0 0 0 -0.1384 0.6321 -1.6943 0.6284 -0.1346 -2.4723 -0.1085 2.2292 -1.6831 0 0 2 0 0 2 0 0 4 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 0 0 2 0.00374 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 C C C C C C C O C 1 V2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 255 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 6 0 7 0 1 0 8 0 9 0 2 0 3 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Molfile for product
  • 47. Chapter 7: Rxnfiles Reactants/Products A line identifying the number of reactants and products, in that order. The format is: rrrppp where the variables represent: rrr Number of reactants* ppp Number of products* * MDL ISIS/Host has a limit of 8 reactants and 8 products. MDL Direct does not impose any limits. Molfile Blocks A series of blocks, each starting with $MOL as a delimiter, giving the molfile for each reactant and product in turn. The molfile blocks are always in the same order as the molecules in the reaction; reactants first and products second. The rxnfile in Figure 14 on page 46 corresponds to the following reaction: O O + CH3 Cl 47
  • 49. Chapter 8: RDfiles Overview An RDfile (reaction-data file) consists of a set of editable “records.” Each record defines a molecule or reaction, and its associated data. An example RDfile incorporating the rxnfile described in Chapter 7 is shown later in this chapter (see Figure 15 on page 51).The f m atf or or an RD fl i : ie s [RDfile Header] [Molecule or Reaction Identifier] *d [Data-field Identifier] [Data] *r where: *d is repeated for each data item *r is repeated for each reaction or molecule Each logical line in an RDfile starts with a keyword in column 1 of a physical line. One or more blanks separate the first argument (if any) from the keyword. The blanks are ignored when the line is read. After the first argument, blanks are significant. An argument longer than 80 characters breaks at column 80 and continues in column 1 of the next line. (The argument may continue on additional lines up to the physical limits on text length imposed by the database.) The RDfile must not contain any blank lines except as part of embedded molfiles, rxnfiles, or data. An identifier separates records. RDfile Header Line 1: $RDFILE 1: The [RDfile Header] must occur at the beginning of the physical file and identifies the file as an RDfile. The version stamp “1” is intended for future expansion of the format. Line 2: $DATM: Date/time (M/D/Y, c) stamp. This line is treated as a comment and ignored when the program is read. Molecule and Reaction Identifiers A [Molecule or Reaction Identifier] defines the start of each complete record in an RDfile. The form of a molecule identifier must be one of the following: $MFMT [$MIREG internal-regno [$MEREG external-regno]] embedded molfile $MIREG internal-regno $MEREG external-regno where: • $MFMT defines a molecule by specifying its connection table as a molfile • $MIREG internal-regno is the internal registry number (sequence number in the database) of the molecule
  • 50. CTFile Formats • $MEREG external-regno is the external registry number of the molecule (any uniquely identifying character string known to the database, for example, CAS number) • Square brackets ( [] ) enclose optional parameters • An embedded molfile (see Chapter 4) follows immediately after the $MFMT line The forms of a reaction identifier closely parallel that of a molecule: $RFMT [$RIREG internal-regno [$REREG external-regno]] embedded rxnfile $RIREG internal-regno $REREG external-regno where: • $RFMT defines a reaction by specifying its description as a rxnfile • $RIREG internal-regno is the internal registry number (sequence number in the database) of the reaction • $REREG external-regno is the external registry number of the reaction (any uniquely identifying character string known to the database) • Square brackets ( [] ) enclose optional parameters • An embedded rxnfile (see Chapter 7) follows immediately after the $RFMT line Data-field Identifier The [Data-field Identifier] specifies the name of a data field in the database. The format is: $DTYPE field name Data Data associated with a field follows the field name on the next line and has the form: $DATUM datum The format of datum depends upon the data type of the field as defined in the database. For example: integer, real number, real range, text, molecule regno. For fields whose data type is “molecule regno,” the datum must specify a molecule and, with the exception noted below, use one of the formats defined above for a molecular identifier. For example: $DATUM $MFMT embedded molfile $DATUM $MEREG external-regno $DATUM $MIREG internal-regno In addition, the following special format is accepted: $DATUM molecule-identifier Here, molecule-identifier acts in the same way as external-regno in that it can be any text string known to the database that uniquely identifies a molecule. (It is usually associated with a data field different from the external-regno.) 50
  • 51. Chapter 8: RDfiles Figure 15 Example of a reaction RDfile $RDFILE 1 $DATM 10/17/91 10:41 $RFMT $RIREG 7439 $RXN REACCS81 RDfile header 1017911041 Rxnfile header 7439 #Reactants and #Products 2 1 $MOL REACCS8110179110412D 1 4 1 $MOL 3 . 4 0 1 0 . 0 0 0 0 . 0 0 0 5 $MOL 6 . 6 0 2 0 . 0 0 0 0 . 0 0 0 0.00000 315 0 Molfile for first reactant First Rxn record 4 REACCS8110179110412D 1 6 0.00380 0 0 0.00371 0 0 0.00000 8 Molfile for second reactant 0 2 REACCS8110179110412D 1 0.00374 0.00000 255 Molfile for product 9 9 0 0 0 0 0 0 0 0 0 . . . 6 9 2 0 0 0 2 $DTYPE rxn:VARIATION(1):rxnTEXT(1) $DATUM CrCl3 $DTYPE rxn:VARIATION(1):LITTEXT(1) $DATUM A G Repin, Y Y Makarov-Zemlyanskii, Zur Russ Fiz-Chim, 44, p.2360, 1974 . . . . . $DTYPE rxn:VARIATION(1):CATALYST(1):REGNO $DATUM $MFMT $MIREG 688 REACCS8110179110412D 1 0.00371 0.00000 Data block for reaction 0 4 3 0 0 0 0 0 0 0 0 0 . . . 1 4 1 0 0 0 0 $DTYPE rxn:VARIATION(1):PRODUCT(1):YIELD $DATUM 70.0 . . . $RFMT $RIREG 8410 $RXN REACCS81 1017911041 8410 Start of next Rxn record 2 1 $MOL ... 51
  • 53. Chapter 9: XDfiles Overview An XDfile (XML-data file) uses a standard set of XML elements that represent records of data. The XDfile format also provides: • Metadata or information about the origin of the data. Unlike the other CTfile formats such as the SDfile or RDfile, the XDfile enables the consumer of the data to correctly interpret it. • The ability to handle generalized data models, such as multiple structures and nonstructure fields per record, multiple reactions per record, multiline data, and binary data. None of the other CTfile formats such as SDFiles or RDFiles have this ability. • Very few restrictions on data formatting within the actual content. Data formatting is based on XML, which does not have restrictions on line length or blank lines. See “Data Formatting” on page 54. • Fast and easy parsing by using any XML parser. The XML data can be validated by using a DTD (Document Type Definition) or an XML schema that defines primitive rules which the data must follow. You can download the DTD and XML schema from the CTFile Formats download page at the Elsevier MDL web site (www.mdl.com). From the Elsevier MDL web site, click Downloads > Download Products > Select a Product > MDL CTFile Formats no-fee > MDL CTFile Formats. Note: Due to limitations in the capabilities of DTDs and XML schemas, an XDfile that is validated by the DTD and XML schema is not guaranteed to be correct. For example, it is possible to create a record with duplicate field values. The DTD and XML schema only provide a low level of validation. Applications which process XDfiles must provide high level checks on the consistency of the data. • Flexibility in creating application-specific XML tags. Note, however, that it is the responsibility of the client application to interpret these custom tags. The Data Source Service of MDL® Core Interface can read an XDfile and load it into an XML data source. It also provides tools for converting SDfiles and RDfiles to XDfiles. For information about these tools, see the "Utilities" section in the "Data Source Service" chapter of MDL Core Interface Developer’s Guide. Note: Although it is possible to convert SDfiles and RDfiles to XDfiles, there are risks involved in converting an XDfile to the original format. This is because the backward conversion will lose the metadata which is not supported in the other CTfile formats. The rest of this chapter contains reference information about the XML elements in an XDfile. For the structure of an XDfile, see “Hierarchy of Elements” on page 55. For an alphabetic list of elements in an XDfile, see “Alphabetic List of Elements” on page 57.
