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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyPDBFiles.html" title="ModifyPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Next</a></td><td width="34%" align="middle"><strong>ModifySDFilesDataFields.pl</strong></td><td width="33%" align="right"><a href="././code/ModifySDFilesDataFields.html" title="View source code">Code</a> | <a href="./../pdf/ModifySDFilesDataFields.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ModifySDFilesDataFields.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ModifySDFilesDataFields.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ModifySDFilesDataFields.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>ModifySDFilesDataFields.pl - Modify data fields in SDFile(s)</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>ModifySDFilesDataFields.pl SDFile(s)...</p>
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26 <p>ModifySDFilesDataFields.pl [<strong>-d, --detail</strong> infolevel]
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27 [<strong>--datafieldscommon</strong> newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]]
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28 [<strong>--datafieldsmap</strong> newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]]
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29 [<strong>--datafieldsmapfile</strong> filename] [<strong>--datafieldURL</strong> URLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel]
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30 [<strong>-h, --help</strong>] [<strong>-k, --keepolddatafields</strong> all | unmappedonly | none] [<strong>-m, --mode</strong> molname | datafields | both]
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31 [<strong>--molnamemode</strong> datafield | labelprefix] [<strong>--molname</strong> datafieldname or prefixstring]
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32 [<strong>--molnamereplace</strong> always | empty] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname]
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33 [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p>
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34 <p>
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35 </p>
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36 <h2>DESCRIPTION</h2>
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37 <p>Modify molname line and data fields in <em>SDFile(s)</em>. Molname line can be replaced by a
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38 data field value or assigned a sequential ID prefixed with a specific string. For data
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39 fields and modification of their values, these types of options are supported: replace
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40 data field labels by another set of labels; combine values of multiple data fields and
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41 assign a new label; add specific set of data field labels and values to all compound
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42 records; and others.</p>
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43 <p>The file names are separated by space.The valid file extensions are <em>.sdf</em> and <em>.sd</em>.
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44 All other file names are ignored. All the SD files in a current directory can be specified
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45 either by <em>*.sdf</em> or the current directory name.</p>
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46 <p>
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47 </p>
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48 <h2>OPTIONS</h2>
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49 <dl>
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50 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt>
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51 <dd>
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52 <p>Level of information to print about compound records being ignored. Default: <em>1</em>. Possible
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53 values: <em>1, 2 or 3</em>.</p>
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54 </dd>
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55 <dt><strong><strong>--datafieldscommon</strong> <em>newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]</em></strong></dt>
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56 <dd>
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57 <p>Specify data field labels and values for addition to each compound record. It's a comma delimited
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58 list of data field label and values pair. Default: <em>none</em>.</p>
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59 <p>Examples:</p>
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60 <div class="OptionsBox">
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61 DepositionDate,YYYY-MM-DD
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62 <br/> Source,www.domainname.org,ReleaseData,YYYY-MM-DD</div>
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63 </dd>
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64 <dt><strong><strong>--datafieldsmap</strong> <em>newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]</em></strong></dt>
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65 <dd>
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66 <p>Specify how various data field labels and values are combined to generate a new data field
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67 labels and their values. All the comma delimited data fields, with in a semicolon delimited set,
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68 are mapped to the first new data field label along with the data field values joined via new
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69 line character. Default: <em>none</em>.</p>
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70 <p>Examples:</p>
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71 <div class="OptionsBox">
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72 Synonym,Name,SystematicName,Synonym;CmpdID,Extreg
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73 <br/> HBondDonors,SumNHOH</div>
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74 </dd>
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75 <dt><strong><strong>--datafieldsmapfile</strong> <em>filename</em></strong></dt>
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76 <dd>
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77 <p>Filename containing mapping of data fields. Format of data fields line in this file corresponds
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78 to <strong>--datafieldsmap</strong> option. Example:</p>
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79 <div class="OptionsBox">
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80 Line 1: Synonym,Name,SystematicName,Synonym;CmpdID,Extreg
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81 <br/> Line 2: HBondDonors,SumNHOH</div>
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82 </dd>
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83 <dt><strong><strong>--datafieldURL</strong> <em>URLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel</em></strong></dt>
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84 <dd>
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85 <p>Specify how to generate a URL for retrieving compound data from a web server and add it
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86 to each compound record. <em>URLDataFieldLabel</em> is used as the data field label for URL value
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87 which is created by combining <em>CGIScriptPath,CGIParamName,CmpdIDFieldLabel</em> values:
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88 CGIScriptPath?CGIParamName=CmpdIDFieldLabelValue. Default: <em>none</em>.</p>
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89 <p>Example:</p>
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90 <div class="OptionsBox">
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91 Source,<a href="http://www.yourdomain.org/GetCmpd.pl">http://www.yourdomain.org/GetCmpd.pl</a>,Reg_ID,Mol_ID</div>
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92 </dd>
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93 <dt><strong><strong>-h, --help</strong></strong></dt>
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94 <dd>
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95 <p>Print this help message.</p>
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96 </dd>
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97 <dt><strong><strong>-k, --keepolddatafields</strong> <em>all | unmappedonly | none</em></strong></dt>
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98 <dd>
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99 <p>Specify how to transfer old data fields from input SDFile(s) to new SDFile(s) during
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100 <em>datafields | both</em> value of <strong>-m, --mode</strong> option: keep all old data fields; write out the ones
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101 not mapped to new fields as specified by <strong>--datafieldsmap</strong> or <--datafieldsmapfile> options;
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102 or ignore all old data field labels. For <em>molname</em> <strong>-m --mode</strong>, old datafields are always kept.
