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1 NAME
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2 MoleculeFileIO
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3
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4 SYNOPSIS
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5 use MoleculeFileIO;
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6
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7 use MoleculeFileIO qw(:all);
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8
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9 DESCRIPTION
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10 MoleculeFileIO class provides the following methods:
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11
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12 new, Close, IsSupportedMoleculeFileFormat, Open, ReadMolecule,
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13 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 IsSupportedMoleculeFileFormat
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18
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19 METHODS
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20 new
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21 $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);
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22
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23 Using specified *MoleculeFileIO* property names and values hash, new
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24 method creates a new object and returns a reference to newly created
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25 MoleculeFileIO object. By default, following properties are
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26 initialized:
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27
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28 Name = ""
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29 Mode = ""
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30 FileIORef = ""
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31
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32 Based on extension of specified file *Name*, an input class is
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33 automatically associated to provide molecule read and write methods.
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34
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35 Examples:
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36
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37 $Name = "Water.mol";
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38 $Mode = "Read";
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39 $MoleculeFileIO = new MoleculeFileIO('Name' => $Name,
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40 'Mode' => $Mode);
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41 $MoleculeFileIO->Open();
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42 $Molecule = $MoleculeFileIO->ReadMolecule();
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43 $Molecule->DetectRings();
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44 print "$Molecule\n";
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45 $MoleculeFileIO->Close();
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46
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47 $MoleculeFileIO = new MoleculeFileIO('Name' => 'Sample1.sdf',
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48 'Mode' => 'Read');
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49 $MoleculeFileIO->Open();
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50 while ($Molecule = $MoleculeFileIO1->ReadMolecule()) {
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51 $Molecule->DetectRings();
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52 print "$Molecule\n";
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53
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54 $DataLabelsAndValuesRef =
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55 $Molecule->GetDataFieldLabelAndValues();
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56 for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
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57 $DataValue = $DataLabelsAndValuesRef->{$DataLabel};
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58 print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
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59 }
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60 print "\n";
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61 }
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62 $MoleculeFileIO->Close();
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63
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64 Close
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65 $MoleculeFileIO->Close();
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66
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67 Closes an open file
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68
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69 IsSupportedMoleculeFileFormat
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70 $Status = $MoleculeFileIO->IsSupportedMoleculeFileFormat($Name);
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71 $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
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72 ($Status, $FormatType, $IOClassName) =
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73 $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
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74
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75 Returns 1 or 0 based on whether input file *Name* format is
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76 supported. In list context, value of supported format type and name
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77 of associated IO class is also returned.
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78
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79 File extension is used to determine file format. Currently,
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80 following file extensions are supported:
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81
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82 FileExts - FormatType - AssociatedIOClassName
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83
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84 .mol - MDLMOL - MDLMolFileIO
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85 .sdf, .sd - SDF - SDFileIO
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86
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87 Open
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88 $MoleculeFileIO->Open([$Mode]);
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89
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90 Opens a file in a specified *Mode*. Default mode value: *Read*.
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91 Supported mode values:
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92
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93 Read, Write, Append, <, >, >>, r, w, or a
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94
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95 ReadMolecule
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96 $Molecule = $MoleculeFileIO->ReadMolecule();
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97
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98 Reads molecule data from the file and returns a *Molecule* object.
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99
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100 ReadMoleculeString
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101 $MoleculeString = $MoleculeFileIO->ReadMoleculeString();
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102
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103 Reads molecule data from a file and returns a *Molecule* string.
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104
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105 WriteMolecule
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106 $MoleculeFileIO->WriteMolecule();
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107
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108 Write molecule data to a file for a *Molecule*.
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109
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110 AUTHOR
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111 Manish Sud <msud@san.rr.com>
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112
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113 SEE ALSO
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114 FileIO.pm, MDLMolFileIO.pm, SDFileIO.pm
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115
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116 COPYRIGHT
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117 Copyright (C) 2015 Manish Sud. All rights reserved.
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118
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119 This file is part of MayaChemTools.
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120
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121 MayaChemTools is free software; you can redistribute it and/or modify it
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122 under the terms of the GNU Lesser General Public License as published by
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123 the Free Software Foundation; either version 3 of the License, or (at
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124 your option) any later version.
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125
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