  • 54. CTFile Formats Data Formatting XML puts little or no restrictions on data formatting within the actual content. Data that is sensitive to white space, molfiles and rxnfiles in particular, must be enclosed in a CDATA section. You must set the xml:space attribute to "preserve". The following example is a Field element that contains a molfile: <Field name="Mol" xml:space="preserve"><![CDATA[ -ISIS- 03190310282D 1 0 0 0 0 0 0 -2.1000 -0.1208 M END ]]></Field> 0 0 0999 V2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 Note that for data outside a CDATA section, certain characters must be escaped as described in the following table: Character Representation in XML < &lt; > &gt; " &quot; ’ &apos; & &amp; For example, "mp < 100" becomes "mp &lt; 100". See also the XML specification for more details. 54
  • 55. Chapter 9: XDfiles Hierarchy of Elements The following shows the hierarchy of elements within an XDfile. The attributes of the elements are not shown in order to more clearly show the structure of the XML: <XDfile> <Dataset> <Source> <DataSource /> <ProgramSource /> <CreatorName /> <CreateDate /> <CreateTime /> <Description /> <Copyright /> </Source> <Metadata> <FieldDef /> <ParentDef> <FieldDef /> </ParentDef> </Metadata> <Data> <Record> <Field> </Field <Parent> <Record> <Field> </Field> </Record> </Parent> </Record> </Data> </Dataset> </XDfile> 55
  • 56. CTFile Formats The following XML schema diagram also illustrates the hierarchy of elements in an XDfile: 56
  • 57. Chapter 9: XDfiles Alphabetic List of Elements Element Parent Brief Description Copyright Source A copyright notice for the data CreateDate Source The date the data was created CreateTime Source The time the data was created CreatorName Source The person who created the data Data Dataset Contains records of data Dataset XDfile Contains a collection of data DataSource Source The source of the data Description Source A description or comment about the data Field Record The value of a field in a record FieldDef Metadata The definition of a field in the data ParentDef The root element XDfile Metadata Dataset Contains definitions of fields in the data Parent Record Contains subrecords of data ParentDef Metadata The definition of a parent field in the data ProgramSource Source The program that created the data Record Data The unit of data; contains a set of field values Parent Source Dataset Contains information about the source of data 57
  • 58. CTFile Formats XDfile The root element. XML data that uses the XDfile format must begin with <XDfile> and end with </XDfile>. It contains one or more Dataset elements. Attributes The data type of all attributes is CDATA. Attribute Required Description xmlns Yes The default namespace for elements in the XDfile. The default is http://www.mdl.com/XDfile/NS. version Yes The version number of the XDfile data. The default is 1.2. Parent Element None Child Elements Element Description Dataset 58 Required Yes A single collection of data
  • 59. Chapter 9: XDfiles Example <?xml version="1.0"?> <XDfile xmlns="http://www.mdl.com/XDfile/NS"> <Dataset name="MySource"> <Source> <DataSource>ACD99.1 Hview</DataSource> <ProgramSource>GCS 1.0</ProgramSource> <CreatorName>John Doe</CreatorName> <CreateDate DATEFORMAT="M/D/Y">7/22/99</CreateDate> <CreateTime TIMEFORMAT="24">13:45</CreateTime> </Source> <Metadata> <FieldDef name="Molstructure" type="Structure" molFormat="Chime"/> <FieldDef name="Reaction Vessel ID" type="FixedText" maxLength="15"/> <FieldDef name="Library ID" type="FixedText" maxLength="8"/> <FieldDef name="Tag Id" type="fixedText" maxLength="3"/> <ParentDef name="XYZ Test Results"> <FieldDef name="Dose" type="Double"/> <FieldDef name="Response" type="Double"/> </ParentDef> </Metadata> <Data> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A02</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">yes</Field> <Parent name="XYZ Test Results" totalRecords="2"> <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> <Record> <Field name="Dose">2.0</Field> <Field name="Response">999.0</Field> </Record> </Parent> </Record> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A03</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">no</Field> </Record> </Data> </Dataset> </XDfile> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 59
  • 60. CTFile Formats Dataset A self-contained, single collection of data. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes, if multiple datasets The name of the dataset. If XDfile contains only one dataset, name is optional. If XDfile contains multiple datasets, name is required in order to identify each dataset. Parent Element XDfile Child Elements Element Required Description Source No Describes the source of the data Metadata No Describes the individual fields in the actual data Data Yes The actual data Example <Dataset> <Metadata> <FieldDef name="CTAB" type="Structure" molFormat="Chime"/> <FieldDef name="Regno" type="Integer" isPrimaryKey="true"/> <FieldDef name="Molname" type="FixedText"/> <FieldDef name="Date" type="Date"/> <FieldDef name="DoubleValue" type="Double"/> </Metadata> <Data totalRecords="1"> <Record> <Field name="CTAB">40Aieg6Mprlczdb^fg37JiOh</Field> <Field name="Regno">1</Field> <Field name="Molname">Test Structure</Field> <Field name="Date">05/10/2002</Field> </Record> </Data> </Dataset> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 60
  • 61. Chapter 9: XDfiles Source Contains information that describes the source of the data. Note that although each child element is optional, the order of the child elements is fixed. If a child element does not follow the order specified below, the element is discarded. Attributes None Parent Element Dataset Child Elements Element Required Description DataSource No The source of the data. ProgramSource No The program that created the data. CreatorName No The name of the person who created the data. CreateDate No The date the data was created. The default format is M-D-Y. CreateTime No The time the data was created. The default format is 24-hour. Description No A description or comments about the data. Copyright No A copyright notice for the data. Example <Source> <DataSource>ACD99.1 Hview</DataSource> <ProgramSource>Core Interface 1.1</ProgramSource> <CreatorName>John Doe</CreatorName> <CreateDate dateOrder="M/D/Y">7/22/99</CreateDate> <CreateTime timeFormat="24">13:45</CreateTime> </Source> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 61
  • 62. CTFile Formats DataSource The source of the actual data. Attributes None Parent Element Source Child Elements None Example <DataSource>ACD99.1 Hview</DataSource> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 62
  • 63. Chapter 9: XDfiles ProgramSource The program that created the actual data. Attributes None Parent Element Source Child Elements None Example <ProgramSource>MDL Core Interface 1.0</ProgramSource> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 63
  • 64. CTFile Formats CreatorName The person who created the actual data. Attributes None Parent Element Source Child Elements None Example <CreatorName>John Doe</CreatorName> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 64
  • 65. Chapter 9: XDfiles CreateDate The date the actual data was created. The default format is M-D-Y. Attributes The data type of all attributes is CDATA. Attribute Required Description dateOrder No The format for the date in <CreateDate>. The separator character is specified as part of the format. The valid formats are: M-D-Y D-M-Y Y-M-D Y-D-M The default format is M-D-Y. Parent Element Source Child Elements None Example <CreateDate dateOrder="M/D/Y">7/22/99</CreateDate> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 65
  • 66. CTFile Formats CreateTime The time the actual data was created. The default format is 24-hour. Attributes The data type of all attributes is CDATA. Attribute Required Description timeFormat No The format for the time in <CreateTime>. The valid values are: 24 12 The default format is 24. Parent Element Source Child Elements None Example <CreateTime>24:15</CreateTime> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 66
  • 67. Chapter 9: XDfiles Description A description or comment about the actual data. Attributes None Parent Element Source Child Elements None Example <Description>This is test data.</Description> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 67
  • 68. CTFile Formats Copyright A copyright notice for the data. Attributes None Parent Element Source Child Elements None Example <Copyright>Copyright 2003 by Acme Corporation </Copyright> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 68
  • 69. Chapter 9: XDfiles Metadata Contains information that describes the fields in the data. Applications can use this information to allow automatic creation of database tables or better formatting of data. The hierarchical structure of the Metadata element must match the data model contained in the Data element. Attributes None Parent Element Dataset Child Elements Element Required Description ParentDef No Contains information about a single parent within the data FieldDef No Contains information about a single field within the data Example <Metadata> <FieldDef name="Molstructure" type="Structure" molFormat="Chime"/> <FieldDef name="Reaction Vessel ID" type="FixedText" maxLength="15"/> <FieldDef name="Library ID" type="FixedText" maxLength="8"/> <FieldDef name="Tag Id" type="FixedText"/> <ParentDef name="XYZ Test Results"> <FieldDef name="Dose" type="Double"/> <FieldDef name="Response" type="Double"/> </ParentDef> </Metadata> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 69