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103 Possible values: <em>all | unmappedonly | none</em>. Default: <em>none</em>.</p>
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104 </dd>
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105 <dt><strong><strong>-m, --mode</strong> <em>molname | datafields | both</em></strong></dt>
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106 <dd>
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107 <p>Specify how to modify SDFile(s): <em>molname</em> - change molname line by another datafield or value;
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108 <em>datafield</em> - modify data field labels and values by replacing one label by another, combining
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109 multiple data field labels and values, adding specific set of data field labels and values to all compound, or
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110 inserting an URL for compound retrieval to each record; <em>both</em> - change molname line and datafields
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111 simultaneously. Possible values: <em>molname | datafields | both</em>. Default: <em>molname</em></p>
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112 </dd>
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113 <dt><strong><strong>--molnamemode</strong> <em>datafield | labelprefix</em></strong></dt>
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114 <dd>
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115 <p>Specify how to change molname line for <strong>-m --mode</strong> option values of <em>molname | both</em>: use
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116 a datafield label value or assign a sequential ID prefixed with <em>labelprefix</em>. Possible values:
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117 <em>datafield | labelprefix</em>. Default: <em>labelprefix</em>.</p>
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118 </dd>
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119 <dt><strong><strong>--molname</strong> <em>datafieldname or prefixstring</em></strong></dt>
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120 <dd>
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121 <p>Molname generation method. For <em>datafield</em> value of <strong>--molnamemode</strong> option, it corresponds
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122 to datafield label name whose value is used for molname; otherwise, it's a prefix string used for
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123 generating compound IDs like labelprefixstring<Number>. Default value, <em>Cmpd</em>, generates
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124 compound IDs like Cmpd<Number> for molname.</p>
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125 </dd>
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126 <dt><strong><strong>--molnamereplace</strong> <em>always | empty</em></strong></dt>
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127 <dd>
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128 <p>Specify when to replace molname line for <strong>-m --mode</strong> option values of <em>molname | both</em>:
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129 always replace the molname line using <strong>--molname</strong> option or only when it's empty. Possible
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130 values: <em>always | empty</em>. Default: <em>empty</em>.</p>
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131 </dd>
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132 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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133 <dd>
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134 <p>Overwrite existing files.</p>
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135 </dd>
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136 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
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137 <dd>
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138 <p>New SD file name is generated using the root: <Root>.<Ext>. Default new file
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139 name: <InitialSDFileName>ModifiedDataFields.<Ext>. This option is ignored for multiple
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140 input files.</p>
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141 </dd>
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142 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
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143 <dd>
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144 <p>Location of working directory. Default: current directory.</p>
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145 </dd>
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146 </dl>
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147 <p>
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148 </p>
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149 <h2>EXAMPLES</h2>
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150 <p>To replace empty molname lines by Cmpd<CmpdNumber> and generate a new SD file
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151 NewSample1.sdf, type:</p>
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152 <div class="ExampleBox">
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153 % ModifySDFilesDataFields.pl -o -r NewSample1 Sample1.sdf</div>
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154 <p>To replace all molname lines by Mol_ID data field generate a new SD file
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155 NewSample1.sdf, type:</p>
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156 <div class="ExampleBox">
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157 % ModifySDFilesDataFields.pl --molnamemode datafield
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158 --molnamereplace always -r NewSample1 -o Sample1.sdf</div>
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159 <p>To replace all molname lines by Mol_ID data field, map Name and CompoundName to
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160 a new datafield Synonym, and generate a new SD file NewSample1.sdf, type:</p>
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161 <div class="ExampleBox">
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162 % ModifySDFilesDataFields.pl --molnamemode datafield
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163 --molnamereplace always --molname Mol_ID --mode both
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164 --datafieldsmap "Synonym,Name,CompoundName" -r
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165 NewSample1 -o Sample1.sdf</div>
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166 <p>To replace all molname lines by Mol_ID data field, map Name and CompoundName to
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167 a new datafield Synonym, add common fields ReleaseDate and Source, and
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168 generate a new SD file NewSample1.sdf without keeping any old SD data fields, type:</p>
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169 <div class="ExampleBox">
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170 % ModifySDFilesDataFields.pl --molnamemode datafield
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171 --molnamereplace always --molname Mol_ID --mode both
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172 --datafieldsmap "Synonym,Name,CompoundName"
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173 --datafieldscommon "ReleaseDate,yyyy-mm-dd,Source,
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174 www.mayachemtools.org" --keepolddatafields none -r
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175 NewSample1 -o Sample1.sdf</div>
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176 <p><strong>Preparing SD files PubChem deposition:</strong></p>
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177 <p>Consider a SD file with these fields: Mol_ID, Name, Synonyms and Systematic_Name.
