annotate mayachemtools/lib/FileIO/MDLMolFileIO.pm @ 0:73ae111cf86f draft

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author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
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1 package FileIO::MDLMolFileIO;
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2 #
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3 # $RCSfile: MDLMolFileIO.pm,v $
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4 # $Date: 2015/02/28 20:48:43 $
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5 # $Revision: 1.32 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use Carp;
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31 use Exporter;
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32 use Scalar::Util ();
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33 use TextUtil ();
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34 use FileUtil ();
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35 use SDFileUtil ();
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36 use FileIO::FileIO;
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37 use Molecule;
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38
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39 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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40
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41 @ISA = qw(FileIO::FileIO Exporter);
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42 @EXPORT = qw();
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43 @EXPORT_OK = qw(IsMDLMolFile);
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44
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45 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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46
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47 # Setup class variables...
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48 my($ClassName);
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49 _InitializeClass();
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50
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51 # Class constructor...
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52 sub new {
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53 my($Class, %NamesAndValues) = @_;
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54
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55 # Initialize object...
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56 my $This = $Class->SUPER::new();
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57 bless $This, ref($Class) || $Class;
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58 $This->_InitializeMDLMolFileIO();
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59
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60 $This->_InitializeMDLMolFileIOProperties(%NamesAndValues);
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61
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62 return $This;
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63 }
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64
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65 # Initialize any local object data...
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66 #
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67 sub _InitializeMDLMolFileIO {
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68 my($This) = @_;
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69
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70 # Nothing to do: Base class FileIO handles default class variables...
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71
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72 return $This;
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73 }
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74
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75 # Initialize class ...
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76 sub _InitializeClass {
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77 #Class name...
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78 $ClassName = __PACKAGE__;
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79
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80 }
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81
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82 # Initialize object values...
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83 sub _InitializeMDLMolFileIOProperties {
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84 my($This, %NamesAndValues) = @_;
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85
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86 # All other property names and values along with all Set/Get<PropertyName> methods
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87 # are implemented on-demand using ObjectProperty class.
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88
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89 my($Name, $Value, $MethodName);
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90 while (($Name, $Value) = each %NamesAndValues) {
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91 $MethodName = "Set${Name}";
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92 $This->$MethodName($Value);
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93 }
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94
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95 if (!exists $NamesAndValues{Name}) {
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96 croak "Error: ${ClassName}->New: Object can't be instantiated without specifying file name...";
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97 }
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98
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99 # Make sure it's a MDLMol file...
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100 $Name = $NamesAndValues{Name};
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101 if (!$This->IsMDLMolFile($Name)) {
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102 croak "Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be MDLMol format...";
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103 }
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104
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105 return $This;
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106 }
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107
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108 # Is it a MDLMol file?
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109 sub IsMDLMolFile ($;$) {
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110 my($FirstParameter, $SecondParameter) = @_;
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111 my($This, $FileName, $Status);
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112
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113 if ((@_ == 2) && (_IsMDLMolFileIO($FirstParameter))) {
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114 ($This, $FileName) = ($FirstParameter, $SecondParameter);
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115 }
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116 else {
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117 $FileName = $FirstParameter;
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118 }
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119
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120 # Check file extension...
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121 $Status = FileUtil::CheckFileType($FileName, "mol");
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122
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123 return $Status;
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124 }
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125
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126 # Read molecule from file and return molecule object...
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127 sub ReadMolecule {
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128 my($This) = @_;
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129 my($FileHandle);
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130
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131 $FileHandle = $This->GetFileHandle();
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132 return $This->ParseMoleculeString(SDFileUtil::ReadCmpdString($FileHandle));
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133 }
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134
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135 # Write compound data using Molecule object...
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136 sub WriteMolecule {
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137 my($This, $Molecule) = @_;
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138
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139 if (!(defined($Molecule) && $Molecule->IsMolecule())) {
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140 carp "Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified...";
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141 return $This;
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142 }
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143 my($FileHandle);
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144 $FileHandle = $This->GetFileHandle();
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145
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146 print $FileHandle $This->GenerateMoleculeString($Molecule) . "\n";
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147
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148 return $This;
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149 }
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150
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151 # Retrieve molecule string...
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152 sub ReadMoleculeString {
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153 my($This) = @_;
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154 my($FileHandle);
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155
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156 $FileHandle = $This->GetFileHandle();
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157 return SDFileUtil::ReadCmpdString($FileHandle);
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158 }
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159
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160 # Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class
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161 # method or a package function.
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162 #
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163 sub ParseMoleculeString {
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164 my($FirstParameter, $SecondParameter) = @_;
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165 my($This, $MoleculeString);
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166
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167 if ((@_ == 2) && (_IsMDLMolFileIO($FirstParameter))) {
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168 ($This, $MoleculeString) = ($FirstParameter, $SecondParameter);
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169 }
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170 else {
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171 $MoleculeString = $FirstParameter;
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172 $This = undef;
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173 }
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174 if (!$MoleculeString) {
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175 return undef;
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176 }
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177 my($LineIndex, @MoleculeLines);
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178 @MoleculeLines = split /\n/, $MoleculeString;
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179
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180 # Create molecule object and set molecule level native and MDL properties...
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181 #
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182 my($Molecule);
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183 $Molecule = new Molecule();
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184
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185 # Set valence model for calculating implicit hydrogens...
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186 $Molecule->SetValenceModel('MDLValenceModel');
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187
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188 # Process headers data...