  • 70. CTFile Formats ParentDef Contains information about a single parent field within the data. Note: Do not create unnecessary parent fields at the root. Parent fields should only be used when there is an actual hierarchical structure to the data. For example, an SDFile would not have ParentDef elements, but would only have multiple FieldDef elements directly under the Metadata element. The actual data in the SDFile follows this format by having multiple Record elements directly under the Data element. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the parent field. This is a simple name because the context of the parent in the hierarchy is implied by the XML structure. Parent Element Metadata ParentDef Child Elements Element Required Description FieldDef Yes Contains information about a single field within the data ParentDef No Contains information about a single parent within the data. A parent within a parent creates a hierarchy. Example <ParentDef name="XYZ Test Results"> <FieldDef name="Dose" type="Double"/> <FieldDef name="Response" type="Double"/> </ParentDef> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 70
  • 71. Chapter 9: XDfiles FieldDef Contains information about a single field within the data. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the field. This is a simple name because the context of the field in the hierarchy is implied by the XML structure. type Yes The type of data in the field. Applications can define their own type, but it will be the responsibility of client applications to interpret these. The valid values are: Reaction Structure Integer Double FixedText VariableText Date Time DateTime Binary isKey No “true” if the field is a key. The valid values are: true false The default value is false. isPrimaryKey No “true” if the field is a primary key. The valid values are: true false The default value is false. nativeName No The name of the field specific to the source from which it is derived. For example, a native name for an Oracle database is schema.table.column. encoding No The encoding set used by the data. Sample values are: binhex rot64 71
  • 72. CTFile Formats Attribute Required Description charset No The character set used by the text. A sample value is ISO-8859-1. decimalSeparator No The decimal separator used for floating point numbers. The valid values are: Period Comma The default value is Period. maxLength No The maximum length of the data in this field. For binary fields in a relational data source (such as CLOB and BLOB fields), the maximum length varies depending on the version of the Oracle JDBC driver. molFormat No The format for the structure, if the field contains structures. The valid values are: Molfile Chime Smiles The default value is Molfile. rxnFormat No The format for the reaction, if the field contains reactions. The valid values are: Rxnfile Chime The default value is Rxnfile. molVersion No The version of the data format. molVersion is currently only applicable to structures. The absence of this attribute implies a pre-V2000 molfile. The valid values are: V2000 V3000 dateOrder No The order and format of a date field. The value specifies the separator character. Dates must be specified using numbers only; do not use month names. The valid orders are: M-D-Y D-M-Y Y-M-D Y-D-M The default value is M-D-Y. 72
  • 73. Chapter 9: XDfiles Attribute Required Description timeOrder No The order of a date field. The value specifies the separator character. The valid orders are: h:m m:h The default value is h:m. timeFormat No The format of a time field. The valid values are: 24 12 The default value is 24. precision No The precision for a real number field. This is the total number of digits. scale No The scale for a real number field. This is the number of digits to the right of the decimal point. nullsAllowed No “true” if the field can contain nulls. The valid values are: true false The default value is false. isIndexed No “true” if the field is indexed. The valid values are: true false The default value is false. isHidden No “true” if the field is hidden. The valid values are: true false The default value is false. units No The units of measure associated with the field. javaFormat No The Java format to use when the field value is parsed. This is the Java output format used by the NumberFormat or DateFormat class. Parent Element Metadata, ParentDef Child Elements None 73
  • 74. CTFile Formats Example <FieldDef name="Molstructure" type="Structure" molFormat="Chime"/> <FieldDef name="Reaction Vessel ID" type="FixedText" maxLength="15" /> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 74
  • 75. Chapter 9: XDfiles Data Contains a collection of Record child elements that contain the actual data. Each Record element contains a collection of Parent and Field elements whose hierarchical structure must match the hierarchy in the Metadata element. The Data element can be empty if there is no data or only the metadata is to be transferred. Attributes The data type of all attributes is CDATA. Attribute Required Description totalRecords No The total number of root-level records in the data Parent Element Dataset Child Elements Element Required Description Record No A record of data Example <Data totalRecords="2"> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A02</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">yes</Field> <Parent name="XYZ Test Results" totalRecords="2"> <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> <Record> <Field name="Dose">2.0</Field> <Field name="Response">999.0</Field> </Record> </Parent> </Record> <Record> <Field name="Molstructure" xml:space="preserve"> <![CDATA[7YALEn$Akl$QPbas35quasdfsdf38...]]></Field> <Field name="Reaction Vessel ID">SAR6077R-01A03</Field> <Field name="Library ID">SAR6077R</Field> <Field name="Tag Id">no</Field> </Record> </Data> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 75
  • 76. CTFile Formats Parent Contains child records of data. A Parent can contain other Parent elements, thus, creating a sub-hierarchy of data. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the field. totalRecords No The total number of records under this parent Parent Element Record Child Elements Element Required Description Record No A record of data Example <Parent name="XYZ Test Results" ID="100"> <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> <Record> <Field name="Dose">2.0</Field> <Field name="Response">999.0</Field> </Record> </Parent> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 76
  • 77. Chapter 9: XDfiles Record A record of data, and contains a set of Field elements. Attributes None Parent Element Data Parent Child Elements Element Required Description Field No A single field of data Parent No Contains subrecords of data. A parent within a record creates a hierarchy. Example <Record> <Field name="Dose">1.0</Field> <Field name="Response">99.0</Field> </Record> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 77
  • 78. CTFile Formats Field Contains data for a single field in a record. Note that the molFormat, molVersion, and rxnFormat attributes can be used on individual Field elements to override the format specified in the Metadata element. Attributes The data type of all attributes is CDATA. Attribute Required Description name Yes The name of the parent field. molFormat No The format for the structure, if the field contains structures. This value overrides the molFormat specified in the Metadata element. The valid values are: Molfile Chime Smiles The default value is Molfile. rxnFormat No The format for the reaction, if the field contains reactions. This value overrides the rxnFormat specified in the Metadata element. The valid values are: Rxnfile Chime The default value is Rxnfile. molVersion No The version of the data format. molVersion is currently only applicable to structures. The absence of this attribute implies a pre-V2000 molfile. This value overrides the molVersion specified in the Metadata element. The valid values are: V2000 V3000 Parent Element Record Example <Field name="Dose">1.0</Field> See Also “Alphabetic List of Elements” on page 57, “Hierarchy of Elements” on page 55 78
  • 79. Chapter 10: The Extended Connection Table (V3000) Overview The extended (V3000) molfile consists of a regular molfile “no structure” followed by a single molfile appendix that contains the body of the connection table (Ctab). The following figure shows both an alanine structure and the extended molfile corresponding to it. See Chapter 2 for the V2000 version of this same structure. Figure 16 Extended molfile organization illustrated using alanine L-Alanine C hial r 13 C 3 N + 2 1 O 6 4 O 5 L-Alanine GSMACCS-II07189510252D 1 0.00366 0.00000 0 Figure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 5 0 0 1 M V30 BEGIN ATOM M V30 1 C -0.6622 0.5342 0 0 CFG=2 M V30 2 C 0.6622 -0.3 0 0 M V30 3 C -0.7207 2.0817 0 0 MASS=13 M V30 4 N -1.8622 -0.3695 0 0 CHG=1 M V30 5 O 0.622 -1.8037 0 0 M V30 6 O 1.9464 0.4244 0 0 CHG=-1 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 3 CFG=1 M V30 3 1 1 4 M V30 4 2 2 5 Blocks not used in this Ctab: M V30 5 1 2 6 Sgroup block, Rgroup block, 3D block M V30 END BOND M V30 END CTAB M END Header Block Comment Line Counts Line Atom Block Connection Table (Ctab) Bond Block Note that the “no structure” is flagged with the “V3000” instead of the “V2000” version stamp. There are two other changes to the header in addition to the version: • The number of appendix lines is always written as 999, regardless of how many there actually are. (All current readers will disregard the count and stop at M END.) • The “dimensional code” is maintained more explicitly. Thus “3D” really means 3D, although “2D” will be interpreted as 3D if any non-zero Z-coordinates are found. Unlike the V2000 molfile, the V3000 extended Rgroup molfile has the same header format as a non-Rgroup molfile.
