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1 package Fingerprints::FingerprintsFileUtil;
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2 #
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3 # $RCSfile: FingerprintsFileUtil.pm,v $
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4 # $Date: 2015/02/28 20:48:54 $
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5 # $Revision: 1.14 $
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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 Exporter;
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31 use Carp;
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32 use TextUtil ();
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33 use FileUtil ();
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34 use FileIO::FingerprintsSDFileIO;
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35 use FileIO::FingerprintsTextFileIO;
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36 use FileIO::FingerprintsFPFileIO;
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37
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38 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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39
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40 @ISA = qw(Exporter);
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41 @EXPORT = qw();
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42 @EXPORT_OK = qw(GetFingerprintsFileType ReadAndProcessFingerpritsData NewFingerprintsFileIO);
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43
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44 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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45
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46 # Generate new FingerprintsFileIO object for a SD, FP or Text fingerprints file specified using file name
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47 # along other appropriate parameters...
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48 #
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49 sub NewFingerprintsFileIO {
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50 my(%FingerprintsFileIOParams) = @_;
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51 my($FingerprintsFileIO, $FileType);
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52
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53 if (!(exists($FingerprintsFileIOParams{Name}) && TextUtil::IsNotEmpty($FingerprintsFileIOParams{Name}))) {
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54 carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File name is not specified...\n";
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55 return undef;
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56 }
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57
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58 if (!(exists($FingerprintsFileIOParams{Mode}) && TextUtil::IsNotEmpty($FingerprintsFileIOParams{Mode}))) {
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59 carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File mode is not specified...\n";
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60 return undef;
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61 }
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62
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63 $FileType = GetFingerprintsFileType($FingerprintsFileIOParams{Name});
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64 if (TextUtil::IsEmpty($FileType)) {
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65 carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Can't create new FingerprintsFileIO object: File type is not specified...\n";
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66 return undef;
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67 }
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68
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69 # Generate fingerprints IO object...
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70 FILETYPE: {
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71 if ($FileType =~ /^SD$/i) {
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72 $FingerprintsFileIO = new FileIO::FingerprintsSDFileIO(%FingerprintsFileIOParams);
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73 last FILETYPE;
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74 }
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75 if ($FileType =~ /^FP$/i) {
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76 $FingerprintsFileIO = new FileIO::FingerprintsFPFileIO(%FingerprintsFileIOParams);
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77 last FILETYPE;
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78 }
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79 if ($FileType =~ /^Text$/i) {
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80 $FingerprintsFileIO = new FileIO::FingerprintsTextFileIO(%FingerprintsFileIOParams);
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81 last FILETYPE;
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82 }
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83 $FingerprintsFileIO = undef;
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84 carp "Warning: Fingerprints::FingerprintsFileUtil::NewFingerprintsFileIO: Fingerprints file type, $FileType, is not valid. Supported file types: SD, FP or Text\n";
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85 }
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86
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87 return $FingerprintsFileIO;
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88 }
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89
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90 # Get fingerpritns file type from fingerprints file name...
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91 #
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92 sub GetFingerprintsFileType {
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93 my($FileName) = @_;
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94 my($FileType);
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95
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96 $FileType = '';
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97 FILETYPE: {
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98 if (FileUtil::CheckFileType($FileName, "sdf sd")) {
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99 $FileType = 'SD';
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100 last FILETYPE;
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101 }
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102 if (FileUtil::CheckFileType($FileName, "fpf fp")) {
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103 $FileType = 'FP';
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104 last FILETYPE;
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105 }
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106 if (FileUtil::CheckFileType($FileName, "csv tsv")) {
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107 $FileType = 'Text';
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108 last FILETYPE;
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109 }
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110 $FileType = '';
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111 carp "Warning: Fingerprints::FingerprintsFileUtil::GetFingerprintsFileType: Can't determine fingerprints file type for $FileName: It's not a fingerprints file...\n";
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112 }
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113
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114 return $FileType;
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115 }
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116
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117
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118 # Process fingerprints bit-vector and vector string data in a file using FingerprintsFileIO
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119 # object and return a references to arrays of CompoundIDs and FingerprintsObjects...
