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3 <title>MayaChemTools:Documentation:SDFileUtil.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PseudoHeap.html" title="PseudoHeap.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/SDFileUtil.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/SDFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/SDFileUtil.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/SDFileUtil.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>SDFileUtil</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use SDFileUtil ;</p>
26 <p>use SDFileUtil qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>SDFileUtil</strong> module provides the following functions:</p>
31 <p> <a href="#generatecmpdatomaliaspropertylines">GenerateCmpdAtomAliasPropertyLines</a>, <a href="#generatecmpdatomline">GenerateCmpdAtomLine</a>, <a href="#generatecmpdbondline">GenerateCmpdBondLine</a>
32 , <a href="#generatecmpdchargepropertylines">GenerateCmpdChargePropertyLines</a>, <a href="#generatecmpdcommentsline">GenerateCmpdCommentsLine</a>, <a href="#generatecmpdcountsline">GenerateCmpdCountsLine</a>
33 , <a href="#generatecmpddataheaderlabelsandvalueslines">GenerateCmpdDataHeaderLabelsAndValuesLines</a>, <a href="#generatecmpdisotopepropertylines">GenerateCmpdIsotopePropertyLines</a>
34 , <a href="#generatecmpdmiscinfoline">GenerateCmpdMiscInfoLine</a>, <a href="#generatecmpdmolnameline">GenerateCmpdMolNameLine</a>
35 , <a href="#generatecmpdradicalpropertylines">GenerateCmpdRadicalPropertyLines</a>, <a href="#generateemptyctabblocklines">GenerateEmptyCtabBlockLines</a>
36 , <a href="#generatemisclinedatestamp">GenerateMiscLineDateStamp</a>, <a href="#getallandcommoncmpddataheaderlabels">GetAllAndCommonCmpdDataHeaderLabels</a>
37 , <a href="#getcmpddataheaderlabels">GetCmpdDataHeaderLabels</a>, <a href="#getcmpddataheaderlabelsandvalues">GetCmpdDataHeaderLabelsAndValues</a>, <a href="#getcmpdfragments">GetCmpdFragments</a>
38 , <a href="#getctablinescount">GetCtabLinesCount</a>, <a href="#getinvalidatomnumbers">GetInvalidAtomNumbers</a>, <a href="#getunknownatoms">GetUnknownAtoms</a>
39 , <a href="#internalbondordertomdlbondtype">InternalBondOrderToMDLBondType</a>, <a href="#internalbondstereochemistrytomdlbondstereo">InternalBondStereochemistryToMDLBondStereo</a>
40 , <a href="#internalchargetomdlcharge">InternalChargeToMDLCharge</a>, <a href="#internalspinmultiplicitytomdlradical">InternalSpinMultiplicityToMDLRadical</a>, <a href="#iscmpd2d">IsCmpd2D</a>
41 , <a href="#iscmpd3d">IsCmpd3D</a>, <a href="#mdlbondstereotointernalbondstereochemistry">MDLBondStereoToInternalBondStereochemistry</a>
42 , <a href="#mdlbondtypetointernalbondorder">MDLBondTypeToInternalBondOrder</a>, <a href="#mdlchargetointernalcharge">MDLChargeToInternalCharge</a>
43 , <a href="#mdlradicaltointernalspinmultiplicity">MDLRadicalToInternalSpinMultiplicity</a>, <a href="#parsecmpdatomaliaspropertyline">ParseCmpdAtomAliasPropertyLine</a>
44 , <a href="#parsecmpdatomline">ParseCmpdAtomLine</a>, <a href="#parsecmpdbondline">ParseCmpdBondLine</a>, <a href="#parsecmpdchargepropertyline">ParseCmpdChargePropertyLine</a>
45 , <a href="#parsecmpdcommentsline">ParseCmpdCommentsLine</a>, <a href="#parsecmpdcountsline">ParseCmpdCountsLine</a>, <a href="#parsecmpdisotopepropertyline">ParseCmpdIsotopePropertyLine</a>
46 , <a href="#parsecmpdmiscinfoline">ParseCmpdMiscInfoLine</a>, <a href="#parsecmpdmolnameline">ParseCmpdMolNameLine</a>, <a href="#parsecmpdradicalpropertyline">ParseCmpdRadicalPropertyLine</a>
47 , <a href="#readcmpdstring">ReadCmpdString</a>, <a href="#removecmpddataheaderlabelandvalue">RemoveCmpdDataHeaderLabelAndValue</a>, <a href="#washcmpd">WashCmpd</a>
48 </p><p>
49 </p>
50 <h2>METHODS</h2>
51 <dl>