  • 80. CTFile Formats Note: Do not create a molfile with a pre-V3000 Rgroup header ("$MDL", and so forth) but with V3000 Ctab blocks. This is not allowed. A pre-V3000 Rgroup molfile can only have embedded molfiles that are also pre-V3000 versions, for example, the version is either "V2000" or " ". Specifications For Atom and Bond Descriptions The general syntax of an entry is: M V30 key posval posval ... [keyword=value] [keyword=value] ... or M V30 BEGIN key [blockname] M V30 posval posval ... keyword=value keyword=value ... ... M V30 END key Each line must begin with "M V30 " with the two blank spaces after M and one blank space after 30. Following this is a list of zero or more required positional values (posval). Optional values may follow which use a ’KEYWORD=value’ format. Items are separated by white space. There can also be white space preceding the first item. Trailing white space is ignored. The value of a keyword can be a list containing two or more values: KEYWORD=(N val1 val2 ... valN) where N specifies the number of items that follow. Values (posval, value, or val1, and so forth) can be strings. Strings that contain blank spaces or start with left parenthesis or double quote, must be surrounded by double quotes. A double quote may be entered literally by doubling it. Each entry is one line of no more than 80 characters. To allow continuation when the 80-character line is too short, use a dash (-) as the last character. When read, the line is concatenated with the next line by removing the dash and stripping the initial "M V30" from the following line. For example: M M V30 10 20 30 “abcV30 def” is read as: M V30 10 20 30 "abc def" Generally, each section of the molfile is enclosed in a block that consists of lines such as: M V30 BEGIN key [blockname] ... M V30 END key The ‘key’ value defines the kind of block, for example, CTAB, ATOM, or BOND. Depending upon the type of block, there may or may not be values on the BEGIN line. 80
  • 81. Chapter 10: The Extended Connection Table (V3000) Conventions The new format conventions used in this chapter are as follows: UPPERCASE Literal text, to be entered as shown. Only the position of "M V30 " is significant; white space may be added anywhere else to improve readability. Note that both lower- and uppercase characters, or any combination of them, are acceptable for literals. They are shown here in uppercase only for readability. lowercase A token, which is defined elsewhere. [] An optional item. Do not include the brackets. [ ]* An optional item, where there may be zero, one, two, or more of the item. | Separates two or more options, only one of which is valid. / Separates two or more items. Either or both may appear in any order. {} Braces are used for grouping. They indicate indefinite or definite repeat. The Extended Connection Table The features of the extended connection table are described in this section. CTAB Block A Ctab block defines the basic connection table, which is defined as: M V30 BEGIN CTAB [ctabname] counts-line atom-block [bond-block] [sgroup-block] [3d-block] [link-line]* M V30 END CTAB The atom block, like the counts line, is required. The Sgroup block, 3D block, and link lines may occur in any order after the atom and bond blocks. The counts line, atom block, and bond block must appear in the order indicated. 81
  • 82. CTFile Formats Counts Line A counts line is required, and must be first. It specifies the number of atoms, bonds, 3D objects, and Sgroups. It also specifies whether or not the CHIRAL flag is set. Optionally, the counts line can specify molregno. This is only used when the regno exceeds 999999 (the limit of the format in the molfile header line). The format of the counts line is: M V30 COUNTS na nb nsg n3d chiral [REGNO=regno] where: na = number of atoms nb = number of bonds nsg = number of Sgroups n3d = number of 3D constraints chiral = 1 if molecule is chiral, 0 if not regno = molecule or model regno Atom Block An atom block specifies all node information for the connection table. It must precede the bond block. It has the following format: M V30 M V30 M V30 M V30 M V30 M V30 M V30 M V30 M V30 . . . M V30 BEGIN ATOM index type x y z aamap [CHG=val] [RAD=val] [CFG=val] [MASS=val] [VAL=val] [HCOUNT=val] [STBOX=val] [INVRET=val] [EXACHG=val] [SUBST=val] [UNSAT=val] [RBCNT=val] [ATTCHPT=val] [RGROUPS=(nvals val [val ...])] [ATTCHORD=(nvals nbr1 val1 [nbr2 val2 ...])] END ATOM The values are described in the following table. Figure 17 Meaning of values in the atom block Field Meaning Values Notes index Atom index Integer > 0 Identifies atoms. The actual value of the index does not matter as long as each index is unique to each atom. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Atom type Type = reserved atom or atom or [NOT] ‘[‘atom, atom,...’]’ A character string. If the string contains white space, it must be quoted. It can be a single atom or an atom list enclosed in square brackets with an optional preceding NOT. where reserved atom = R# = Rgroup A = “any” atom Q = any atom but C or H * = “star” atom Atom = character string (For example, ‘C’ or ‘Cl') xyz 82 Atom coordinates Angstroms
  • 83. Chapter 10: The Extended Connection Table (V3000) aamap Atom-atom mapping 0 = no mapping Reaction property > 0 = mapped atom CHG Atom charge Integer Same range as V2000 0 = none (default) RAD Atom radical 0 = none (default) 1 = singlet 2 = doublet 3 = triplet CFG Stereo configuration 0 = none (default) 1 = odd parity 2 = even parity 3 = either parity MASS Atomic weight Default = natural abundance A specified value indicates the absolute atomic weight of the designated atom. VAL Valence Integer > 0 or Abnormal valence 0 = none (default) -1 = zero HCOUNT Query hydrogen count Integer > 0 or Same maximum value as V2000 0 = not specified (default) -1 = zero STBOX Stereo box 0 = ignore the configuration of this double bond atom (default) 1 = consider the stereo configuration of this double bond atom INVRET Configuration inversion 0 = none (default) Both atoms of a double bond must be marked to search double bond stereochemistry. Alternatively, the STBOX bond property can be used. Reaction property 1 = configuration inverts 2 = configuration retained EXACHG Exact change 0 = property not applied (default) Reaction property 1 = exact change as displayed in the reaction SUBST Query substitution count Integer > 0 or Same maximum value as V2000. 0 = not specified (default) -1 = none UNSAT RBCNT Query unsaturation flag 0 = not specified (default) Query ring bond count Integer > 0 or 1 = unsaturated Same maximum value as V2000. 0 = not specified (default) -1 = none 83
  • 84. CTFile Formats ATTCHPT Rgroup member attachment points Attachment points on member: -1 = first and second site 1 = first site only When the Rgroup member atom has two attachment points, the atom with the lowest index number attaches to the first attachment point 2 = second site only RGROUPS Integer > 0 val is the Rgroup number. ATTCHORD nvals is the number of Rgroups that comprise this R# atom. Integer > 0 nvals is the number of values that follow on the ATTCHORD line Integer > 0 A list of atom neighbor index and atom neighbor value pairs that identify the attachment order information at the R# atom nbr1 is atom neighbor index #1, nbr2 is index #2 val1 is the attachment order for the nbr1 attachment. Bond block A bond block specifies all edge information for the connection table. It must precede the Sgroup or 3D blocks. Its format is: M V30 BEGIN BOND M V30 index type atom1 atom2 [CFG=val] [TOPO=val] [RXCTR=val] [STBOX=val] ... M V30 END BOND where the values are described in the following table: Figure 18 Meaning of values in the bond block Field Meaning Values Notes index Bond index Integer > 0 The actual value of the index does not matter as long as all are unique. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Bond type Integer: Types 4 through 8 are for queries only. 1 = single 2 = double 3 = triple 4 = aromatic 5 = single or double 6 = single or aromatic 7 = double or aromatic 8 = any 84
  • 85. Chapter 10: The Extended Connection Table (V3000) atom1,ato m2 Atom indexes Integer > 0 CFG Bond configuration Atom1 and Atom2 are bond end points. 0 = none (default) 1 = up 2 = either 3 = down TOPO Query property 0 = not specified (default) 1 = ring 2 = chain RXCTR Reacting center status 0 = unmarked (default) -1 = not a reacting center 1 = generic reacting center Additional: 2 = no change 4 = bond made or broken 8 = bond order changes 12 =( 4 + 8) bond made or broken and changes 5 = (4 + 1), 9 = (8 + 1), and 13 =(12 + 1) are also possible STBOX Stereo box 0 = ignore the configuration of this double bond (default) A double bond must be marked to search double bond stereochemistry 1 = consider the stereo configuration of this double bond Link atom line There is one link atom line for each link atom in the Ctab. A link atom line has the format: M V30 LINKNODE minrep maxrep nbonds inatom outatom [inatom outatom...] 85
  • 86. CTFile Formats Figure 19 Meaning of values in link lines Field Values Notes minrep Minimum number of group repetitions. 1 For future expansion. Not currently used. maxrep Maximum number of group repetitions. Integer > 0 nbonds Number of directed bonds defining the group. nbonds = # of pairs of inatom-outatom tuples inatom Atom index of atom in the repeating group. Integer > 0 outatom 86 Meaning Atom index of atom bonded to inatom, but outside of repeating group. Integer > 0 Number of tuples is usually two but may be one for link nodes with an attachment point.
