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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="./PseudoHeap.html" title="PseudoHeap.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SequenceFileUtil.html" title="SequenceFileUtil.html">Next</a></td><td width="34%" align="middle"><strong>SDFileUtil.pm</strong></td><td width="33%" align="right"><a href="././code/SDFileUtil.html" title="View source code">Code</a> | <a href="./../pdf/SDFileUtil.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/SDFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/SDFileUtil.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/SDFileUtil.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>SDFileUtil</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>use SDFileUtil ;</p>
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26 <p>use SDFileUtil qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>SDFileUtil</strong> module provides the following functions:</p>
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31 <p> <a href="#generatecmpdatomaliaspropertylines">GenerateCmpdAtomAliasPropertyLines</a>, <a href="#generatecmpdatomline">GenerateCmpdAtomLine</a>, <a href="#generatecmpdbondline">GenerateCmpdBondLine</a>
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32 , <a href="#generatecmpdchargepropertylines">GenerateCmpdChargePropertyLines</a>, <a href="#generatecmpdcommentsline">GenerateCmpdCommentsLine</a>, <a href="#generatecmpdcountsline">GenerateCmpdCountsLine</a>
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33 , <a href="#generatecmpddataheaderlabelsandvalueslines">GenerateCmpdDataHeaderLabelsAndValuesLines</a>, <a href="#generatecmpdisotopepropertylines">GenerateCmpdIsotopePropertyLines</a>
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34 , <a href="#generatecmpdmiscinfoline">GenerateCmpdMiscInfoLine</a>, <a href="#generatecmpdmolnameline">GenerateCmpdMolNameLine</a>
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35 , <a href="#generatecmpdradicalpropertylines">GenerateCmpdRadicalPropertyLines</a>, <a href="#generateemptyctabblocklines">GenerateEmptyCtabBlockLines</a>
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36 , <a href="#generatemisclinedatestamp">GenerateMiscLineDateStamp</a>, <a href="#getallandcommoncmpddataheaderlabels">GetAllAndCommonCmpdDataHeaderLabels</a>
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37 , <a href="#getcmpddataheaderlabels">GetCmpdDataHeaderLabels</a>, <a href="#getcmpddataheaderlabelsandvalues">GetCmpdDataHeaderLabelsAndValues</a>, <a href="#getcmpdfragments">GetCmpdFragments</a>
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38 , <a href="#getctablinescount">GetCtabLinesCount</a>, <a href="#getinvalidatomnumbers">GetInvalidAtomNumbers</a>, <a href="#getunknownatoms">GetUnknownAtoms</a>
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39 , <a href="#internalbondordertomdlbondtype">InternalBondOrderToMDLBondType</a>, <a href="#internalbondstereochemistrytomdlbondstereo">InternalBondStereochemistryToMDLBondStereo</a>
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40 , <a href="#internalchargetomdlcharge">InternalChargeToMDLCharge</a>, <a href="#internalspinmultiplicitytomdlradical">InternalSpinMultiplicityToMDLRadical</a>, <a href="#iscmpd2d">IsCmpd2D</a>
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41 , <a href="#iscmpd3d">IsCmpd3D</a>, <a href="#mdlbondstereotointernalbondstereochemistry">MDLBondStereoToInternalBondStereochemistry</a>
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42 , <a href="#mdlbondtypetointernalbondorder">MDLBondTypeToInternalBondOrder</a>, <a href="#mdlchargetointernalcharge">MDLChargeToInternalCharge</a>
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43 , <a href="#mdlradicaltointernalspinmultiplicity">MDLRadicalToInternalSpinMultiplicity</a>, <a href="#parsecmpdatomaliaspropertyline">ParseCmpdAtomAliasPropertyLine</a>
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44 , <a href="#parsecmpdatomline">ParseCmpdAtomLine</a>, <a href="#parsecmpdbondline">ParseCmpdBondLine</a>, <a href="#parsecmpdchargepropertyline">ParseCmpdChargePropertyLine</a>
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45 , <a href="#parsecmpdcommentsline">ParseCmpdCommentsLine</a>, <a href="#parsecmpdcountsline">ParseCmpdCountsLine</a>, <a href="#parsecmpdisotopepropertyline">ParseCmpdIsotopePropertyLine</a>
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46 , <a href="#parsecmpdmiscinfoline">ParseCmpdMiscInfoLine</a>, <a href="#parsecmpdmolnameline">ParseCmpdMolNameLine</a>, <a href="#parsecmpdradicalpropertyline">ParseCmpdRadicalPropertyLine</a>
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47 , <a href="#readcmpdstring">ReadCmpdString</a>, <a href="#removecmpddataheaderlabelandvalue">RemoveCmpdDataHeaderLabelAndValue</a>, <a href="#washcmpd">WashCmpd</a>
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48 </p><p>
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49 </p>
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50 <h2>METHODS</h2>
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51 <dl>
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52 <dt><strong><a name="generatecmpdatomaliaspropertylines" class="item"><strong>GenerateCmpdAtomAliasPropertyLines</strong></a></strong></dt>
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53 <dd>
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54 <div class="OptionsBox">
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55 @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef);</div>
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56 <p>Returns a formatted atom alias property lines corresponding to successive pairs
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57 of atom number and alias values specified by a refernce to an array. Two lines
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58 are generate for each atom number and alias value pairs: First line - A <AtomNum>;
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59 Second line:<AtomAlias>.</p>
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60 </dd>
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61 <dt><strong><a name="generatecmpdatomline" class="item"><strong>GenerateCmpdAtomLine</strong></a></strong></dt>
