.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "Chemistry::File::MDLMol 3pm" .TH Chemistry::File::MDLMol 3pm "2022-02-06" "perl v5.32.1" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Chemistry::File::MDLMol \- MDL molfile reader/writer .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& use Chemistry::File::MDLMol; \& \& # read a molecule \& my $mol = Chemistry::Mol\->read(\*(Aqmyfile.mol\*(Aq); \& \& # write a molecule \& $mol\->write("myfile.mol"); \& \& # use a molecule as a query for substructure matching \& use Chemistry::Pattern; \& use Chemistry::Ring; \& Chemistry::Ring::aromatize_mol($mol); \& \& my $patt = Chemistry::Pattern\->read(\*(Aqquery.mol\*(Aq); \& if ($patt\->match($mol)) { \& print "it matches!\en"; \& } .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" \&\s-1MDL\s0 Molfile (V2000) reader/writer. .PP This module automatically registers the 'mdl' format with Chemistry::Mol. .PP The first three lines of the molfile are stored as \f(CW$mol\fR\->name, \&\f(CW$mol\fR\->attr(\*(L"mdlmol/line2\*(R"), and \f(CW$mol\fR\->attr(\*(L"mdlmol/comment\*(R"). .PP This version only reads and writes some of the information available in a molfile: it reads coordinates, atom and bond types, charges, isotopes, radicals, and atom lists. It does not read other things such as stereochemistry, 3d properties, etc. .PP This module is part of the PerlMol project, . .SS "Query properties" .IX Subsection "Query properties" The \s-1MDL\s0 molfile format supports query properties such as atom lists, and special bond types such as \*(L"single or double\*(R", \*(L"single or aromatic\*(R", \*(L"double or aromatic\*(R", \*(L"ring bond\*(R", or \*(L"any\*(R". These properties are supported by this module in conjunction with Chemistry::Pattern. However, support for query properties is currently read-only, and the other properties listed in the specification are not supported yet. .PP So that atom and bond objects can use these special query options, the conditions are represented as Perl subroutines. The generated code can be read from the 'mdlmol/test_sub' attribute: .PP .Vb 2 \& $atom\->attr(\*(Aqmdlmol/test_sub\*(Aq); \& $bond\->attr(\*(Aqmdlmol/test_sub\*(Aq); .Ve .PP This may be useful for debugging, such as when an atom doesn't seem to match as expected. .SS "Aromatic Queries" .IX Subsection "Aromatic Queries" To be able to search for aromatic substructures are represented by Kekule structures, molfiles that are read as patterns (with \&\f(CW\*(C`Chemistry::Pattern\-\*(C'\fRread) are aromatized automatically by using the Chemistry::Ring module. The default bond test from Chemistry::Pattern::Bond is overridden by one that checks the aromaticity in addition to the bond order. The test is, .PP .Vb 2 \& $patt\->aromatic ? $bond\->aromatic \& : (!$bond\->aromatic && $patt\->order == $bond\->order); .Ve .PP That is, aromatic pattern bonds match aromatic bonds, and aliphatic pattern bonds match aliphatic bonds with the same bond order. .SH "SOURCE CODE REPOSITORY" .IX Header "SOURCE CODE REPOSITORY" .SH "SEE ALSO" .IX Header "SEE ALSO" Chemistry::Mol .PP The \s-1MDL\s0 file format specification. , , , or Arthur Dalby et al., J. Chem. Inf. Comput. Sci, 1992, 32, 244\-255. . .SH "AUTHOR" .IX Header "AUTHOR" Ivan Tubert-Brohman .SH "COPYRIGHT" .IX Header "COPYRIGHT" Copyright (c) 2009 Ivan Tubert-Brohman. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.