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120 #
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121 # Note:
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122 # . The file open and close is automatically performed during processing.
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123 #
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124 sub ReadAndProcessFingerpritsData {
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125 my($FingerprintsFileIO, $CheckCompoundIDs) = @_;
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126 my($CompoundID, $FingerprintsCount, $IgnoredFingerprintsCount, @CompundIDs, @FingerprintsObjects, %UniqueCompoundIDs);
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127
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128 if (!$FingerprintsFileIO) {
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129 return (undef, undef);
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130 }
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131 $CheckCompoundIDs = defined $CheckCompoundIDs ? $CheckCompoundIDs : 0;
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132
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133 print "\nReading and processing fingerprints data...\n";
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134
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135 ($FingerprintsCount, $IgnoredFingerprintsCount) = (0) x 3;
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136
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137 @CompundIDs = ();
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138 @FingerprintsObjects = ();
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139
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140 %UniqueCompoundIDs = ();
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141
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142 # Check and open file for reading...
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143 if (!$FingerprintsFileIO->GetStatus()) {
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144 $FingerprintsFileIO->Open();
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145 }
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146
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147 FINGERPRINTS: while ($FingerprintsFileIO->Read()) {
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148 $FingerprintsCount++;
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149
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150 if (!$FingerprintsFileIO->IsFingerprintsDataValid()) {
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151 $IgnoredFingerprintsCount++;
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152 next FINGERPRINTS;
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153 }
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154
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155 if ($CheckCompoundIDs) {
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156 $CompoundID = $FingerprintsFileIO->GetCompoundID();
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157 if (exists $UniqueCompoundIDs{$CompoundID}) {
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158 warn "Warning: Ignoring fingerprints data for compound ID $CompoundID: Multiple entries for compound ID in fingerprints file.\n";
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159 $IgnoredFingerprintsCount++;
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160 next FINGERPRINTS;
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161 }
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162 $UniqueCompoundIDs{$CompoundID} = $CompoundID;
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163 }
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164
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165 push @FingerprintsObjects, $FingerprintsFileIO->GetFingerprints();
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166 push @CompundIDs, $FingerprintsFileIO->GetCompoundID();
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167 }
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168 $FingerprintsFileIO->Close();
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169
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170 print "Number of fingerprints data entries: $FingerprintsCount\n";
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171 print "Number of fingerprints date entries processed successfully: ", ($FingerprintsCount - $IgnoredFingerprintsCount) , "\n";
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172 print "Number of fingerprints data entries ignored due to missing/invalid data: $IgnoredFingerprintsCount\n\n";
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173
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174 return (\@CompundIDs, \@FingerprintsObjects);
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175 }
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176
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177
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178 1;
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179
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180 __END__
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181
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182 =head1 NAME
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183
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184 FingerprintsFileUtil
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185
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186 =head1 SYNOPSIS
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187
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188 use Fingerprints::FingerprintsFileUtil;
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189
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190 use Fingerprints::FingerprintsFileUtil qw(:all);
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191
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192 =head1 DESCRIPTION
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193
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194 B<FingerprintsFileUtil> module provides the following functions:
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195
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196 GetFingerprintsFileType, NewFingerprintsFileIO, ReadAndProcessFingerpritsData
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197
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198 B<FingerprintsFileUtil> module provides function to handle fingerprints data strings
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199 in FP, SD and CSV/TSV text files present in one of the following two types: fingerprints
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200 bit-vectors and fingerprints vector strings
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201
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202 Example of B<FP> file format containing fingerprints bit-vector string data:
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203
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204 #
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205 # Package = MayaChemTools 7.4
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206 # ReleaseDate = Oct 21, 2010
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207 #
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208 # TimeStamp = Mon Mar 7 15:14:01 2011
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209 #
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210 # FingerprintsStringType = FingerprintsBitVector
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211 #
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212 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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213 # Size = 1024
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214 # BitStringFormat = HexadecimalString
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215 # BitsOrder = Ascending
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216 #
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217 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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218 Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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219 ... ...
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220 ... ..