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62 <dd>
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63 <div class="OptionsBox">
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64 $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY,
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65 $AtomZ, [$MassDifference, $Charge, $StereoParity]);</div>
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66 <p>Returns a formatted atom data line containing all the input values.</p>
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67 </dd>
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68 <dt><strong><a name="generatecmpdbondline" class="item"><strong>GenerateCmpdBondLine</strong></a></strong></dt>
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69 <dd>
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70 <div class="OptionsBox">
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71 $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum,
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72 $BondType, [$BondStereo]);</div>
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73 <p>Returns a formatted bond data line containing all the input values.</p>
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74 </dd>
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75 <dt><strong><a name="generatecmpdchargepropertylines" class="item"><strong>GenerateCmpdChargePropertyLines</strong></a></strong></dt>
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76 <dd>
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77 <div class="OptionsBox">
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78 @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef);</div>
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79 <p>Returns a formatted M CHG property lines corresponding to successive pairs of
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80 atom number and charge values specified by a refernce to an array.</p>
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81 </dd>
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82 <dt><strong><a name="generatecmpdcommentsline" class="item"><strong>GenerateCmpdCommentsLine</strong></a></strong></dt>
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83 <dd>
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84 <div class="OptionsBox">
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85 $Line = GenerateCmpdCommentsLine($Comments);</div>
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86 <p>Returns a formatted comments data line.</p>
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87 </dd>
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88 <dt><strong><a name="generatecmpdcountsline" class="item"><strong>GenerateCmpdCountsLine</strong></a></strong></dt>
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89 <dd>
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90 <div class="OptionsBox">
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91 $Line = GenerateCmpdCountsLine($AtomCount, $BondCount,
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92 $ChiralFlag, [$PropertyCount, $Version]);</div>
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93 <p>Returns a formatted line containing all the input values. The default values of 999
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94 and V2000 are used for <em>PropertyCount</em> and <em>Version</em>.</p>
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95 </dd>
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96 <dt><strong><a name="generatecmpddataheaderlabelsandvalueslines" class="item"><strong>GenerateCmpdDataHeaderLabelsAndValuesLines</strong></a></strong></dt>
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97 <dd>
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98 <div class="OptionsBox">
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99 @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines(
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100 $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef,
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101 [$SortDataLabels]);</div>
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102 <p>Returns formatted data lines containing header label and values lines corresponding to
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103 all data header labels in array reference <em>DataHeaderLabelsRef</em> with values in hash
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104 reference <em>DataHeaderLabelsAndValuesRef</em>. By default, data header labels are
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105 not sorted and correspond to the label order in array reference <em>DataHeaderLabelsRef</em>.</p>
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106 </dd>
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107 <dt><strong><a name="generatecmpdisotopepropertylines" class="item"><strong>GenerateCmpdIsotopePropertyLines</strong></a></strong></dt>
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108 <dd>
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109 <div class="OptionsBox">
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110 @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef);</div>
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111 <p>Returns a formatted M ISO property lines corresponding to successive pairs of
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112 atom number and isotope values specified by a refernce to an array.</p>
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113 </dd>
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114 <dt><strong><a name="generatecmpdmiscinfoline" class="item"><strong>GenerateCmpdMiscInfoLine</strong></a></strong></dt>
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115 <dd>
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116 <div class="OptionsBox">
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117 $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial,
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118 $Code]);</div>
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119 <p>Returns a formatted line containing specified user initial, program name, date and code.