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189 $LineIndex = 0;
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190 my($MoleculeName) = SDFileUtil::ParseCmpdMolNameLine($MoleculeLines[$LineIndex]);
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191 $MoleculeName = TextUtil::RemoveTrailingWhiteSpaces($MoleculeName);
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192 $Molecule->SetName($MoleculeName);
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193
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194 $LineIndex++;
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195 my($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2, $Energy, $RegistryNum) = SDFileUtil::ParseCmpdMiscInfoLine($MoleculeLines[$LineIndex]);
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196 $Molecule->SetProperties('MDLUserInitial' => $UserInitial, 'MDLProgramName' => $ProgramName, 'MDLDate' => $Date, 'MDLCode' => $Code, 'MDLScalingFactor1' => $ScalingFactor1, 'MDLScalingFactor2' => $ScalingFactor2, 'MDLEnergy' => $Energy, 'MDLRegistryNum' => $RegistryNum);
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197
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198 $LineIndex++;
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199 my($Comments) = SDFileUtil::ParseCmpdCommentsLine($MoleculeLines[$LineIndex]);
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200 $Molecule->SetProperties('MDLComments' => $Comments);
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201
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202 $LineIndex++;
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203 my($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) = SDFileUtil::ParseCmpdCountsLine($MoleculeLines[$LineIndex]);
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204
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205 $Molecule->SetProperties('MDLChiralFlag' => $ChiralFlag, 'MDLPropertyCount' => $PropertyCount, 'MDLVersion' => $Version);
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206
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207 # Process atom data...
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208 my($FirstAtomLineIndex, $LastAtomLineIndex, $AtomNum, $AtomX, $AtomY, $AtomZ, $AtomSymbol, $MassDifference, $Charge, $StereoParity, $Atom, %AtomNumToAtomMap);
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209
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210 $AtomNum = 0;
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211 %AtomNumToAtomMap = ();
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212 $FirstAtomLineIndex = 4; $LastAtomLineIndex = $FirstAtomLineIndex + $AtomCount - 1;
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213
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214 for ($LineIndex = $FirstAtomLineIndex; $LineIndex <= $LastAtomLineIndex; $LineIndex++) {
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215 $AtomNum++;
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216 ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge, $StereoParity) = SDFileUtil::ParseCmpdAtomLine($MoleculeLines[$LineIndex]);
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217
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218 $Atom = new Atom('AtomSymbol' => $AtomSymbol, 'XYZ' => [$AtomX, $AtomY, $AtomZ]);
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219
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220 if ($MassDifference && $MassDifference != 0) {
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parents:
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221 _ProcessMassDifference($Atom, $MassDifference);
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222 }
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parents:
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223 if ($Charge && $Charge != 0) {
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parents:
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224 _ProcessCharge($Atom, $Charge);
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225 }
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parents:
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226 if ($StereoParity && $StereoParity != 0) {
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parents:
diff changeset
227 _ProcessStereoParity($Atom, $StereoParity);
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parents:
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228 }
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229
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parents:
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230 $AtomNumToAtomMap{$AtomNum} = $Atom;
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parents:
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231 $Molecule->AddAtom($Atom);
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232 }
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233
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234 # Process bond data...
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parents:
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235 my($FirstBondLineIndex, $LastBondLineIndex, $FirstAtomNum, $SecondAtomNum, $BondType, $BondStereo, $InternalBondOrder, $InternalBondType, $Bond, $Atom1, $Atom2);
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parents:
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236
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237 $FirstBondLineIndex = $FirstAtomLineIndex + $AtomCount;
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parents:
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238 $LastBondLineIndex = $FirstAtomLineIndex + $AtomCount + $BondCount - 1;
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parents:
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239
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parents:
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240 for ($LineIndex = $FirstBondLineIndex; $LineIndex <= $LastBondLineIndex; $LineIndex++) {
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parents:
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241 ($FirstAtomNum, $SecondAtomNum, $BondType, $BondStereo) = SDFileUtil::ParseCmpdBondLine($MoleculeLines[$LineIndex]);
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242
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243 $Atom1 = $AtomNumToAtomMap{$FirstAtomNum};
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244 $Atom2 = $AtomNumToAtomMap{$SecondAtomNum};
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245
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parents:
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246 ($InternalBondOrder, $InternalBondType) = SDFileUtil::MDLBondTypeToInternalBondOrder($BondType);
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parents:
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247 $Bond = new Bond('Atoms' => [$Atom1, $Atom2], 'BondOrder' => $InternalBondOrder);
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248 $Bond->SetBondType($InternalBondType);
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249
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250 if ($BondStereo && $BondStereo != 0) {
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251 _ProcessBondStereo($Bond, $BondStereo);
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252 }
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253
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254 $Molecule->AddBond($Bond);
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255 }
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256
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257 # Process available property block lines starting with A aaa, M CHG, M ISO and M RAD. All other property blocks
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258 # lines are for query or specific display purposes and are ignored for now.