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221
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222 Example of B<FP> file format containing fingerprints vector string data:
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223
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224 #
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225 # Package = MayaChemTools 7.4
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226 # ReleaseDate = Oct 21, 2010
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227 #
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228 # TimeStamp = Mon Mar 7 15:14:01 2011
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229 #
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230 # FingerprintsStringType = FingerprintsVector
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231 #
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232 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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233 # VectorStringFormat = IDsAndValuesString
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234 # VectorValuesType = NumericalValues
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235 #
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236 Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
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237 N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
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238 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
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239 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
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240 Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C
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241 O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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242 15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2
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243 1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ...
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244 ... ...
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245 ... ...
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246
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247 Example of B<SD> file format containing fingerprints vector string data:
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248
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249 ... ...
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250 ... ...
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251 $$$$
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252 ... ...
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253 ... ...
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254 ... ...
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255 41 44 0 0 0 0 0 0 0 0999 V2000
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256 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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257 ... ...
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258 2 3 1 0 0 0 0
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259 ... ...
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260 M END
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261 > <CmpdID>
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262 Test
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263
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264 > <PathLengthFingerprints>
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265 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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266 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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267 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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268 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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269 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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270 aa0660a11014a011d46
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271
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272 $$$$
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273 ... ...
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274 ... ...
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275
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276 Example of CSV B<text> file format containing fingerprints bit-vector string data:
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277
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278 "CompoundID","PathLengthFingerprints"
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279 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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280 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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281 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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282 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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283 ... ...
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284 ... ...
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285
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286 The current release of MayaChemTools supports the following types of fingerprint
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287 bit-vector and vector strings:
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288
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289 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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290 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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291 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
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292 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
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293 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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294 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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295
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296 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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297 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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298 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
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299 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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300
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301 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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302 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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303 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
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304
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305 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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306 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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307 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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308 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
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309 O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
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310 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...
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311
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312 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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313 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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314 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
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315 .024 -2.270
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316
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317 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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318 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
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319 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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320 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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321 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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322
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323 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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324 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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325 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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326 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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327 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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328 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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329
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330 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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331 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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332 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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333 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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334 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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335 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
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336
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337 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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338 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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339 0000000001010000000110000011000000000000100000000000000000000000100001
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340 1000000110000000000000000000000000010011000000000000000000000000010000
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341 0000000000000000000000000010000000000000000001000000000000000000000000
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342 0000000000010000100001000000000000101000000000000000100000000000000...
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343
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344 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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345 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
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346 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
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347 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
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348 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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349 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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350
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351 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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352 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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353 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
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354 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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355 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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|
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356 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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357
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358 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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|
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359 0000000000000000000000000000000001001000010010000000010010000000011100
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360 0100101010111100011011000100110110000011011110100110111111111111011111
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361 11111111111110111000
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362
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|
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363 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
|
|
|
364 1110011111100101111111000111101100110000000000000011100010000000000000
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365 0000000000000000000000000000000000000000000000101000000000000000000000
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366 0000000000000000000000000000000000000000000000000000000000000000000000
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367 0000000000000000000000000000000000000011000000000000000000000000000000
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368 0000000000000000000000000000000000000000
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369
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370 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
|
|
|
371 ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
372 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
|
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|
373 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
|
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374 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
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|
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375 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1
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376
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|
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377 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
|
|
|
378 ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
|
|
|
379 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
|
|
|
380 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
381 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
|
|
|
382 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
|
|
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383
|
|
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384 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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|
|
385 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
386 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
387 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
388 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
389 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
390
|
|
|
391 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
392 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
393 C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
|
|
|
394 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
395 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
396 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
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|
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397
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|
|
398 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
399 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
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|
400 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
|
|
|
401 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
402 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
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|
403 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
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404
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|
405 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
406 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
407 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
408 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
409 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
410 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
|
411
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|
|
412 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
413 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
|
|
|
414 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
|
|
|
415 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
|
|
|
416 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
|
|
|
417 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
|
|
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418
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|
419 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
420 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
|
|
|
421 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
|
|
|
422 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
|
|
|
423 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
|
|
|
424
|
|
|
425 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
426 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
|
|
|
427 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
|
|
|
428 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
|
|
|
429 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
|
|
|
430
|
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|
431 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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|
|
432 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
433 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
|
|
|
434 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
|
|
|
435 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
|
|
|
436 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
|
|
|
437 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
|
|
|
438
|
|
|
439 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
|
|
|
440 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
|
|
|
441 .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
|
|
|
442 D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
|
|
|
443 -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
|
|
|
444 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...