  • 87. Chapter 10: The Extended Connection Table (V3000) Sgroup block The Sgroup block contains general Sgroup information and information on each Sgroup structure as shown here. For the V2000 version of this Sgroup structure and connection table, see Chapter 2. Figure 20 Connection Table Organization of an Sgroup Structure Pol er ym 7 5 2 1 * 6 n 3 4C l n * r an Polymer GSMACCS-II07189510252D 1 0.00374 0.00000 0 Figure 5, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 6 3 0 0 M V30 BEGIN ATOM M V30 1 * 2.9463 0.3489 0 0 M V30 2 C 1.6126 1.1189 0 0 M V30 3 C 0.2789 0.3489 0 0 CFG=3 Blocks not used in this Ctab: M V30 4 Cl 0.2789 -1.1911 0 0 Rgroup block, 3D block M V30 5 C -1.0548 1.119 0 0 M V30 6 C -2.3885 0.349 0 0 M V30 7 * -3.9246 1.147 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 4 1 5 6 M V30 5 1 5 3 M V30 6 1 7 6 M V30 END BOND M V30 BEGIN SGROUP M V30 1 SRU 5 ATOMS=(2 5 6) XBONDS=(2 5 6) BRKXYZ=(9 -0.6103 1.2969 0 -0.6103 M V30 0.171 0 0 0 0) BRKXYZ=(9 -3.1565 0.185 0 -3.1565 1.311 0 0 0 0) M V30 CONNECT=HT M V30 2 SRU 6 ATOMS=(3 2 3 4) XBONDS=(2 1 5) BRKXYZ=(9 2.2794 1.2969 0 2.2794 M V30 0.1709 0 0 0 0) BRKXYZ=(9 -0.1657 0.171 0 -0.1657 1.2969 0 0 0 0) M V30 CONNECT=HT M V30 3 COP 7 ATOMS=(7 1 2 3 4 5 6 7) BRKXYZ=(9 3.6382 1.6391 0 3.6382 M V30 -1.7685 0 0 0 0) BRKXYZ=(9 -4.707 -1.7685 0 -4.707 1.6391 0 0 0 0) M V30 SUBTYPE=RAN M V30 END SGROUP M V30 END CTAB M END Header Block Comment Line Counts Line Atom Block Connection Table (Ctab) Bond Block Sgroup Block Sgroup 1 Properties Sgroup 2 Properties Sgroup 3 Properties 87
  • 88. CTFile Formats An Sgroup block defines all Sgroups in the molecule, including superatoms. The format is as follows: M V30 BEGIN SGROUP [M V30 DEFAULT [CLASS=class] -] M V30 index type extindex M V30 [ATOMS=(natoms atom [atom ...])] M V30 [XBONDS=(nxbonds xbond [xbond ...])] M V30 [CBONDS=(ncbonds cbond [cbond ...])] M V30 [PATOMS=(npatoms patom [patom ...])] M V30 [SUBTYPE=subtype] [MULT=mult] M V30 [CONNECT=connect] [PARENT=parent] [COMPNO=compno] M V30 [XBHEAD=(nxbonds xbond [xbond ...])] M V30 [XBCORR=(nxbpairs xb1 xb2 [xb1 xb2 ...])] M V30 [LABEL=label] M V30 [BRKXYZ=(9 bx1 by1 bz1 bx2 by2 bz2 bx3 by3 bz3])* M V30 [ESTATE=estate] [CSTATE=(4 xbond cbvx cbvy cbvz)]* M V30 [FIELDNAME=fieldname] [FIELDINFO=fieldinfo] M V30 [FIELDDISP=fielddisp] M V30 [QUERYTYPE=querytype] [QUERYOP=queryop] M V30 [FIELDDATA=fielddata] ... M V30 [CLASS=class] M V30 [SAP=(3 aidx lvidx id)]* M V30 [BRKTYP=bracketType] ... M V30 END SGROUP The DEFAULT field provides a way to specify default values for keyword options. The same keyword options and values as defined in the following table. Figure 21 Meaning of values in the Sgroup block Field Meaning Values Notes index Sgroup index Integer > 0 The actual value of the index does not matter as long as all indexes are unique. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Sgroup type String. Only first 3 letters are significant: SUPeratom MULtiple SRU MONomer COPolymer CROsslink MODification GRAft COMponent MIXture FORmulation DATa ANY GENeric extindex Integer => 0: Use 0 to autogenerate a number. If 0, positive integer assigned 88 External index value This is the V2000 Sgroup label
  • 89. Chapter 10: The Extended Connection Table (V3000) ATOMS natoms is the number of atoms that define the Sgroup. atom is the atom index. XBONDS Integer > 0 Integer > 0 Integer > 0 ncbonds is the number of containment bonds. Integer > 0 cbond is the containment-bond index PATOMS Integer > 0 xbond is the crossing-bond index. CBONDS nxbonds is the number of crossing bonds. Integer > 0 npatom is the number of paradigmatic repeating unit atoms. Integer > 0 Only used for Data Sgroups. This field is expected to become obsolete and is retained for compatibility with MACCS-II. The field is only used for multiple groups. patom is the atom index of an atom in the paradigmatic repeating unit for a multiple group. SUBTYPE subtype is the Sgroup subtype. String. Only the first 3 letters are significant: ALTernate RANdom BLOck MULT mult is the multiple group multiplier. Integer > 0 CONNECT connect is the connectivity. String values are as follows: EU (default) The default, if missing, is EU. The MDL V2000 writer never writes an EU entry. HH HT PARENT parent is the parent Sgroup index. Integer > 0 COMPNO compno is the component order number. Integer > 0 XBHEAD nxbonds is the number of crossing bonds that cross the “head” bracket. Integer > 0 xbond is the crossing-bond index. Integer > 0 If XBHEAD is missing, no bonds are paired as the head or tail of the repeating unit 89
  • 90. CTFile Formats XBCORR nxbpairs 2 x the number of pairs of crossing-bond correspondence, that is, the number of values in list. xb1 - xb2 is the pairs of crossing-bond correspondence, that is, xb1 connects to xb2. Integer > 0 LABEL label is the display label for this Sgroup. String For example, superatom name BRKXYZ bx1 - bz3 are the double (X,Y,Z) display coordinates in each bracket. Angstroms By specifying 3 triples, the format allows a 3D display. estate is the expanded display state information for superatoms. String xbond is the crossing bond of the expanded superatom. Integer > 0 Display vector information for the contracted superatom. cbvx - cvbz is the vector to contracted superatom. Angstroms Only present for expanded superatoms. One CSTATE entry per crossing bond. FIELDNAME fieldname is the name of data field for Data Sgroup. String FIELDINFO fieldinfo is the program-specific field information. Free-format string Example: In MACCS-II this is: “<type> <units/format>” FIELDDISP fielddisp is the Data Sgroup field display information. Free-format string This string is interpreted by V3000 as identical to V2000 appendix for Data Sgroup display (‘M SDD’) except for the index value. QUERYTYPE querytype is the type of query or no query if missing. String ESTATE CSTATE However, only the first two (X, Y) coordinates are currently used. The Z value and last (X, Y) coordinates are currently ignored and should be set to zero. E = expanded superatom or multiple group Only superatoms and multiple groups (shortcuts) in an expanded internal state are supported. This field defines whether a superatom or multiple group is displayed as expanded or contracted. This field is expected to become obsolete. ‘ ’ = not a query (default) ‘MQ’ = MACCS-II query ‘IQ’ = ISIS query <p>Q’ = <program> query QUERYOP queryop is the query operator. String. Example: “=” or “LIKE” in ISIS ISIS: query operator MACCS-II: blank or missing FIELDDATA fielddata is the query or field data. Free-format string Only one entry per query, but can be more than one for actual data. The order of the entries is important. CLASS class is the character string for superatom class. String Example: PEPTIDE 90