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259 #
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260 #
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261 my($PropertyLineIndex, $PropertyLine, $FirstChargeOrRadicalLine, @ValuePairs);
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262
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263 $PropertyLineIndex = $FirstAtomLineIndex + $AtomCount + $BondCount;
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264 $PropertyLine = $MoleculeLines[$PropertyLineIndex];
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265 $FirstChargeOrRadicalLine = 1;
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266
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267 PROPERTYLINE: while ($PropertyLine !~ /^M END/i ) {
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parents:
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268 if ($PropertyLine =~ /\$\$\$\$/) {
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269 last PROPERTYLINE;
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270 }
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271 if ($PropertyLine =~ /^(M CHG|M RAD)/i) {
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parents:
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272 if ($FirstChargeOrRadicalLine) {
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273 $FirstChargeOrRadicalLine = 0;
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274 _ZeroOutAtomsChargeAndRadicalValues(\%AtomNumToAtomMap);
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275 }
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parents:
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276 if ($PropertyLine =~ /^M CHG/i) {
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parents:
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277 @ValuePairs = SDFileUtil::ParseCmpdChargePropertyLine($PropertyLine);
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parents:
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278 _ProcessChargeProperty(\@ValuePairs, \%AtomNumToAtomMap);
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parents:
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279 }
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parents:
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280 elsif ($PropertyLine =~ /^M RAD/i) {
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parents:
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281 @ValuePairs = SDFileUtil::ParseCmpdRadicalPropertyLine($PropertyLine);
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parents:
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282 _ProcessRadicalProperty(\@ValuePairs, \%AtomNumToAtomMap);
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283 }
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284 }
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parents:
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285 elsif ($PropertyLine =~ /^M ISO/i) {
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parents:
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286 @ValuePairs = SDFileUtil::ParseCmpdIsotopePropertyLine($PropertyLine);
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parents:
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287 _ProcessIsotopeProperty(\@ValuePairs, \%AtomNumToAtomMap);
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288 }
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parents:
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289 elsif ($PropertyLine =~ /^A /i) {
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parents:
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290 my($NextPropertyLine);
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parents:
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291 $PropertyLineIndex++;
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parents:
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292 $NextPropertyLine = $MoleculeLines[$PropertyLineIndex];
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parents:
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293 @ValuePairs = SDFileUtil::ParseCmpdAtomAliasPropertyLine($PropertyLine, $NextPropertyLine);
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parents:
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294 _ProcessAtomAliasProperty(\@ValuePairs, \%AtomNumToAtomMap);
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parents:
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295 }
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parents:
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296 $PropertyLineIndex++;
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parents:
diff changeset
297 $PropertyLine = $MoleculeLines[$PropertyLineIndex];
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parents:
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298 }
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parents:
diff changeset
299 # Store input molecule string as generic property of molecule...
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parents:
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300 $Molecule->SetInputMoleculeString($MoleculeString);
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parents:
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301
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parents:
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302 return $Molecule;
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parents:
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303 }
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parents:
diff changeset
304
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parents:
diff changeset
305 # Generate molecule string using molecule object...
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parents:
diff changeset
306 sub GenerateMoleculeString {
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parents:
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307 my($FirstParameter, $SecondParameter) = @_;
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parents:
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308 my($This, $Molecule);
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parents:
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309
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parents:
diff changeset
310 if ((@_ == 2) && (_IsMDLMolFileIO($FirstParameter))) {
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parents:
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311 ($This, $Molecule) = ($FirstParameter, $SecondParameter);
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parents:
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312 }
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parents:
diff changeset
313 else {
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parents:
diff changeset
314 $Molecule = $FirstParameter;
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parents:
diff changeset
315 $This = undef;
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parents:
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316 }
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parents:
diff changeset
317 if (!defined($Molecule)) {
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parents:
diff changeset
318 return undef;
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parents:
diff changeset
319 }
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parents:
diff changeset
320 my(@MoleculeLines);
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parents:
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321 @MoleculeLines = ();
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parents:
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322
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parents:
diff changeset
323 # First line: Molname line...
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parents:
diff changeset
324 push @MoleculeLines, SDFileUtil::GenerateCmpdMolNameLine($Molecule->GetName());
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325
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parents:
diff changeset
326 # Second line: Misc info...
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parents:
diff changeset
327 my($ProgramName, $UserInitial, $Code);
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parents:
diff changeset
328 $ProgramName = ''; $UserInitial = ''; $Code = '';
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329
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330 $Code = $Molecule->IsThreeDimensional() ? '3D' : '2D';
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parents:
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331
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parents:
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332 push @MoleculeLines, SDFileUtil::GenerateCmpdMiscInfoLine($ProgramName, $UserInitial, $Code);
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parents:
diff changeset
333
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parents:
diff changeset
334 # Third line: Comments line...
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parents:
diff changeset
335 my($Comments);
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parents:
diff changeset
336 $Comments = $Molecule->HasProperty('MDLComments') ? $Molecule->GetMDLComments() : ($Molecule->HasProperty('Comments') ? $Molecule->GetComments() : '');
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parents:
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337 push @MoleculeLines, SDFileUtil::GenerateCmpdCommentsLine($Comments);
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parents:
diff changeset
338
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parents:
diff changeset
339 # Fourth line: Counts line for V2000
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parents:
diff changeset
340 my($AtomCount, $BondCount, $ChiralFlag);
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parents:
diff changeset
341 $AtomCount = $Molecule->GetNumOfAtoms();
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parents:
diff changeset
342 $BondCount = $Molecule->GetNumOfBonds();
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parents:
diff changeset
343 $ChiralFlag = 0;
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parents:
diff changeset
344 push @MoleculeLines, SDFileUtil::GenerateCmpdCountsLine($AtomCount, $BondCount, $ChiralFlag);
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parents:
diff changeset
345
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parents:
diff changeset
346 # Atom lines...