|
|
|
445
|
|
|
446 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
447 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
|
|
|
448 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
|
|
|
449 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
|
|
|
450 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
|
|
|
451 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
|
|
|
452 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
453
|
|
|
454 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
455 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
456 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
457 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
|
|
|
458 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
|
|
|
459 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
|
|
|
460
|
|
|
461 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
462 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
|
|
|
463 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
|
|
|
464 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
|
|
|
465 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
|
|
|
466 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
|
|
|
467 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
|
|
|
468 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
|
|
|
469
|
|
|
470 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
471 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
472 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
|
|
|
473 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
|
|
|
474 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
|
|
|
475 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...
|
|
|
476
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|
477 =head1 FUNCTIONS
|
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478
|
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|
479 =over 4
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480
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481 =item B<GetFingerprintsFileType>
|
|
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482
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|
|
483 $FileType = GetFingerprintsFileType($FileName);
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484
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|
|
485 Returns fingerprints B<FileType> of I<FileName> determined using extension of file name.
|
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|
486 Possible B<FileType> values: I<FP, SD, Text>. Supported file name extensions for various
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|
|
487 file types are: B<FP> - I<fpf, fp>; B<SD> - I<sdf, sd>; B<Text> - I<csv, tsv>.
|
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488
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489 =item B<NewFingerprintsFileIO>
|
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490
|
|
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491 $FingerprintsFileIO = NewFingerprintsFileIO(%IOParameters);
|
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|
492
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493 Using specified I<IOParameters> property names and values hash, B<NewFingerprintsFileIO>
|
|
|
494 method creates a new object using appropriate fingerprints file IO class - B<FingerprintsFPFileIO,
|
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|
495 FingerprintsSDFileIO, or FingerprintsTextFileIO> - and returns a reference to a newly created
|
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|
496 B<FingerprintsFileIO> object.
|
|
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497
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498 The I<IOParameters> hash must contain I<Name> and I<Mode> as key/value pairs to create
|
|
|
499 a new B<FingerprintsFileIO> object.
|
|
|
500
|
|
|
501 Based on type of file - B<FP, SD or Text> - B<NewFingerprintsFileIO> use B<new> method
|
|
|
502 from appropriate class - B<FingerprintsFPFileIO> - along with I<IOParameters> to create
|
|
|
503 B<FingerprintsFileIO> object.
|
|
|
504
|
|
|
505 =item B<ReadAndProcessFingerpritsData>
|
|
|
506
|
|
|
507 ($CompoundIDsRef, $FingerprintsObjectRef) =
|
|
|
508 ReadAndProcessFingerpritsData($FingerprintsFileIO);
|
|
|
509
|
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|
510 Processes fingerprints bit-vector and vector string data in a file using I<FingerprintsFileIO>
|
|
|
511 object and returns a references to arrays of B<CompoundIDs> and I<FingerprintsObjects>.
|
|
|
512
|
|
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513 The file open and close is automatically performed during processing.
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514
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515 =back
|
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516
|
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|
517 =head1 AUTHOR
|
|
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518
|
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519 Manish Sud <msud@san.rr.com>
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|
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520
|
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|
521 =head1 SEE ALSO
|
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522
|
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523 FingerprintsFPFileIO.pm, FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm
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524
|
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525 =head1 COPYRIGHT
|
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526
|
|
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527 Copyright (C) 2015 Manish Sud. All rights reserved.
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528
|
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529 This file is part of MayaChemTools.
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530
|
|
|
531 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
532 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
533 Software Foundation; either version 3 of the License, or (at your option)
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534 any later version.
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535
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536 =cut
|