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178 And Mol_ID data field uniquely identifies your compound.</p>
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179 <p>To prepare a new SD file CmpdDataForPubChem.sdf containing only required
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180 PUBCHEM_EXT_DATASOURCE_REGID field, type:</p>
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181 <div class="ExampleBox">
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182 % ModifySDFilesDataFields.pl --m datafields
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183 --datafieldsmap
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184 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID"
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185 -r CmpdDataForPubChem -o Sample1.sdf</div>
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186 <p>To prepare a new SD file CmpdDataForPubChem.sdf containing only required
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187 PUBCHEM_EXT_DATASOURCE_REGID field and replace molname line with Mol_ID, type:</p>
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188 <div class="ExampleBox">
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189 % ModifySDFilesDataFields.pl --molnamemode datafield
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190 --molnamereplace always --molname Mol_ID --mode both
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191 --datafieldsmap
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192 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID"
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193 -r CmpdDataForPubChem -o Sample1.sdf</div>
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194 <p>In addition to required PubChem data field, you can also add optional PubChem data
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195 fields.</p>
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196 <p>To map your Name, Synonyms and Systematic_Name data fields to optional
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197 PUBCHEM_SUBSTANCE_SYNONYM data field along with required ID field, type:</p>
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198 <div class="ExampleBox">
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199 % ModifySDFilesDataFields.pl --molnamemode datafield
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200 --molnamereplace always --molname Mol_ID --mode both
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201 --datafieldsmap
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202 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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203 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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204 -r CmpdDataForPubChem -o Sample1.sdf</div>
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205 <p>To add your <domain.org> as PUBCHEM_EXT_SUBSTANCE_URL and link substance
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206 retrieval to your CGI script <http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID>
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207 via PUBCHEM_EXT_DATASOURCE_REGID field along with optional and required
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208 data fields, type:</p>
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209 <div class="ExampleBox">
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210 % ModifySDFilesDataFields.pl --molnamemode datafield
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211 --molnamereplace always --molname Mol_ID --mode both
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212 --datafieldsmap
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213 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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214 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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215 --datafieldscommon
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216 "PUBCHEM_EXT_SUBSTANCE_URL,domain.org"
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217 --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL,
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218 <a href="http://www.yourdomain.org/GetCmpd.pl">http://www.yourdomain.org/GetCmpd.pl</a>,Reg_ID,Mol_ID"
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219 -r CmpdDataForPubChem -o Sample1.sdf</div>
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220 <p>And to add a publication date and request a release data using
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221 PUBCHEM_PUBLICATION_DATE and PUBCHEM_DEPOSITOR_RECORD_DATE data fields
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222 along with all the data fields in earlier examples, type:
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223 optional fields, type:</p>
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224 <div class="ExampleBox">
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225 % ModifySDFilesDataFields.pl --molnamemode datafield
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226 --molnamereplace always --molname Mol_ID --mode both
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227 --datafieldsmap
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228 "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID;
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229 PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName"
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230 --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL,
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231 <a href="http://www.yourdomain.org/GetCmpd.pl">http://www.yourdomain.org/GetCmpd.pl</a>,Reg_ID,Mol_ID"
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232 --datafieldscommon
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233 "PUBCHEM_EXT_SUBSTANCE_URL,domain.org,
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234 PUBCHEM_PUBLICATION_DATE,YYY-MM-DD,
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235 PUBCHEM_DEPOSITOR_RECORD_DATE,YYYY-MM-DD"
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236 -r CmpdDataForPubChem -o Sample1.sdf</div>
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237 <p>
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238 </p>
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239 <h2>AUTHOR</h2>
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240 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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241 <p>
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242 </p>
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243 <h2>SEE ALSO</h2>
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244 <p><a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./JoinSDFiles.html">JoinSDFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.pl</a>, <a href="./SDFilesToHTML.html">SDFilesToHTML.pl</a>
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245 </p>
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246 <p>
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247 </p>
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248 <h2>COPYRIGHT</h2>
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249 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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250 <p>This file is part of MayaChemTools.</p>
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251 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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252 the terms of the GNU Lesser General Public License as published by the Free
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253 Software Foundation; either version 3 of the License, or (at your option)
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254 any later version.</p>
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255 <p> </p><p> </p><div class="DocNav">
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256 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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257 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ModifyPDBFiles.html" title="ModifyPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ModifySDFilesDataFields.pl</strong></td></tr>
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258 </table>
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259 </div>
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260 <br />
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261 <center>
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262 <img src="../../images/h2o2.png">
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263 </center>
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264 </body>
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265 </html>
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