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parents:
diff changeset
347 my($Atom, $AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge, $StereoParity, $AtomNum, $AtomID, @Atoms, %AtomIDToNum);
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parents:
diff changeset
348 my($ChargePropertyValue, $IsotopePropertyValue, $RadicalPropertyValue, $AtomAliasPropertyValue, @IsotopePropertyValuePairs, @ChargePropertyValuePairs, @RadicalPropertyValuePairs, @AtomAliasPropertyValuePairs);
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parents:
diff changeset
349
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parents:
diff changeset
350 @ChargePropertyValuePairs = ();
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parents:
diff changeset
351 @IsotopePropertyValuePairs = ();
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parents:
diff changeset
352 @RadicalPropertyValuePairs = ();
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parents:
diff changeset
353 @AtomAliasPropertyValuePairs = ();
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parents:
diff changeset
354
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parents:
diff changeset
355 @Atoms = $Molecule->GetAtoms();
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parents:
diff changeset
356
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parents:
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357 $AtomNum = 0;
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parents:
diff changeset
358 for $Atom (@Atoms) {
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parents:
diff changeset
359 $AtomNum++;
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parents:
diff changeset
360 $AtomID = $Atom->GetID();
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parents:
diff changeset
361 $AtomIDToNum{$AtomID} = $AtomNum;
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parents:
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362
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parents:
diff changeset
363 $AtomSymbol = $Atom->GetAtomSymbol();
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parents:
diff changeset
364 ($AtomX, $AtomY, $AtomZ) = $Atom->GetXYZ();
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parents:
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365
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parents:
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366 # Setup mass difference...
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parents:
diff changeset
367 $MassDifference = _GetMassDifference($Atom);
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parents:
diff changeset
368 if ($MassDifference) {
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parents:
diff changeset
369 # Hold it for M ISO property lines...
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parents:
diff changeset
370 $IsotopePropertyValue = _GetIsotopePropertyValue($Atom);
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parents:
diff changeset
371 if ($IsotopePropertyValue) {
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parents:
diff changeset
372 push @IsotopePropertyValuePairs, ($AtomNum, $IsotopePropertyValue);
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parents:
diff changeset
373 }
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parents:
diff changeset
374 }
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parents:
diff changeset
375
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parents:
diff changeset
376 # Setup charge...
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parents:
diff changeset
377 $Charge = _GetCharge($Atom);
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parents:
diff changeset
378 if ($Charge) {
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parents:
diff changeset
379 # Hold it for M CHG property lines...
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parents:
diff changeset
380 $ChargePropertyValue = _GetChargePropertyValue($Atom);
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deepakjadmin
parents:
diff changeset
381 if ($ChargePropertyValue) {
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deepakjadmin
parents:
diff changeset
382 push @ChargePropertyValuePairs, ($AtomNum, $ChargePropertyValue);
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deepakjadmin
parents:
diff changeset
383 }
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parents:
diff changeset
384 }
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parents:
diff changeset
385
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parents:
diff changeset
386 # Hold any radical values for for M RAD property lines...
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parents:
diff changeset
387 $RadicalPropertyValue = _GetRadicalPropertyValue($Atom);
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deepakjadmin
parents:
diff changeset
388 if ($RadicalPropertyValue) {
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deepakjadmin
parents:
diff changeset
389 push @RadicalPropertyValuePairs, ($AtomNum, $RadicalPropertyValue);
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deepakjadmin
parents:
diff changeset
390 }
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parents:
diff changeset
391
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deepakjadmin
parents:
diff changeset
392 # Hold any atom alias value for A xxx property lines....
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parents:
diff changeset
393 $AtomAliasPropertyValue = _GetAtomAliasPropertyValue($Atom);
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deepakjadmin
parents:
diff changeset
394 if ($AtomAliasPropertyValue) {
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deepakjadmin
parents:
diff changeset
395 push @AtomAliasPropertyValuePairs, ($AtomNum, $AtomAliasPropertyValue);
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deepakjadmin
parents:
diff changeset
396
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deepakjadmin
parents:
diff changeset
397 # Set AtomSymbol to carbon as atom alias would override its value during parsing...
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deepakjadmin
parents:
diff changeset
398 $AtomSymbol = "C";
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deepakjadmin
parents:
diff changeset
399 }
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deepakjadmin
parents:
diff changeset
400
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deepakjadmin
parents:
diff changeset
401 # Setup stereo parity...
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deepakjadmin
parents:
diff changeset
402 $StereoParity = _GetStereoParity($Atom);
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deepakjadmin
parents:
diff changeset
403
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deepakjadmin
parents:
diff changeset
404 push @MoleculeLines, SDFileUtil::GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge, $StereoParity);
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deepakjadmin
parents:
diff changeset
405 }
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deepakjadmin
parents:
diff changeset
406
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deepakjadmin
parents:
diff changeset
407 # Bond lines...
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deepakjadmin
parents:
diff changeset
408 my($FirstAtomID, $FirstAtom, $FirstAtomNum, $SecondAtomID, $SecondAtom, $SecondAtomNum, $MDLBondType, $BondOrder, $BondType, $MDLBondStereo, $Bond, @Bonds);
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parents:
diff changeset
409 for $FirstAtom (@Atoms) {
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deepakjadmin
parents:
diff changeset
410 $FirstAtomID = $FirstAtom->GetID();
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deepakjadmin
parents:
diff changeset
411 $FirstAtomNum = $AtomIDToNum{$FirstAtomID};
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deepakjadmin
parents:
diff changeset
412
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deepakjadmin
parents:
diff changeset
413 @Bonds = ();
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deepakjadmin
parents:
diff changeset
414 @Bonds = $FirstAtom->GetBonds();
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deepakjadmin
parents:
diff changeset
415 BOND: for $Bond (@Bonds) {
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deepakjadmin
parents:
diff changeset
416 $SecondAtom = $Bond->GetBondedAtom($FirstAtom);
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deepakjadmin
parents:
diff changeset
417 $SecondAtomID = $SecondAtom->GetID();
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deepakjadmin
parents:
diff changeset
418 $SecondAtomNum = $AtomIDToNum{$SecondAtomID};
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deepakjadmin
parents:
diff changeset
419 if ($FirstAtomNum >= $SecondAtomNum) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
420 next BOND;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
421 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
422 # Setup BondType...