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120 Default values are: <em>ProgramName - MayaChem; UserInitial - NULL; Code - 2D</em>.</p>
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121 </dd>
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122 <dt><strong><a name="generatecmpdmolnameline" class="item"><strong>GenerateCmpdMolNameLine</strong></a></strong></dt>
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123 <dd>
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124 <div class="OptionsBox">
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125 $Line = GenerateCmpdMolNameLine($MolName);</div>
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126 <p>Returns a formatted molecule name data line.</p>
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127 </dd>
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128 <dt><strong><a name="generatecmpdradicalpropertylines" class="item"><strong>GenerateCmpdRadicalPropertyLines</strong></a></strong></dt>
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129 <dd>
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130 <div class="OptionsBox">
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131 @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef);</div>
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132 <p>Returns a formatted M CHG property lines corresponding to successive pairs of
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133 atom number and multiplicity values specified by a refernce to an array.</p>
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134 </dd>
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135 <dt><strong><a name="generateemptyctabblocklines" class="item"><strong>GenerateEmptyCtabBlockLines</strong></a></strong></dt>
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136 <dd>
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137 <div class="OptionsBox">
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138 $Lines = GenerateCmpdMiscInfoLine([$Date]);</div>
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139 <p>Returns formatted lines representing empty CTAB block.</p>
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140 </dd>
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141 <dt><strong><a name="generatemisclinedatestamp" class="item"><strong>GenerateMiscLineDateStamp</strong></a></strong></dt>
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142 <dd>
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143 <div class="OptionsBox">
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144 $Line = GenerateMiscLineDateStamp();</div>
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145 <p>Returns date stamp for misc line.</p>
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146 </dd>
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147 <dt><strong><a name="getallandcommoncmpddataheaderlabels" class="item"><strong>GetAllAndCommonCmpdDataHeaderLabels</strong></a></strong></dt>
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148 <dd>
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149 <div class="OptionsBox">
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150 ($CmpdCount, $DataFieldLabelsArrayRef,
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151 $CommonDataFieldLabelsArrayRef) =
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152 GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);</div>
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153 <p>Returns number of comopunds, a reference to an array containing all unique data header
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154 label and a reference to an array containing common data field labels for all compounds
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155 in SD file.</p>
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156 </dd>
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157 <dt><strong><a name="getcmpddataheaderlabels" class="item"><strong>GetCmpdDataHeaderLabels</strong></a></strong></dt>
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158 <dd>
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159 <div class="OptionsBox">
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160 (@Labels) = GetCmpdDataHeaderLabels(\@CmpdLines);</div>
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161 <p>Returns an array containg data header labels for a compound</p>
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162 </dd>
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163 <dt><strong><a name="getcmpddataheaderlabelsandvalues" class="item"><strong>GetCmpdDataHeaderLabelsAndValues</strong></a></strong></dt>
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164 <dd>
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165 <div class="OptionsBox">
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166 (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);</div>
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167 <p>Returns a hash conating data header labes and values for a compound.</p>
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168 </dd>
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169 <dt><strong><a name="getcmpdfragments" class="item"><strong>GetCmpdFragments</strong></a></strong></dt>
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170 <dd>
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171 <div class="OptionsBox">
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172 ($FragmentCount, $FragmentString) = GetCmpdFragments(\@CmpLines);</div>
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173 <p>Figures out the number of disconnected fragments and return their values along
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174 with the atom numbers in a string delimited by new line character. Fragment data
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175 in <strong>FragmentString</strong> is sorted on based on its size.</p>
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176 </dd>
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177 <dt><strong><a name="getctablinescount" class="item"><strong>GetCtabLinesCount</strong></a></strong></dt>
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178 <dd>
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179 <div class="OptionsBox">
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180 $CtabLinesCount = GetCtabLinesCount(\@CmpdLines);</div>
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181 <p>Returns number of lines present between the 4th line and the line containg "M END".</p>
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182 </dd>
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183 <dt><strong><a name="getinvalidatomnumbers" class="item"><strong>GetInvalidAtomNumbers</strong></a></strong></dt>
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184 <dd>
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185 <div class="OptionsBox">
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186 ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) =
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187 GetInvalidAtomNumbers(\@CmpdLines);</div>
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188 <p>Returns a list of values containing information about invalid atom numbers present
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189 in block or atom property lines.</p>
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190 </dd>
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191 <dt><strong><a name="getunknownatoms" class="item"><strong>GetUnknownAtoms</strong></a></strong></dt>
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192 <dd>
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193 <div class="OptionsBox">
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194 ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) =
