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.IX Title "Chemistry::File::SDF 3pm"
.TH Chemistry::File::SDF 3pm "2022-02-06" "perl v5.32.1" "User Contributed Perl Documentation"
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.SH "NAME"
Chemistry::File::SDF \- MDL Structure Data File reader/writer
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Chemistry::File::SDF;
\&
\&    # Simple interface (all at once)
\&    # read all the molecules in the file
\&    my @mols = Chemistry::Mol\->read(\*(Aqmyfile.sdf\*(Aq);
\&
\&    # assuming that the file includes a <PKA> data item...
\&    print $mols[0]\->attr("sdf/data")\->{PKA}; 
\&
\&    # write a bunch of molecules to an SDF file
\&    Chemistry::Mol\->write(\*(Aqmyfile.sdf\*(Aq, mols => \e@mols);
\&
\&    # or write just one molecule
\&    $mol\->write(\*(Aqmyfile.sdf\*(Aq);
\&
\&
\&    # Low level interface (one at a time)
\&    # create reader
\&    my $reader = Chemistry::Mol\->file(\*(Aqmyfile.sdf\*(Aq);
\&    $reader\->open(\*(Aq<\*(Aq);
\&    while (my $mol = $reader\->read_mol($reader\->fh)) {
\&        # do something with $mol
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1MDL SDF\s0 (V2000) reader.
.PP
This module automatically registers the 'sdf' format with Chemistry::Mol.
.PP
The parser returns a list of Chemistry::Mol objects.  \s-1SDF\s0 data can be accessed
by the \f(CW$mol\fR\->attr method. Attribute names are stored as a hash ref at the
\&\*(L"sdf/data\*(R" attribute, as shown in the synopsis. When a data item has a single
line in the \s-1SDF\s0 file, the attribute is stored as a string; when there's more
than one line, they are stored as an array reference. The rest of the
information on the line that holds the field name is ignored.
.PP
This module is part of the PerlMol project, <https://github.com/perlmol>.
.SH "CAVEATS"
.IX Header "CAVEATS"
Note that by storing the \s-1SDF\s0 data as a hash, there can be only one field with
a given name. The \s-1SDF\s0 format description is not entirely clear in this regard.
Also note that \s-1SDF\s0 data field names are considered to be case-sensitive.
.SH "SOURCE CODE REPOSITORY"
.IX Header "SOURCE CODE REPOSITORY"
<https://github.com/perlmol/Chemistry\-File\-MDLMol>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Chemistry::Mol
.PP
The \s-1MDL\s0 file format specification.
<http://www.mdl.com/downloads/public/ctfile/ctfile.pdf> or
Arthur Dalby et al., J. Chem. Inf. Comput. Sci, 1992, 32, 244\-255.
.SH "AUTHOR"
.IX Header "AUTHOR"
Ivan Tubert-Brohman <itub@cpan.org>
.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.