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deepakjadmin
parents:
diff changeset
423 $BondOrder = $Bond->GetBondOrder();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
424 $BondType = $Bond->GetBondType();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
425 $MDLBondType = SDFileUtil::InternalBondOrderToMDLBondType($BondOrder, $BondType);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
426
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
427 # Setup BondStereo...
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deepakjadmin
parents:
diff changeset
428 $MDLBondStereo = _GetBondStereo($Bond);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
429
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deepakjadmin
parents:
diff changeset
430 push @MoleculeLines, SDFileUtil::GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum, $MDLBondType, $MDLBondStereo);
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deepakjadmin
parents:
diff changeset
431 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
432 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
433 # Property lines...
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deepakjadmin
parents:
diff changeset
434 if (@IsotopePropertyValuePairs) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
435 push @MoleculeLines, SDFileUtil::GenerateCmpdIsotopePropertyLines(\@IsotopePropertyValuePairs);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
436 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
437 if (@ChargePropertyValuePairs) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
438 push @MoleculeLines, SDFileUtil::GenerateCmpdChargePropertyLines(\@ChargePropertyValuePairs);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
439 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
440 if (@RadicalPropertyValuePairs) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
441 push @MoleculeLines, SDFileUtil::GenerateCmpdRadicalPropertyLines(\@RadicalPropertyValuePairs);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
442 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
443 if (@AtomAliasPropertyValuePairs) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
444 push @MoleculeLines, SDFileUtil::GenerateCmpdAtomAliasPropertyLines(\@AtomAliasPropertyValuePairs);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
445 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
446
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deepakjadmin
parents:
diff changeset
447 push @MoleculeLines, "M END";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
448
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
449 return join "\n", @MoleculeLines;
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deepakjadmin
parents:
diff changeset
450 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
451
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deepakjadmin
parents:
diff changeset
452 # Process MassDifference value and set atom's mass number...
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deepakjadmin
parents:
diff changeset
453 #
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deepakjadmin
parents:
diff changeset
454 sub _ProcessMassDifference {
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deepakjadmin
parents:
diff changeset
455 my($Atom, $MassDifference) = @_;
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deepakjadmin
parents:
diff changeset
456 my($MassNumber, $NewMassNumber, $AtomicNumber);
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deepakjadmin
parents:
diff changeset
457
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deepakjadmin
parents:
diff changeset
458 $AtomicNumber = $Atom->GetAtomicNumber();
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deepakjadmin
parents:
diff changeset
459
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deepakjadmin
parents:
diff changeset
460 if (!$AtomicNumber) {
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deepakjadmin
parents:
diff changeset
461 carp "Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Assigned to non standard element...";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
462 return;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
463 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
464 $MassNumber = $Atom->GetMassNumber();
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deepakjadmin
parents:
diff changeset
465 if (!$MassDifference) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
466 carp "Warning: ${ClassName}->_ProcessMassDifference: Ignoring specified mass difference value, $MassDifference, in SD file: Unknown MassNumber value...";
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deepakjadmin
parents:
diff changeset
467 return;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
468 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
469 $NewMassNumber = $MassNumber + $MassDifference;
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deepakjadmin
parents:
diff changeset
470 if (!PeriodicTable::IsElementNaturalIsotopeMassNumber($AtomicNumber, $NewMassNumber)) {
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deepakjadmin
parents:
diff changeset
471 my($AtomSymbol) = $Atom->GetAtomSymbol();
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deepakjadmin
parents:
diff changeset
472 carp "Warning: ${ClassName}->_ProcessMassDifference: Unknown mass number, $MassNumber, corresponding to specified mass difference value, $MassDifference, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n";
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deepakjadmin
parents:
diff changeset
473 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
474
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deepakjadmin
parents:
diff changeset
475 # Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...
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deepakjadmin
parents:
diff changeset
476 $Atom->SetProperty('MassNumber', $NewMassNumber);
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deepakjadmin
parents:
diff changeset
477 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
478
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
479 # Get mass difference value...
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deepakjadmin
parents:
diff changeset
480 sub _GetMassDifference {
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deepakjadmin
parents:
diff changeset
481 my($Atom) = @_;
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deepakjadmin
parents:
diff changeset
482 my($MassDifference, $MassNumber, $MostAbundantMassNumber, $AtomicNumber);
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deepakjadmin
parents:
diff changeset
483
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deepakjadmin
parents:
diff changeset
484 $MassDifference = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
485 $MassNumber = $Atom->GetMassNumber();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
486 if (defined $MassNumber) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
487 $AtomicNumber = $Atom->GetAtomicNumber();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
488 if (defined $AtomicNumber) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
489 $MostAbundantMassNumber = PeriodicTable::GetElementMostAbundantNaturalIsotopeMassNumber($AtomicNumber);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
490 if (defined($MostAbundantMassNumber) && $MassNumber != $MostAbundantMassNumber) {
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deepakjadmin
parents:
diff changeset
491 $MassDifference = $MassNumber - $MostAbundantMassNumber;
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deepakjadmin
parents:
diff changeset
492 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
493 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
494 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
495 return $MassDifference;
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deepakjadmin
parents:
diff changeset
496 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
497
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deepakjadmin
parents:
diff changeset
498 # Process formal charge value and assign it to atom as formal charge...