52 <dt><strong><a name="generatecmpdatomaliaspropertylines" class="item"><strong>GenerateCmpdAtomAliasPropertyLines</strong></a></strong></dt>
53 <dd>
54 <div class="OptionsBox">
55 @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef);</div>
56 <p>Returns a formatted atom alias property lines corresponding to successive pairs
57 of atom number and alias values specified by a refernce to an array. Two lines
58 are generate for each atom number and alias value pairs: First line - A &lt;AtomNum&gt;;
59 Second line:&lt;AtomAlias&gt;.</p>
60 </dd>
61 <dt><strong><a name="generatecmpdatomline" class="item"><strong>GenerateCmpdAtomLine</strong></a></strong></dt>
62 <dd>
63 <div class="OptionsBox">
64 $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY,
65 $AtomZ, [$MassDifference, $Charge, $StereoParity]);</div>
66 <p>Returns a formatted atom data line containing all the input values.</p>
67 </dd>
68 <dt><strong><a name="generatecmpdbondline" class="item"><strong>GenerateCmpdBondLine</strong></a></strong></dt>
69 <dd>
70 <div class="OptionsBox">
71 $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum,
72 $BondType, [$BondStereo]);</div>
73 <p>Returns a formatted bond data line containing all the input values.</p>
74 </dd>
75 <dt><strong><a name="generatecmpdchargepropertylines" class="item"><strong>GenerateCmpdChargePropertyLines</strong></a></strong></dt>
76 <dd>
77 <div class="OptionsBox">
78 @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef);</div>
79 <p>Returns a formatted M CHG property lines corresponding to successive pairs of
80 atom number and charge values specified by a refernce to an array.</p>
81 </dd>
82 <dt><strong><a name="generatecmpdcommentsline" class="item"><strong>GenerateCmpdCommentsLine</strong></a></strong></dt>
83 <dd>
84 <div class="OptionsBox">
85 $Line = GenerateCmpdCommentsLine($Comments);</div>
86 <p>Returns a formatted comments data line.</p>
87 </dd>
88 <dt><strong><a name="generatecmpdcountsline" class="item"><strong>GenerateCmpdCountsLine</strong></a></strong></dt>
89 <dd>
90 <div class="OptionsBox">
91 $Line = GenerateCmpdCountsLine($AtomCount, $BondCount,
92 $ChiralFlag, [$PropertyCount, $Version]);</div>
93 <p>Returns a formatted line containing all the input values. The default values of 999
94 and V2000 are used for <em>PropertyCount</em> and <em>Version</em>.</p>
95 </dd>
96 <dt><strong><a name="generatecmpddataheaderlabelsandvalueslines" class="item"><strong>GenerateCmpdDataHeaderLabelsAndValuesLines</strong></a></strong></dt>
97 <dd>
98 <div class="OptionsBox">
99 @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines(
100 $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef,
101 [$SortDataLabels]);</div>
102 <p>Returns formatted data lines containing header label and values lines corresponding to
103 all data header labels in array reference <em>DataHeaderLabelsRef</em> with values in hash
104 reference <em>DataHeaderLabelsAndValuesRef</em>. By default, data header labels are
105 not sorted and correspond to the label order in array reference <em>DataHeaderLabelsRef</em>.</p>
106 </dd>
107 <dt><strong><a name="generatecmpdisotopepropertylines" class="item"><strong>GenerateCmpdIsotopePropertyLines</strong></a></strong></dt>
108 <dd>
109 <div class="OptionsBox">
110 @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef);</div>
111 <p>Returns a formatted M ISO property lines corresponding to successive pairs of
112 atom number and isotope values specified by a refernce to an array.</p>
113 </dd>
114 <dt><strong><a name="generatecmpdmiscinfoline" class="item"><strong>GenerateCmpdMiscInfoLine</strong></a></strong></dt>
115 <dd>
116 <div class="OptionsBox">
117 $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial,
118 $Code]);</div>
119 <p>Returns a formatted line containing specified user initial, program name, date and code.
