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