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deepakjadmin
parents:
diff changeset
499 sub _ProcessCharge {
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deepakjadmin
parents:
diff changeset
500 my($Atom, $Charge) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
501 my($InternalCharge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
502
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
503 $InternalCharge = SDFileUtil::MDLChargeToInternalCharge($Charge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
504 $Atom->SetFormalCharge($InternalCharge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
505 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
506
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
507 # Get MDL formal charge value ...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
508 sub _GetCharge {
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deepakjadmin
parents:
diff changeset
509 my($Atom) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
510 my($InternalCharge, $Charge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
511
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
512 $Charge = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
513 if ($Atom->HasProperty('FormalCharge')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
514 $InternalCharge = $Atom->GetFormalCharge();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
515 if ($InternalCharge) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
516 $Charge = SDFileUtil::InternalChargeToMDLCharge($InternalCharge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
517 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
518 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
519 return $Charge;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
520 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
521
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
522 # Process stereo parity value and assign it to atom as MDL property...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
523 #
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
524 # Notes:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
525 # . Mark atom as chiral center
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deepakjadmin
parents:
diff changeset
526 # . Assign any explicit Clockwise (parity 1), CounterClockwise (parity 2) or either value (parity 3) as property of atom.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
527 # . MDL values of Clockwise and CounterClockwise don't correspond to priority assigned to ligands around
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
528 # stereo center using CIP scheme; consequently, these values can't be used to set internal Stereochemistry for
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
529 # an atom.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
530 #
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
531 sub _ProcessStereoParity {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
532 my($Atom, $StereoParity) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
533
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
534 $Atom->SetStereoCenter('1');
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
535 $Atom->SetMDLStereoParity($StereoParity);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
536 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
537
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
538 # Set stereo parity value to zero for now: The current release of MayaChemTools hasn't implemented
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
539 # functionality to determine chirality.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
540 #
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
541 sub _GetStereoParity {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
542 my($Atom) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
543 my($StereoParity);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
544
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
545 $StereoParity = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
546
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
547 return $StereoParity;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
548 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
549
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
550 # Process bond stereo value...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
551 sub _ProcessBondStereo {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
552 my($Bond, $BondStereo) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
553 my($InternalBondStereo);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
554
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
555 $InternalBondStereo = SDFileUtil::MDLBondStereoToInternalBondStereochemistry($BondStereo);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
556 if ($InternalBondStereo) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
557 $Bond->SetBondStereochemistry($InternalBondStereo);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
558 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
559 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
560
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
561 # Get MDLBondStereo value...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
562 sub _GetBondStereo {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
563 my($Bond) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
564 my($InternalBondStereo, $BondStereo);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
565
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
566 $BondStereo = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
567
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
568 $InternalBondStereo = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
569 BONDSTEREO: {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
570 if ($Bond->IsUp()) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
571 $InternalBondStereo = 'Up';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
572 last BONDSTEREO;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
573 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
574 if ($Bond->IsDown()) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
575 $InternalBondStereo = 'Down';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
576 last BONDSTEREO;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
577 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
578 if ($Bond->IsUpOrDown()) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
579 $InternalBondStereo = 'UpOrDown';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
580 last BONDSTEREO;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
581 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
582 if ($Bond->IsCisOrTrans() || $Bond->IsCis() || $Bond->IsTrans()) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
583 $InternalBondStereo = 'CisOrTrans';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
584 last BONDSTEREO;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
585 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
586 $InternalBondStereo = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
587 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
588
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
589 if ($InternalBondStereo) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
590 $BondStereo = SDFileUtil::InternalBondStereochemistryToMDLBondStereo($InternalBondStereo);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
591 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
592
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
593 return $BondStereo;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
594 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
595
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
596 # Zero out charge and radical values specified for atoms...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
597 sub _ZeroOutAtomsChargeAndRadicalValues {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
598 my($AtomNumToAtomMapRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
599 my($Atom);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
600
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
601 for $Atom (values %{$AtomNumToAtomMapRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
602 if ($Atom->HasProperty('FormalCharge')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
603 $Atom->DeleteProperty('FormalCharge');
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
604 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
605 elsif ($Atom->HasProperty('SpinMultiplicity')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
606 $Atom->DeleteProperty('SpinMultiplicity');
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
607 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
608 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
609 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
610
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
611 # Process charge property value pairs...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
612 sub _ProcessChargeProperty {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
613 my($ValuePairsRef, $AtomNumToAtomMapRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
614
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
615 if (!(defined($ValuePairsRef) && @{$ValuePairsRef})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
616 return;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
617 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
618 my($Index, $ValuePairsCount, $AtomNum, $Charge, $Atom);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
619
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
620 $ValuePairsCount = scalar @{$ValuePairsRef};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
621 VALUEPAIRS: for ($Index = 0; $Index < $ValuePairsCount; $Index +=2) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
622 $AtomNum = $ValuePairsRef->[$Index]; $Charge = $ValuePairsRef->[$Index + 1];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
623 if (!$Charge) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
624 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
625 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
626 if (!exists $AtomNumToAtomMapRef->{$AtomNum}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
627 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
628 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
629 $Atom = $AtomNumToAtomMapRef->{$AtomNum};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
630 if ($Atom->HasProperty('SpinMultiplicity')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
631 carp "Warning: ${ClassName}->_ProcessChargeProperty: Setting formal charge on atom number, $AtomNum, with already assigned spin multiplicity value...";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
632 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
633 $Atom->SetFormalCharge($Charge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
634 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
635 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
636
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
637 # Get charge property value for an atom...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
638 sub _GetChargePropertyValue {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
639 my($Atom) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