  • 91. Chapter 10: The Extended Connection Table (V3000) SAP aidx is the index of attachment point or potential attachment point atom. Integer > 0 lvidx is the index of leaving atom. Allowed integers are: 0 = none or implied H ‘aidx’ = atom index number of attachment point atom > 0 = atom index number of atom bonded to ‘aidx’ id is the attachment identifier. BRKTYP String (two chars in V2000) There must be multiple entries if superatom has more than one attachment point. The order of the entries defines the order of the attachment points. Note that SAP entries may or may not include the actual attachment points, depending on the particular superatom and its representation on MDL ISIS/Desktop. bracketType is the displayed bracket style. Allowed values for this string are: This information supports Sgroup enhancements on MDL ISIS/Desktop. BRACKET (default) PAREN Correspondence with existing V2000 appendices M M M M M M M M M M M M M M M M M M M M M STY SST SLB SCN SDS SAL SBL SPA SMT CRS SDI SBV SDT SDD SCD SED SPL SNC SAP SCL SBT = = = = = = = = = = = = = = = = = = = = = type SUBTYPE extindex CONNECT ESTATE ATOMS XBONDS or CBONDS PATOMS LABEL and MULT XBHEAD,XBCORR BRKXYZ CSTATE FIELDNAME, FIELDINFO, QUERYTYPE, QUERYOP FIELDDISP (not required) FIELDDATA PARENT COMPNO SAP CLASS BRKTYP 91
  • 92. CTFile Formats Collection block A collection block specifies all collection information for objects in the current connection table context. Collection blocks must be provided after the blocks that define the objects included in the collection to minimize the amount of forward object references that must be maintained by the file reader. M V30 BEGIN COLLECTION [M V30 DEFAULT -]M V30 name/subname M V30 [ATOMS=(natoms atom [atom ...])] M V30 [BONDS=(nbonds bond [bond ...])] M V30 [SGROUPS=(nsgroups sgrp [sgrp ...])] M V30 [OBJ3DS=(nobj3ds obj3d [obj3d ...])] M V30 [MEMBERS=(nmembers member [member ...])] M V30 [RGROUPS=(nrgroups rgroup [rgroup ...])] ... M V30 END COLLECTION Figure 22 Meaning of values in the collection block Field Meaning Value name/subname Collection id Nonblank string ATOMS natoms is the number of atoms included in the collection Integer > 0 atom is the atom index Integer > 0 nbonds is the number of bonds included in the collection Integer > 0 bond is the bond index Integer > 0 nsgroups is the number of sgroups included in the collection Integer > 0 sgrp is the sgroup index Integer > 0 nobj3ds is the number of 3D features included in the collection Integer > 0 obj3d is the 3D feature index Integer > 0 nmembers is the number of members included in the collection Integer > 0 member is the member identifier ROOT or RrMm nrgroups is the number of rgroups included in the collection Integer > 0 rgroup is the rgroup identifier Rr BONDS SGROUPS OBJ3DS MEMBERS RGROUPS Notes r > 0, m > 0 r>0 • Collections can be named in a semi-arbitrary fashion. • A two part name is supported for collections on import and export. • The subname designation is required. • The name is the unique identifier for the collection contents. • All collections of the same name are presumed to indicate various pieces of the same collection, which may be provided in one or more COLLECTION block entries provided within various subblocks of the full connection table. • Collection names are not case sensitive, must contain only printable characters, and must begin with an alphanumeric character. 92
  • 93. Chapter 10: The Extended Connection Table (V3000) • Collection objects are presumed to be unordered, and no preservation of input order is necessary or required on subsequent file writes. • Future enhancements to the collection block information will provide ordered collection support. The default delimiter for the collection name is the '/' character. If the name begins with a non-alphanumeric character, it is presumed to indicate an alternate delimiter character, thus a collection name that contains a '/' character might be designed as '|name|/subname/|', for example. In addition, if the first character is ‘”’,it is presumed that the collection name is being quoted due to the presence of spaces. The name MDLV30 is a reserved name used to designate internal collections. User specified collections may use any other arbitrary naming conventions. The default action for all MDL provided V3000 readers and writers is to preserve all user collection information for CTfile import/export operations. Internal collections may also be preserved if their contents have been validated as correct input for the specified internal representation. There is no implied validation for user collections other than requiring the collection to refer to valid objects. Collections may not contain other collections in their definition. The default action on registration is to strip user collection information without error, but possibly with status or warning messages being issued. The internal collection types are: MDLV30/HILITE Highlighting collection. Default action for renderers is to provide a "highlighted" display of the specified objects. All object types are allowed in this collection: atoms, bonds, Sgroups, 3Dfeatures, Rgroups, members, and components. MDLV30/STEABS Absolute stereochemistry collection. This collection defines the set of stereocenters in the structure that have absolute configurations. This is an atom collection. MDLV30/STERACn "Racemic" stereochemistry collection (n >0). This collection defines a set of stereogenic centers whose relative configuration is known. A mixture of the two enantiomeric relative configurations is present. This is an atom collection. MDLV30/STERELn Relative stereochemistry collection (n>0). This collection defines a set of stereogenic centers whose relative configuration is known. Only one of the two enantiomeric relative configurations is present. There is no assumption about which of the two configurations is present. This is an atom collection. 93
  • 94. CTFile Formats 3D block The 3D block contains 3D information as shown below. For the V2000 version of this 3D query and its connection table, see Chapter 2.3D Block Normal 3D Query Exclusion sphere Point Angle Centroid Plane Benzene ring o 75-105 4.4-5.7 N Distance Nitrogen atom 3D Query MACCS-II07189510253D 1 1.00000 0.00000 0 Figure 6, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 7 0 7 0 M V30 BEGIN ATOM M V30 1 C 1.0252 0.2892 1.1122 0 M V30 2 C -0.4562 0.6578 1.3156 0 M V30 3 C -1.4813 0.3687 0.2033 0 M V30 4 C -1.0252 -0.2892 -1.1122 0 M V30 5 C 0.4562 -0.6578 -1.3156 0 M V30 6 C 1.4813 -0.3687 -0.2033 0 M V30 7 N 4.1401 -0.1989 1.3456 0 M V30 8 C 4.6453 0.5081 1.7417 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 2 3 M V30 3 1 3 4 Blocks not used in this Ctab: Sgroup block, M V30 4 2 4 5 Rgroup block M V30 5 1 5 6 M V30 6 2 6 1 M V30 7 1 7 8 M V30 END BOND M V30 BEGIN OBJ3D M V30 1 -7 6 "" 0 0 BASIS=(3 6 4 2) M V30 2 -5 13 "" 0 0 BASIS=(6 1 2 3 4 5 6) M V30 3 -8 7 "" 0 0 BASIS=(2 O3D.1 O3D.2) M V30 4 -3 6 "" -2 0 BASIS=(2 O3D.1 O3D.3) PNTDIR=1 M V30 5 -16 12 "" 1.5 0 BASIS=(1 O3D.4) UNCONNOK=1 M V30 6 -12 10 "" 75 105 BASIS=(3 O3D.4 O3D.1 7) M V30 7 -9 3 "" 4.4 5.7 BASIS=(2 7 O3D.1) M V30 END OBJ3D M V30 END CTAB M END Header Block Comment Line Counts Line Atom Block Connection Table (Ctab) Bond Block 3D object block A 3D block specifies information for all 3D objects in the connection table. It must follow the atom and bond blocks. As in V2000 molfiles, there can be only one fixed-atom constraint. 94
