0
|
1 NAME
|
|
2 SDFileIO
|
|
3
|
|
4 SYNOPSIS
|
|
5 use FileIO::SDFileIO;
|
|
6
|
|
7 use FileIO::SDFileIO qw(:all);
|
|
8
|
|
9 DESCRIPTION
|
|
10 SDFIleIO class provides the following methods:
|
|
11
|
|
12 new, GenerateMoleculeString, IsSDFile, ParseMoleculeString,
|
|
13 ReadMolecule, ReadMoleculeString, WriteMolecule
|
|
14
|
|
15 The following methods can also be used as functions:
|
|
16
|
|
17 GenerateMoleculeString, IsSDFile, ParseMoleculeString
|
|
18
|
|
19 Data specific to SDFileIO class not directly used by Molecule, Atom and
|
|
20 Bond objects - data label/value pairs, atom SteroParity and so on - is
|
|
21 associated to and retrieved from approptiate objects using following
|
|
22 methods:
|
|
23
|
|
24 SetMDL<PropertyName>
|
|
25 GetMDL<PropertyName>.
|
|
26
|
|
27 SD data label and values are attached to Molecule object as a refernece
|
|
28 to a hash using SetDataFieldLabelAndValues and can be retrieved using
|
|
29 GetDataFieldLabelAndValues method.
|
|
30
|
|
31 SDFileIO class is derived from *FileIO* class and uses its methods to
|
|
32 support generic file related functionality.
|
|
33
|
|
34 METHODS
|
|
35 new
|
|
36 $NewSDFileIO = new FileIO::SDFileIO(%NamesAndValues);
|
|
37
|
|
38 Using specified *SDFileIO* property names and values hash, new
|
|
39 method creates a new object and returns a reference to newly created
|
|
40 SDFileIO object.
|
|
41
|
|
42 GenerateMoleculeString
|
|
43 $MoleculeString = $SDFileIO->GenerateMoleculeString($Molecule);
|
|
44 $MoleculeString = FileIO::SDFileIO::GenerateMoleculeString($Molecule);
|
|
45
|
|
46 Returns a MoleculeString in SD format corresponding to *Molecule*.
|
|
47
|
|
48 IsSDFile
|
|
49 $Status = $SDFileIO->IsSDFile($FileName);
|
|
50 $Status = FileIO::SDFileIO::IsSDFile($FileName);
|
|
51
|
|
52 Returns 1 or 0 based on whether *FileName* is a SD file.
|
|
53
|
|
54 ParseMoleculeString
|
|
55 $Molecule = $SDFileIO->ParseMoleculeString($MoleculeString);
|
|
56 $Molecule = FileIO::SDFileIO::ParseMoleculeString($MoleculeString);
|
|
57
|
|
58 Parses *MoleculeString* and returns a Molecule object. SD data field
|
|
59 label and value pairs are associated to Molecule object as a
|
|
60 reference to a hash using:
|
|
61
|
|
62 $Molecule->SetDataFieldLabelAndValues(\%DataLabelsAndValues)
|
|
63
|
|
64 The reference to hash can be retrieved by:
|
|
65
|
|
66 $DataLabelsAndValues = $Molecule->GetDataFieldLabelAndValues();
|
|
67 for $DataLabel (sort keys %{$DataLabelsAndValues}) {
|
|
68 $DataValue = $DataLabelsAndValues->{$DataLabel};
|
|
69 }
|
|
70
|
|
71 ReadMolecule
|
|
72 $Molecule = $SDFileIO->ReadMolecule($FileHandle);
|
|
73
|
|
74 Reads data for the next compound in a file using already opened
|
|
75 *FileHandle*, creates, and returns a Molecule object.
|
|
76
|
|
77 ReadMoleculeString
|
|
78 $MoleculeString = $SDFileIO->ReadMoleculeString($FileHandle);
|
|
79
|
|
80 Reads data for the next compound in a file using already opened
|
|
81 *FileHandle* and returns a MoleculeString corresponding to compound
|
|
82 structure and other associated data.
|
|
83
|
|
84 WriteMolecule
|
|
85 $SDFileIO->WriteMolecule($Molecule);
|
|
86
|
|
87 Writes *Molecule* data to a file in MDLMol format and returns
|
|
88 SDFileIO.
|
|
89
|
|
90 AUTHOR
|
|
91 Manish Sud <msud@san.rr.com>
|
|
92
|
|
93 SEE ALSO
|
|
94 MoleculeFileIO.pm, MDLMolFileIO.pm
|
|
95
|
|
96 COPYRIGHT
|
|
97 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
98
|
|
99 This file is part of MayaChemTools.
|
|
100
|
|
101 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
102 under the terms of the GNU Lesser General Public License as published by
|
|
103 the Free Software Foundation; either version 3 of the License, or (at
|
|
104 your option) any later version.
|
|
105
|