640 my($Charge);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
641
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
642 $Charge = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
643 if ($Atom->HasProperty('FormalCharge')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
644 $Charge = $Atom->GetFormalCharge();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
645 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
646 return $Charge;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
647 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
648
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
649 # Process charge property value pairs...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
650 sub _ProcessRadicalProperty {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
651 my($ValuePairsRef, $AtomNumToAtomMapRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
652
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
653 if (!(defined($ValuePairsRef) && @{$ValuePairsRef})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
654 return;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
655 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
656 my($Index, $ValuePairsCount, $AtomNum, $Radical, $SpinMultiplicity, $Atom);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
657
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
658 $ValuePairsCount = scalar @{$ValuePairsRef};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
659 VALUEPAIRS: for ($Index = 0; $Index < $ValuePairsCount; $Index +=2) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
660 $AtomNum = $ValuePairsRef->[$Index]; $Radical = $ValuePairsRef->[$Index + 1];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
661 if (!$Radical) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
662 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
663 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
664 if (!exists $AtomNumToAtomMapRef->{$AtomNum}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
665 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
666 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
667 $Atom = $AtomNumToAtomMapRef->{$AtomNum};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
668 if ($Atom->HasProperty('FormalCharge')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
669 carp "Warning: ${ClassName}->_ProcessRadicalProperty: Setting spin multiplicity on atom number, $AtomNum, with already assigned formal charge value...";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
670 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
671 $SpinMultiplicity = SDFileUtil::MDLRadicalToInternalSpinMultiplicity($Radical);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
672 $Atom->SetSpinMultiplicity($SpinMultiplicity);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
673 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
674 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
675
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
676 # Get radical property value for an atom...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
677 sub _GetRadicalPropertyValue {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
678 my($Atom) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
679 my($Radical, $SpinMultiplicity);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
680
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
681 $Radical = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
682 if ($Atom->HasProperty('SpinMultiplicity')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
683 $SpinMultiplicity = $Atom->GetSpinMultiplicity();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
684 $Radical = SDFileUtil::InternalSpinMultiplicityToMDLRadical($SpinMultiplicity);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
685 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 return $Radical;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
687 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
688
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 # Process isotope property value pairs...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
690 sub _ProcessIsotopeProperty {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
691 my($ValuePairsRef, $AtomNumToAtomMapRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
692
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 if (!(defined($ValuePairsRef) && @{$ValuePairsRef})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
694 return;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
695 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
696 my($Index, $ValuePairsCount, $AtomNum, $MassNumber, $Atom, $AtomicNumber);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698 $ValuePairsCount = scalar @{$ValuePairsRef};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
699 VALUEPAIRS: for ($Index = 0; $Index < $ValuePairsCount; $Index +=2) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
700 $AtomNum = $ValuePairsRef->[$Index]; $MassNumber = $ValuePairsRef->[$Index + 1];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
701 if (!$MassNumber) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
702 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
703 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
704 if (!exists $AtomNumToAtomMapRef->{$AtomNum}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
705 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
706 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
707 $Atom = $AtomNumToAtomMapRef->{$AtomNum};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
708 $AtomicNumber = $Atom->GetAtomicNumber();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
710 if (!PeriodicTable::IsElementNaturalIsotopeMassNumber($AtomicNumber, $MassNumber)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711 my($AtomSymbol) = $Atom->GetAtomSymbol();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
712 carp "Warning: ${ClassName}->_ProcessProcessIsotopeProperty: Unknown mass number, $MassNumber, specified on M ISO property line for atom number, $AtomNum, in SD for atom with atomic number, $AtomicNumber, and atomic symbol, $AtomSymbol. The mass number value has been assigned. Don't forget to Set ExactMass property explicitly; otherwise, GetExactMass method would return mass of most abundant isotope...\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
713 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
714
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
715 # Use SetProperty method instead of SetMassNumber to skip explicit checks on MassNumber value...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
716 $Atom->SetProperty('MassNumber', $MassNumber);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
717 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
718 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
719
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
720 # Get isotope property value for an atom...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
721 sub _GetIsotopePropertyValue {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
722 my($Atom) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
723 my($MassNumber);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
724
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
725 $MassNumber = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
726 if ($Atom->HasProperty('MassNumber')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
727 $MassNumber = $Atom->GetMassNumber();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
728 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
729 return $MassNumber;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
730 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
731
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
732 # Process atom alias property value pairs...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
733 sub _ProcessAtomAliasProperty {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
734 my($ValuePairsRef, $AtomNumToAtomMapRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
735
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
736 if (!(defined($ValuePairsRef) && @{$ValuePairsRef})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
737 return;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
738 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
739 my($Index, $ValuePairsCount, $AtomNum, $AtomAlias, $Atom);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
740
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
741 $ValuePairsCount = scalar @{$ValuePairsRef};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
742 VALUEPAIRS: for ($Index = 0; $Index < $ValuePairsCount; $Index +=2) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
743 $AtomNum = $ValuePairsRef->[$Index]; $AtomAlias = $ValuePairsRef->[$Index + 1];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
744 if (!$AtomNum) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
745 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
746 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
747 if (!exists $AtomNumToAtomMapRef->{$AtomNum}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
748 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
749 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
750 $AtomAlias = TextUtil::RemoveLeadingAndTrailingWhiteSpaces($AtomAlias);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
751 if (TextUtil::IsEmpty($AtomAlias)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
752 carp("Warning: ${ClassName}->_ProcessAtomAliasProperty: Ignoring atom alias property line: No Atom alias value specified...");
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
753 next VALUEPAIRS;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
754 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
755
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
756 # Set atom symbol to atom alias which sets atomic number automatically...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
757 $Atom = $AtomNumToAtomMapRef->{$AtomNum};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
758 $Atom->SetAtomSymbol($AtomAlias);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
759
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
760 $Atom->SetProperty('AtomAlias', $AtomAlias);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
761 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
762 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
763
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
764 # Get atom alias property value for an atom...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
765 sub _GetAtomAliasPropertyValue {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
766 my($Atom) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
767 my($AtomAlias);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
768
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
769 $AtomAlias = undef;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
770 if ($Atom->HasProperty('AtomAlias')) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
771 $AtomAlias = $Atom->GetAtomAlias();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
772 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
773 return $AtomAlias;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
774 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
775
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
776 # Is it a MDLMolFileIO object?