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195 GetUnknownAtoms(\@CmpdLines);</div>
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196 <p>Returns a list of values containing information about atoms which contain special element
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197 symbols not present in the periodic table.</p>
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198 </dd>
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199 <dt><strong><a name="internalbondordertomdlbondtype" class="item"><strong>InternalBondOrderToMDLBondType</strong></a></strong></dt>
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200 <dd>
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201 <div class="OptionsBox">
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202 $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder);</div>
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203 <p>Returns value of <em>MDLBondType</em> corresponding to <em>InternalBondOrder</em>.</p>
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204 <div class="OptionsBox">
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205 InternalBondOrder MDLBondType</div>
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206 <div class="OptionsBox">
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207 1 1
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208 2 2
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209 3 3
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210 1.5 4</div>
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211 </dd>
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212 <dt><strong><a name="internalbondstereochemistrytomdlbondstereo" class="item"><strong>InternalBondStereochemistryToMDLBondStereo</strong></a></strong></dt>
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213 <dd>
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214 <div class="OptionsBox">
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215 $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo(
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216 $InternalBondStereo);</div>
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217 <p>Returns value of <em>MDLBondStereo</em> corresponding to <em>InternalBondStereo</em> using following
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218 mapping:</p>
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219 <div class="OptionsBox">
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220 InternalBondStereo MDLBondStereo</div>
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221 <div class="OptionsBox">
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222 Up 1
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223 UpOrDown 4
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224 Down 6
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225 CisOrTrans 3
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226 Other 0</div>
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227 </dd>
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228 <dt><strong><a name="internalchargetomdlcharge" class="item"><strong>InternalChargeToMDLCharge</strong></a></strong></dt>
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229 <dd>
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230 <div class="OptionsBox">
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231 $MDLCharge = InternalChargeToMDLCharge($InternalCharge);</div>
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232 <p>Returns value of <em>MDLCharge</em> corresponding to <em>InternalCharge</em> using following
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233 mapping:</p>
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234 <div class="OptionsBox">
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235 InternalCharge MDLCharge</div>
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236 <div class="OptionsBox">
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237 3 1
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238 2 2
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239 1 3
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240 <br/> -1 5
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241 <br/> -2 6
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242 <br/> -3 7</div>
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243 </dd>
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244 <dt><strong><a name="internalspinmultiplicitytomdlradical" class="item"><strong>InternalSpinMultiplicityToMDLRadical</strong></a></strong></dt>
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245 <dd>
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246 <div class="OptionsBox">
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247 $MDLRadical = InternalSpinMultiplicityToMDLRadical(
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248 $InternalSpinMultiplicity);</div>
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249 <p>Returns value of <em>MDLRadical</em> corresponding to <em>InternalSpinMultiplicity</em>. These
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250 value are equivalent.</p>
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251 </dd>
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252 <dt><strong><a name="mdlbondstereotointernalbondtype" class="item"><strong>MDLBondStereoToInternalBondType</strong></a></strong></dt>
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253 <dd>
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254 <div class="OptionsBox">
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255 $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo);</div>
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256 <p>Returns value of <em>InternalBondType</em> corresponding to <em>MDLBondStereo</em> using
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257 mapping shown for <strong>InternalBondTypeToMDLBondStereo</strong> function.</p>
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258 </dd>
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259 <dt><strong><a name="iscmpd2d" class="item"><strong>IsCmpd2D</strong></a></strong></dt>
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260 <dd>
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261 <div class="OptionsBox">
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262 $Status = IsCmpd2D();</div>
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263 <p>Returns 1 or 0 based on whether z-coordinate of any atom is non-zero.</p>
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264 </dd>
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265 <dt><strong><a name="iscmpd3d" class="item"><strong>IsCmpd3D</strong></a></strong></dt>
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266 <dd>
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267 <div class="OptionsBox">
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268 $Status = IsCmpd3D();</div>
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269 <p>Returns 1 or 0 based on whether z-coordinate of any atom is non-zero.</p>
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270 </dd>
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271 <dt><strong><a name="mdlbondstereotointernalbondstereochemistry" class="item"><strong>MDLBondStereoToInternalBondStereochemistry</strong></a></strong></dt>
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272 <dd>
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273 <div class="OptionsBox">
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274 $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry(
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275 $MDLBondStereo);</div>
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276 <p>Returns value of <em>InternalBondStereo</em> corresponding to <em>MDLBondStereo</em> using