120 Default values are: <em>ProgramName - MayaChem; UserInitial - NULL; Code - 2D</em>.</p>
121 </dd>
122 <dt><strong><a name="generatecmpdmolnameline" class="item"><strong>GenerateCmpdMolNameLine</strong></a></strong></dt>
123 <dd>
124 <div class="OptionsBox">
125 $Line = GenerateCmpdMolNameLine($MolName);</div>
126 <p>Returns a formatted molecule name data line.</p>
127 </dd>
128 <dt><strong><a name="generatecmpdradicalpropertylines" class="item"><strong>GenerateCmpdRadicalPropertyLines</strong></a></strong></dt>
129 <dd>
130 <div class="OptionsBox">
131 @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef);</div>
132 <p>Returns a formatted M CHG property lines corresponding to successive pairs of
133 atom number and multiplicity values specified by a refernce to an array.</p>
134 </dd>
135 <dt><strong><a name="generateemptyctabblocklines" class="item"><strong>GenerateEmptyCtabBlockLines</strong></a></strong></dt>
136 <dd>
137 <div class="OptionsBox">
138 $Lines = GenerateCmpdMiscInfoLine([$Date]);</div>
139 <p>Returns formatted lines representing empty CTAB block.</p>
140 </dd>
141 <dt><strong><a name="generatemisclinedatestamp" class="item"><strong>GenerateMiscLineDateStamp</strong></a></strong></dt>
142 <dd>
143 <div class="OptionsBox">
144 $Line = GenerateMiscLineDateStamp();</div>
145 <p>Returns date stamp for misc line.</p>
146 </dd>
147 <dt><strong><a name="getallandcommoncmpddataheaderlabels" class="item"><strong>GetAllAndCommonCmpdDataHeaderLabels</strong></a></strong></dt>
148 <dd>
149 <div class="OptionsBox">
150 ($CmpdCount, $DataFieldLabelsArrayRef,
151 $CommonDataFieldLabelsArrayRef) =
152 GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);</div>
153 <p>Returns number of comopunds, a reference to an array containing all unique data header
154 label and a reference to an array containing common data field labels for all compounds
155 in SD file.</p>
156 </dd>
157 <dt><strong><a name="getcmpddataheaderlabels" class="item"><strong>GetCmpdDataHeaderLabels</strong></a></strong></dt>
158 <dd>
159 <div class="OptionsBox">
160 (@Labels) = GetCmpdDataHeaderLabels(\@CmpdLines);</div>
161 <p>Returns an array containg data header labels for a compound</p>
162 </dd>
163 <dt><strong><a name="getcmpddataheaderlabelsandvalues" class="item"><strong>GetCmpdDataHeaderLabelsAndValues</strong></a></strong></dt>
164 <dd>
165 <div class="OptionsBox">
166 (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);</div>
167 <p>Returns a hash conating data header labes and values for a compound.</p>
168 </dd>
169 <dt><strong><a name="getcmpdfragments" class="item"><strong>GetCmpdFragments</strong></a></strong></dt>
170 <dd>
171 <div class="OptionsBox">
172 ($FragmentCount, $FragmentString) = GetCmpdFragments(\@CmpLines);</div>
173 <p>Figures out the number of disconnected fragments and return their values along
174 with the atom numbers in a string delimited by new line character. Fragment data
175 in <strong>FragmentString</strong> is sorted on based on its size.</p>
176 </dd>
177 <dt><strong><a name="getctablinescount" class="item"><strong>GetCtabLinesCount</strong></a></strong></dt>
178 <dd>
179 <div class="OptionsBox">
180 $CtabLinesCount = GetCtabLinesCount(\@CmpdLines);</div>
181 <p>Returns number of lines present between the 4th line and the line containg &quot;M END&quot;.</p>
182 </dd>
183 <dt><strong><a name="getinvalidatomnumbers" class="item"><strong>GetInvalidAtomNumbers</strong></a></strong></dt>
184 <dd>
185 <div class="OptionsBox">
186 ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) =
187 GetInvalidAtomNumbers(\@CmpdLines);</div>
188 <p>Returns a list of values containing information about invalid atom numbers present
189 in block or atom property lines.</p>
190 </dd>
191 <dt><strong><a name="getunknownatoms" class="item"><strong>GetUnknownAtoms</strong></a></strong></dt>
192 <dd>
193 <div class="OptionsBox">
194 ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) =
195 GetUnknownAtoms(\@CmpdLines);</div>
196 <p>Returns a list of values containing information about atoms which contain special element
197 symbols not present in the periodic table.</p>
198 </dd>
199 <dt><strong><a name="internalbondordertomdlbondtype" class="item"><strong>InternalBondOrderToMDLBondType</strong></a></strong></dt>
200 <dd>
201 <div class="OptionsBox">
202 $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder);</div>
203 <p>Returns value of <em>MDLBondType</em> corresponding to <em>InternalBondOrder</em>.</p>
204 <div class="OptionsBox">
205 InternalBondOrder MDLBondType</div>