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
777 sub _IsMDLMolFileIO {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
778 my($Object) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
779
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
780 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
781 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
782
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
783
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
784 1;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
785
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
786 __END__
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
787
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
788 =head1 NAME
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
789
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
790 MDLMolFileIO
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
791
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
792 =head1 SYNOPSIS
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
793
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
794 use FileIO::MDLMolFileIO;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
795
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
796 use FileIO::MDLMolFileIO qw(:all);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
797
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
798 =head1 DESCRIPTION
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
799
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
800 B<MDLMolFIleIO> class provides the following methods:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
801
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
802 new, GenerateMoleculeString, IsMDLMolFile, ParseMoleculeString, ReadMolecule,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
803 ReadMoleculeString, WriteMolecule
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
804
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
805 The following methods can also be used as functions:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
806
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
807 GenerateMoleculeString, IsMDLMolFile, ParseMoleculeString
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
808
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
809 Data specific to B<MDLMolFileIO> class not directly used by B<Molecule>, B<Atom> and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
810 B<Bond> objects - data label/value pairs, atom SteroParity and so on - is associated to
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
811 and retrieved from appropriate objects using following methods:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
812
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
813 SetMDL<PropertyName>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
814 GetMDL<PropertyName>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
815
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
816 B<MDLMolFileIO> class is derived from I<FileIO> class and uses its methods to support
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
817 generic file related functionality.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
818
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
819 =head2 METHODS
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
820
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
821 =over 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
822
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
823 =item B<new>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
824
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
825 $NewMDLMolFileIO = new FileIO::MDLMolFileIO(%NamesAndValues);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
826
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
827 Using specified I<MDLMolFileIO> property names and values hash, B<new> method creates a new object
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
828 and returns a reference to newly created B<MDLMolFileIO> object.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
829
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
830 =item B<GenerateMoleculeString>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
831
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
832 $MoleculeString = $MDLMolFileIO->GenerateMoleculeString($Molecule);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
833 $MoleculeString = FileIO::MDLMolFileIO::GenerateMoleculeString($Molecule);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
834
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
835 Returns a B<MoleculeString> in MDLMol format corresponding to I<Molecule>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
836
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
837 =item B<IsMDLMolFile>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
838
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
839 $Status = $MDLMolFileIO->IsMDLMolFile($FileName);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
840 $Status = FileIO::MDLMolFileIO::IsMDLMolFile($FileName);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
841
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
842 Returns 1 or 0 based on whether I<FileName> is a MDLMol file.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
843
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
844 =item B<ParseMoleculeString>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
845
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deepakjadmin
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846 $Molecule = $MDLMolFileIO->ParseMoleculeString($MoleculeString);
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847 $Molecule = FileIO::MDLMolFileIO::ParseMoleculeString($MoleculeString);
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848
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849 Parses I<MoleculeString> and returns a B<Molecule> object.
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850
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851 =item B<ReadMolecule>
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852
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853 $Molecule = $MDLMolFileIO->ReadMolecule($FileHandle);
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854
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855 Reads data for the compound in a file using already opened I<FileHandle>, creates,
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deepakjadmin
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856 and returns a B<Molecule> object.
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857
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858 =item B<ReadMoleculeString>
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859
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860 $MoleculeString = $MDLMolFileIO->ReadMoleculeString($FileHandle);
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861
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862 Reads data for the compound in a file using already opened I<FileHandle> and
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863 returns a B<MoleculeString> corresponding to compound structure and other associated
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864 data.
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865
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866 =item B<WriteMolecule>
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867
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868 $MDLMolFileIO->WriteMolecule($Molecule);
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869
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870 Writes I<Molecule> data to a file in MDLMol format and returns B<MDLMolFileIO>.
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deepakjadmin
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871
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872 =back
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873
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874 =head1 AUTHOR
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875
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876 Manish Sud <msud@san.rr.com>
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877
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878 =head1 SEE ALSO
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879
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880 MoleculeFileIO.pm, SDFileIO.pm
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881
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882 =head1 COPYRIGHT
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883
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deepakjadmin
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884 Copyright (C) 2015 Manish Sud. All rights reserved.
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885
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deepakjadmin
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886 This file is part of MayaChemTools.
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deepakjadmin
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887
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888 MayaChemTools is free software; you can redistribute it and/or modify it under
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parents:
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889 the terms of the GNU Lesser General Public License as published by the Free
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deepakjadmin
parents:
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890 Software Foundation; either version 3 of the License, or (at your option)
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deepakjadmin
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891 any later version.
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892
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893 =cut