  • 95. Chapter 10: The Extended Connection Table (V3000) The format of the 3D block is as follows: M V30 M V30 M V30 M V30 M V30 M V30 ... M V30 BEGIN OBJ3D index type color name value1 value2 BASIS=(nbvals bval [bval ...]) [ALLOW=(nvals val [val ...])] [PNTDIR=val] [ANGDIR=val] [UNCONNOK=val] [DATA=strval] [COMMENT=comment] END OBJ3D Figure 23 Meaning of values in the 3D block Field Meaning Values Notes index 3D object index Integer > 0 The actual value of the index does not matter as long as all indexes are unique. However, extremely large numbers used as indexes can cause the program to fail to allocate memory for the correspondence array. type Object type Integer < 0 for geometric constraints and for data constraints This format is the same as V2000. Integer > 0 are field IDs color Color value Integer > 0 name Object name or, for data query, the field name. String value1 Distance, radius, deviation, or minimum value. Floating point, value1 = 0 if constraint has no floating values value2 Maximum value for range constraints. Floating point, value2 = 0 if not a range constraint BASIS nbvals is the number of objects in basis. Integer > 0 bval is the atom number or 3D object index Integer or O3D.integer nvals is the number of atoms allowed in an exclusion sphere. Integer > 0 val is the atom number. Integer > 0 ALLOW PNTDIR For objects where order is important, for example, in an angle constructed from three points, the order must be the same as in V2000 molfiles. 0 = point has no direction 1 = point has direction ANGDIR 0 = dihedral angle has no direction MACCS-II uses ‘Chiral’. 1 = dihedral angle has direction UNCONNOK 0 = unconnected atoms are not OK 1 = unconnected atoms are OK DATA strval is the data query string String COMMENT string comment String. Normally uses the MACCS-II DASP, DISP, and BOX values Same as V2000 molfile 95
  • 96. CTFile Formats The Extended Rgroup Query Molfile A single molecule or Rgroup molecule connection table. The header is contained in the normal header location, that is, in the first three lines of the file. The body of the new molecule is contained in new appendixes, organized as follows:A molecule block consists of a main Ctab, plus optionally one or more Rgroup definitions. ctab-block [rgroup-block]* Rgroup block The Rgroup file shown in the next figure corresponds to the following Rgroup query. For the V2000 version of the Rgroup query and its connection table, see Chapter 5 Figure 24 Connection table organization of an Rgroup query. I R 1 TH EN R 2 F R1 R2 * R2 R1 = R1 > 0 C * * R2 = R2 = 0 C 96 O N
  • 97. Chapter 10: The Extended Connection Table (V3000) GSMACCS-II07189510252D 1 0 M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M 0 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 END 0.00353 0.00000 0 0 0 999 V3000 BEGIN CTAB COUNTS 9 9 0 0 0 BEGIN ATOM 1 C 1.3337 0.77 0 0 2 C 0 1.54 0 0 3 C -1.3337 0.77 0 0 4 C -1.3337 -0.77 0 0 5 C 0 -1.54 0 0 6 C 1.3337 -0.77 0 0 7 R# 0 3.08 0 0 RGROUPS=(1 1) 8 R# 2.6674 1.54 0 0 RGROUPS=(1 2) 9 R# -2.6674 1.54 0 0 RGROUPS=(1 2) END ATOM BEGIN BOND 1 1 1 2 2 2 2 3 3 1 3 4 4 2 4 5 5 1 5 6 6 2 6 1 7 1 1 8 8 1 2 7 9 1 3 9 END BOND END CTAB BEGIN RGROUP 1 RLOGIC 2 0 "" BEGIN CTAB COUNTS 1 0 0 0 0 BEGIN ATOM 1 C 12.21 14.3903 0 0 ATTCHPT=1 END ATOM END CTAB END RGROUP BEGIN RGROUP 2 RLOGIC 0 0 0 BEGIN CTAB COUNTS 2 1 0 0 0 BEGIN ATOM 1 C -1.4969 0.0508 0 0 ATTCHPT=1 2 O 0.0431 0.0508 0 0 END ATOM BEGIN BOND 1 2 1 2 END BOND END CTAB BEGIN CTAB COUNTS 1 0 0 0 0 BEGIN ATOM 1 N 12.21 14.3903 0 0 ATTCHPT=1 END ATOM END CTAB END RGROUP Header Block 0 Counts Line Atom Block for root Ctab for Rgroup root Bond Block for root Rgroup logic Line Counts Line Atom Block Ctab for Rgroup 1 Member 1 Block for Rgroup 1 Rgroup logic Line Counts Line Atom Block Ctab for Rgroup 2 Member 1 Bond Block Counts Line Atom Block Block for Rgroup 2 Ctab for Rgroup 2 Member 2 97
  • 98. CTFile Formats An Rgroup block defines one Rgroup. Each Ctab block specifies one member. M V30 BEGIN RGROUP rgroup-number [rgroup-logic-line] ctab-block [ctab-block]* M V30 END RGROUP Figure 25 Meaning of values in the Rgroup block Field Meaning Values rgroup-number Index of this rgroup Notes Integer > 0 Rgroup logic lines There is zero or one Rgroup logic line for each Rgroup in the molecule. If present, the Rgroup logic line specifies if-then logic between Rgroups, the convention about unfilled valence sites, and the Rgroup occurrence information. Its format is: M V30 RLOGIC thenR RestH Occur Figure 26 Meaning of values in Rgroup logic line Field Meaning Values thenR Number of a “then” Rgroup 0 = none (default) RestH Attachment(s) at Rgroup position 0 = off, that is, any molecule fragment at any unsatisfied Rgroup location (default) 1 = only hydrogen or a member of Rgroup is allowed Occur String specifying number (range) of Rgroup occurrence sites that need to be satisfied. String ‘> 0’ = default Notes Similar to MACCS-II and ISIS: [N[,[N[,...]]]] Automatic V3000 output Current Elsevier MDL products support reading and writing of V2000 and V3000 formats. These products will preferentially write V2000 molfiles to maximize interoperability with third party applications. However, because of the limitations imposed by the V2000 format, there are situations when the V3000 format will be automatically used. The following are cases in which the V3000 format is automatically written instead of the V2000 format: • • 98 Structure highlighting - The V3000 format is required for molecule or collection highlighting. See the “Collection block” on page 92 which contains information about structure highlighting. Enhanced stereochemistry features - The V3000 format is required when using the enhanced stereochemical representations. See the “Collection block” on page 92 which contains information about the enhanced stereochemistry features.
  • 99. Chapter 10: The Extended Connection Table (V3000) • The maximum length of a field with a fixed width is exceeded - If any of the fields with fixed widths for any connection table properties are exceeded, then the V3000 format will be used. For example, if the number of atoms (or bonds) exceeds 999, the V3000 format will be used. This is because the number of atoms (or bonds) on the V2000 counts line cannot exceed 3 columns (see “The Counts Line” on page 12). For more details about the fixed field widths in the V2000 format, see “Chapter 2: The Connection Table [CTAB] (V2000)” on page 11. 99
  • 101. Chapter 11: The Extended Reaction File Overview Rxnfiles contain structural data for the reactants and products of a reaction. For the V2000 version of this reaction file, see Chapter 7. The first line of the file begins with $RXN to identify the file as a reaction file. The V3000 version follows the $RXN token to indicate the extended version of the reaction file. There are two new block types introduced: REACTANT and PRODUCT.