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277 mapping shown for <strong>InternalBondStereochemistryToMDLBondStereo</strong> function.</p>
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278 </dd>
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279 <dt><strong><a name="mdlbondtypetointernalbondorder" class="item"><strong>MDLBondTypeToInternalBondOrder</strong></a></strong></dt>
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280 <dd>
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281 <div class="OptionsBox">
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282 $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType);</div>
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283 <p>Returns value of <em>InternalBondOrder</em> corresponding to <em>MDLBondType</em> using
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284 mapping shown for <strong>InternalBondOrderToMDLBondType</strong> function.</p>
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285 </dd>
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286 <dt><strong><a name="mdlchargetointernalcharge" class="item"><strong>MDLChargeToInternalCharge</strong></a></strong></dt>
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287 <dd>
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288 <div class="OptionsBox">
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289 $InternalCharge = MDLChargeToInternalCharge($MDLCharge);</div>
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290 <p>Returns value of <em>$InternalCharge</em> corresponding to <em>MDLCharge</em> using
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291 mapping shown for <strong>InternalChargeToMDLCharge</strong> function.</p>
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292 </dd>
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293 <dt><strong><a name="mdlradicaltointernalspinmultiplicity" class="item"><strong>MDLRadicalToInternalSpinMultiplicity</strong></a></strong></dt>
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294 <dd>
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295 <div class="OptionsBox">
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296 $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity(
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297 $MDLRadical);</div>
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298 <p>Returns value of <em>InternalSpinMultiplicity</em> corresponding to <em>MDLRadical</em>. These
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299 value are equivalent.</p>
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300 </dd>
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301 <dt><strong><a name="parsecmpdatomaliaspropertyline" class="item"><strong>ParseCmpdAtomAliasPropertyLine</strong></a></strong></dt>
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302 <dd>
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303 <div class="OptionsBox">
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304 @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine(
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305 $CurrentLine, $NexLine);</div>
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306 <p>Parses atom alias propery lines in CTAB generic properties block and returns an array
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307 with successive pairs of values corresponding to atom number and its alias.</p>
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308 </dd>
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309 <dt><strong><a name="parsecmpdatomline" class="item"><strong>ParseCmpdAtomLine</strong></a></strong></dt>
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310 <dd>
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311 <div class="OptionsBox">
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312 ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge,
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313 $StereoParity) = ParseCmpdAtomLine($AtomDataLine);</div>
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314 <p>Parses compound data line containing atom information and returns a list
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315 of values.</p>
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316 </dd>
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317 <dt><strong><a name="parsecmpdbondline" class="item"><strong>ParseCmpdBondLine</strong></a></strong></dt>
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318 <dd>
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319 <div class="OptionsBox">
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320 ($FirstAtomNum, $SecondAtomNum, $BondType) =
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321 ParseCmpdBondLine($BondDataLine);</div>
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322 <p>Parses compound data line containing bond information and returns a list of
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323 values.</p>
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324 </dd>
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325 <dt><strong><a name="parsecmpdcommentsline" class="item"><strong>ParseCmpdCommentsLine</strong></a></strong></dt>
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326 <dd>
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327 <div class="OptionsBox">
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328 $Comments = ParseCmpdCommentsLine($CommentsDataLine);</div>
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329 <p>Returns the comment string.</p>
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330 </dd>
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331 <dt><strong><a name="parsecmpdchargepropertyline" class="item"><strong>ParseCmpdChargePropertyLine</strong></a></strong></dt>
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332 <dd>
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333 <div class="OptionsBox">
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334 @AtomNumAndValuePairs = ParseCmpdChargePropertyLine(
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335 $ChargeDataLine);</div>
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336 <p>Parses charge propery line in CTAB generic properties block and returns an array
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337 with successive pairs of values corresponding to atom number and its charge.</p>
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338 </dd>
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339 <dt><strong><a name="parsecmpdcountsline" class="item"><strong>ParseCmpdCountsLine</strong></a></strong></dt>
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340 <dd>
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341 <div class="OptionsBox">
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342 ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) =
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343 ParseCmpdCountsLine(\@CountDataLines);</div>
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344 <p>Returns a list of values containing count information.</p>
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345 </dd>
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346 <dt><strong><a name="parsecmpdmiscinfoline" class="item"><strong>ParseCmpdMiscInfoLine</strong></a></strong></dt>
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347 <dd>
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348 <div class="OptionsBox">
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349 ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2,
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350 $Energy, $RegistryNum) = ParseCmpdMiscInfoLine($Line);</div>
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351 <p>Returns a list of values containing miscellaneous information.</p>