  • 102. CTFile Formats Figure 27 V3000 Rxnfile for the acylation of benzene $RXN V3000 0503021738 M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M 102 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 V30 END Header Block 7439 COUNTS 2 1 BEGIN REACTANT BEGIN CTAB COUNTS 4 3 0 0 0 BEGIN ATOM 1 C 0.323 -0.2377 0 1 2 C -1.0362 -0.9618 0 2 3 O 0.323 1.4154 0 3 4 Cl 1.6423 -1.0307 0 0 END ATOM BEGIN BOND 1 1 1 2 RXCTR=2 2 2 1 3 RXCTR=2 3 1 1 4 RXCTR=4 END BOND END CTAB BEGIN CTAB COUNTS 6 6 0 0 0 BEGIN ATOM 1 C 1.3331 -0.7694 0 5 2 C 1.3331 0.7694 0 6 3 C 0 -1.5417 0 7 4 C 0 1.5417 0 8 5 C -1.3331 -0.7694 0 9 6 C -1.3331 0.7694 0 10 END ATOM BEGIN BOND 1 1 1 2 RXCTR=2 2 2 1 3 RXCTR=2 3 2 2 4 RXCTR=2 4 1 3 5 RXCTR=2 5 1 4 6 RXCTR=2 6 2 5 6 RXCTR=2 END BOND END CTAB END REACTANT BEGIN PRODUCT BEGIN CTAB COUNTS 9 9 0 0 0 BEGIN ATOM 1 C -0.5331 -0.1358 0 5 2 C -1.8606 0.633 0 6 3 C -0.5331 -1.6992 0 7 4 C 0.8201 0.6305 0 1 5 C -3.2189 -0.1358 0 8 6 C -1.8811 -2.4731 0 9 7 C 2.1297 -0.1128 0 2 8 O 0.8534 2.2297 0 3 9 C -3.2292 -1.6863 0 10 END ATOM BEGIN BOND 1 1 1 2 RXCTR=2 2 2 1 3 RXCTR=2 3 1 1 4 RXCTR=4 4 2 2 5 RXCTR=2 5 1 3 6 RXCTR=2 6 1 4 7 RXCTR=2 7 2 4 8 RXCTR=2 8 1 5 9 RXCTR=2 9 2 6 9 RXCTR=2 END BOND END CTAB END PRODUCT Counts Line Counts Line Atom Block Ctab for first reactant Bond Block Counts Line Reactant block Atom Block Ctab for second reactant Bond Block Counts Line Atom Block Ctab for product Bond Block Product block
  • 103. Appendix A: Stereo Notes Parity is illustrated as follows: Mark a bond attached at a stereo center Up or Down to define the configuration Number the atoms surrounding the stereo center with 1, 2, 3, and 4 in order of increasing atom number (position in the atom block) (a hydrogen atom should be considered the highest numbered atom, in this case atom 4). View the center from a position such that the bond connecting the highest-numbered atom (4) projects behind the plane formed by atoms 1, 2, and 3. Note: In the figure, atoms 1, 2, and 4 are all in the plane of the paper, and atom 3 is above the plane. 3 4 C 2 1 Sighting towards atom number 4 through the plane (123), you see that the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order. 1 3 2 3 Part = 2 iy Part = 1 iy 2 1 The Ctab lists a parity value of 1 for a clockwise arrangement at the stereo center and 2 for counterclockwise. A center with an Either bond has a parity value of 3. An unmarked stereo center is also assigned a value of 3. The first example above has a parity value of 2.
  • 105. 105 Index Numbers 3D block (V3000 molfiles) 94 3D features (ctab) count line 24 data constraints 31 data line 26 detail lines 24 identification line 25 properties block 23 type identifiers 25 A atom alias (ctab) 16 atom attachment order (ctab) 18 atom block (ctab) 12 atom block (V3000 molfiles) 82 atom descriptions (V3000 molfiles) 80 atom limit enhancements 33 atom list (ctab) 17 atom list block (query) 14 atom value (ctab) 16 atom, phantom extra 33 attachment point (ctab) 17 attachment point, superatom 33 B blank lines in SDfiles 43 bond block (ctab) 14 bond block (V3000 molfiles) 84 bond descriptions (V3000 molfiles) 80 bracket style, Sgroup 34 C charge (ctab) 16 collection block (V3000 molfiles) 92 connection table 11 Copyright (XDfile) 68 correspondence, Sgroup 21 counts line (ctab) 12 counts line (V3000 molfiles) 82 CreateDate (XDfile) 65 CreateTime (XDfile) 66 CreatorName (XDfile) 64 ctab atom block 12 atom list block (query) 14 bond block 14 counts line 12 end of block 23 extended connection table (V3000 molfiles) 81 overview 11 properties block 15 stext block 15 ctab block (V3000 molfiles) 81 3D block 94 atom block 82 bond block 84 collection block 92 counts line 82 link atom line 85 Sgroup block 87 ctab properties 3D data constraints 31 3D features count line 24 3D features detail lines 24 3D properties block 23 atom alias 16 atom attachment order 18 atom list 17 atom value 16 attachment point 17 charge 16 data Sgroup data 22 data Sgroup display information 22 data Sgroup field description 22 group abbreviation 16 isotope 17 large REGNO 34 link atom 17 multiple group parent atom list 21 phantom extra atom 33 radical 16 range of occurence 18 Rgroup label location 18 Rgroup logic 18 ring bond count 17 Sgroup atom list 21 Sgroup bond list 21 Sgroup bracket style 34 Sgroup component numbers 23 Sgroup connectivity 21 Sgroup correspondence 21
  • 106. 106 CTFile Formats Sgroup display information 21 Sgroup expansion 21 Sgroup hierarchy information 23 Sgroup labels 20 Sgroup subscript 21 Sgroup subtype 20 Sgroup type 19 substitution count 17 superatom attachment point 33 superatom bond and vector 22 superatom class 34 unsatisfied sites 18 unsaturated atoms 17 CTfile formats 7 D Data (XDfile) 75 data line (3D) 26 data Sgroup data (ctab) 22 data Sgroup display information (ctab) 22 data Sgroup field description (ctab) 22 Dataset (XDfile) 60 DataSource (XDfile) 62 Description (XDfile) 67 E end of block (ctab) 23 escaped characters (XDfile) 54 extended connection table (V3000 molfiles) 81 extended molfiles 79 extended Rgroup query molecule (V3000 molfiles) 96 extended rxnfiles 101 extra atom, phantom 33 F Field (XDfile) 78 FieldDef (XDfile) 71 I isotope (ctab) 17 L large REGNO 34 link atom (ctab) 17 link atom line (V3000 molfiles) 85 list of elements, XDfile 57 M MDLV30, reserved name (V3000) 93 Metadata (XDfile) 69 molfile blocks (Rxnfiles) 47 molfiles 35 extended 79 header block 36 multiple group parent atom list (ctab) 21 P Parent (XDfile) 76 ParentDef (XDfile) 70 parity 103 phantom extra atom 33 preserve CDATA (XDfile) 54 products (Rxnfiles) 47 ProgramSource (XDfile) 63 properties block - 3D (ctab) 23 properties block (ctab) 15 Q query properties 3D data constraints 31 atom list 17 link atoms 17 ring bond count 17 substitution count 17 unsaturated atoms 17 G group abbreviation (ctab) 16 H header (RDfiles) 49 header block (molfiles) 36 header block (Rxnfiles) 45 hierarchy of elements, XDfile 55 R radical (ctab) 16 range of occurence (ctab) 18 RDfiles header 49 reactants (Rxnfiles) 47 Record (XDfile) 77 REGNO, large 34 RGfiles 37 Rgroup block (V3000 molfiles) 96 Rgroup label location (ctab) 18 Rgroup logic (ctab) 18
  • 107. Index Rgroup logic lines (V3000 molfiles) 98 Rgroup properties (ctab) atom attachment order 18 attachment point 17 range of occurence 18 Rgroup label location 18 Rgroup logic 18 unsatisfied sites 18 ring bond count (ctab) 17 Rxnfiles 45 header block 45 molfile blocks 47 reactants and products 47 V3000 101 V V2000 11 V3000 molfiles 79 atoms 80 bonds 80 compared with V2000 6 correspondence with existing V2000 appendices 91 ctab block 81 extended connection table 81 extended Rgroup query molecule 96 V3000 Rxnfiles 101 X S SDfiles 41 after a CFS search 43 blank lines 43 Sgroup block (V3000 molfiles) 87 Sgroup bracket style 34 Sgroup properties (ctab) data Sgroup data 22 data Sgroup display information 22 data Sgroup field description 22 multiple group parent atom list 21 phantom extra atom 33 Sgroup atom list 21 Sgroup bond list 21 Sgroup bracket style 34 Sgroup component numbers 23 Sgroup connectivity 21 Sgroup correspondence 21 Sgroup display information 21 Sgroup expansion 21 Sgroup hierarchy information 23 Sgroup labels 20 Sgroup subscript 21 Sgroup subtype 20 Sgroup type 19 superatom attachment point 33 superatom bond and vector 22 superatom class 34 Source (XDfile) 61 stereo parity 103 stext block 15 substitution count (ctab) 17 superatom attachment point 33 superatom bond and vector (ctab) 22 superatom class 34 U unsatisfied sites (ctab) 18 unsaturated atoms (ctab) 17 107 XDfile data formatting 54 example 59 hierarchy of elements 55 list of elements 57 overview 53 preserve CDATA 54 root element 58