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352 </dd>
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353 <dt><strong><a name="parsecmpdisotopepropertyline" class="item"><strong>ParseCmpdIsotopePropertyLine</strong></a></strong></dt>
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354 <dd>
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355 <div class="OptionsBox">
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356 @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine(
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357 $IsotopeDataLine);</div>
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358 <p>Parses isotopic propery line in CTAB generic properties block and returns an array
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359 with successive pairs of values corresponding to atom number and absolute mass of
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360 atom isotope.</p>
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361 </dd>
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362 <dt><strong><a name="parsecmpdmolnameline" class="item"><strong>ParseCmpdMolNameLine</strong></a></strong></dt>
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363 <dd>
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364 <div class="OptionsBox">
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365 $MolName = ParseCmpdMolNameLine($Line);</div>
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366 <p>Returns a string containing molecule name.</p>
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367 </dd>
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368 <dt><strong><a name="parsecmpdradicalpropertyline" class="item"><strong>ParseCmpdRadicalPropertyLine</strong></a></strong></dt>
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369 <dd>
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370 <div class="OptionsBox">
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371 @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine(
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372 $RadicalDataLine);</div>
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373 <p>Parses radical propery line in CTAB generic properties block and returns an array
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374 with successive pairs of values corresponding to atom number and radical number
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375 value.</p>
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376 </dd>
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377 <dt><strong><a name="removecmpddataheaderlabelandvalue" class="item"><strong>RemoveCmpdDataHeaderLabelAndValue</strong></a></strong></dt>
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378 <dd>
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379 <div class="OptionsBox">
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380 $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString,
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381 $DataHeaderLabel);</div>
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382 <p>Returns a <strong>NewCmpdString</strong> after removing <em>DataHeaderLabel</em> along with its
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383 value from <em>CmpdString</em>.</p>
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384 </dd>
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385 <dt><strong><a name="readcmpdstring" class="item"><strong>ReadCmpdString</strong></a></strong></dt>
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386 <dd>
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387 <div class="OptionsBox">
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388 $CmpdString = ReadCmpdString(\*SDFILEHANDLE);</div>
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389 <p>Returns a string containing all the data lines for the next available compound
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390 in an already open file indicated by SDFILEHANDLE. A NULL string is returned
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391 on EOF.</p>
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392 </dd>
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393 <dt><strong><a name="washcmpd" class="item"><strong>WashCmpd</strong></a></strong></dt>
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394 <dd>
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395 <div class="OptionsBox">
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396 ($FragmentCount, $Fragments, $WashedCmpdString) =
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397 WashCmpd(\@CmpdLines);</div>
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398 <p>Figures out the number of disconnected fragments and return their values along
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399 with the atom numbers in a string delimited by new line character. Fragment data
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400 in <strong>FragmentString</strong> is sorted on based on its size.</p>
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401 </dd>
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402 </dl>
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403 <p>
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404 </p>
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405 <h2>AUTHOR</h2>
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406 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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407 <p>
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408 </p>
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409 <h2>SEE ALSO</h2>
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410 <p><a href="./TextUtil.html">TextUtil.pm</a>
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411 </p>
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412 <p>
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413 </p>
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414 <h2>COPYRIGHT</h2>
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415 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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416 <p>This file is part of MayaChemTools.</p>
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417 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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418 the terms of the GNU Lesser General Public License as published by the Free
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419 Software Foundation; either version 3 of the License, or (at your option)
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420 any later version.</p>
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421 <p> </p><p> </p><div class="DocNav">
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422 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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423 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PseudoHeap.html" title="PseudoHeap.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SequenceFileUtil.html" title="SequenceFileUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>SDFileUtil.pm</strong></td></tr>
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424 </table>
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425 </div>
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426 <br />
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427 <center>
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428 <img src="../../images/h2o2.png">
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429 </center>
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430 </body>
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431 </html>
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