206 <div class="OptionsBox">
207 &nbsp; 1 1
208 2 2
209 3 3
210 1.5 4</div>
211 </dd>
212 <dt><strong><a name="internalbondstereochemistrytomdlbondstereo" class="item"><strong>InternalBondStereochemistryToMDLBondStereo</strong></a></strong></dt>
213 <dd>
214 <div class="OptionsBox">
215 $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo(
216 $InternalBondStereo);</div>
217 <p>Returns value of <em>MDLBondStereo</em> corresponding to <em>InternalBondStereo</em> using following
218 mapping:</p>
219 <div class="OptionsBox">
220 InternalBondStereo MDLBondStereo</div>
221 <div class="OptionsBox">
222 &nbsp; Up 1
223 UpOrDown 4
224 Down 6
225 CisOrTrans 3
226 Other 0</div>
227 </dd>
228 <dt><strong><a name="internalchargetomdlcharge" class="item"><strong>InternalChargeToMDLCharge</strong></a></strong></dt>
229 <dd>
230 <div class="OptionsBox">
231 $MDLCharge = InternalChargeToMDLCharge($InternalCharge);</div>
232 <p>Returns value of <em>MDLCharge</em> corresponding to <em>InternalCharge</em> using following
233 mapping:</p>
234 <div class="OptionsBox">
235 InternalCharge MDLCharge</div>
236 <div class="OptionsBox">
237 &nbsp; 3 1
238 2 2
239 1 3
240 <br/> -1 5
241 <br/> -2 6
242 <br/> -3 7</div>
243 </dd>
244 <dt><strong><a name="internalspinmultiplicitytomdlradical" class="item"><strong>InternalSpinMultiplicityToMDLRadical</strong></a></strong></dt>
245 <dd>
246 <div class="OptionsBox">
247 $MDLRadical = InternalSpinMultiplicityToMDLRadical(
248 $InternalSpinMultiplicity);</div>
249 <p>Returns value of <em>MDLRadical</em> corresponding to <em>InternalSpinMultiplicity</em>. These
250 value are equivalent.</p>
251 </dd>
252 <dt><strong><a name="mdlbondstereotointernalbondtype" class="item"><strong>MDLBondStereoToInternalBondType</strong></a></strong></dt>
253 <dd>
254 <div class="OptionsBox">
255 $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo);</div>
256 <p>Returns value of <em>InternalBondType</em> corresponding to <em>MDLBondStereo</em> using
257 mapping shown for <strong>InternalBondTypeToMDLBondStereo</strong> function.</p>
258 </dd>
259 <dt><strong><a name="iscmpd2d" class="item"><strong>IsCmpd2D</strong></a></strong></dt>
260 <dd>
261 <div class="OptionsBox">
262 $Status = IsCmpd2D();</div>
263 <p>Returns 1 or 0 based on whether z-coordinate of any atom is non-zero.</p>
264 </dd>
265 <dt><strong><a name="iscmpd3d" class="item"><strong>IsCmpd3D</strong></a></strong></dt>
266 <dd>
267 <div class="OptionsBox">
268 $Status = IsCmpd3D();</div>
269 <p>Returns 1 or 0 based on whether z-coordinate of any atom is non-zero.</p>
270 </dd>
271 <dt><strong><a name="mdlbondstereotointernalbondstereochemistry" class="item"><strong>MDLBondStereoToInternalBondStereochemistry</strong></a></strong></dt>
272 <dd>
273 <div class="OptionsBox">
274 $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry(
275 $MDLBondStereo);</div>
276 <p>Returns value of <em>InternalBondStereo</em> corresponding to <em>MDLBondStereo</em> using
277 mapping shown for <strong>InternalBondStereochemistryToMDLBondStereo</strong> function.</p>
278 </dd>
279 <dt><strong><a name="mdlbondtypetointernalbondorder" class="item"><strong>MDLBondTypeToInternalBondOrder</strong></a></strong></dt>
280 <dd>
281 <div class="OptionsBox">
282 $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType);</div>
283 <p>Returns value of <em>InternalBondOrder</em> corresponding to <em>MDLBondType</em> using
284 mapping shown for <strong>InternalBondOrderToMDLBondType</strong> function.</p>
285 </dd>
286 <dt><strong><a name="mdlchargetointernalcharge" class="item"><strong>MDLChargeToInternalCharge</strong></a></strong></dt>
287 <dd>
288 <div class="OptionsBox">
289 $InternalCharge = MDLChargeToInternalCharge($MDLCharge);</div>
290 <p>Returns value of <em>$InternalCharge</em> corresponding to <em>MDLCharge</em> using
291 mapping shown for <strong>InternalChargeToMDLCharge</strong> function.</p>
292 </dd>
293 <dt><strong><a name="mdlradicaltointernalspinmultiplicity" class="item"><strong>MDLRadicalToInternalSpinMultiplicity</strong></a></strong></dt>
294 <dd>
295 <div class="OptionsBox">
296 $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity(
297 $MDLRadical);</div>
298 <p>Returns value of <em>InternalSpinMultiplicity</em> corresponding to <em>MDLRadical</em>. These
299 value are equivalent.</p>
300 </dd>
301 <dt><strong><a name="parsecmpdatomaliaspropertyline" class="item"><strong>ParseCmpdAtomAliasPropertyLine</strong></a></strong></dt>
302 <dd>
303 <div class="OptionsBox">
304 @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine(
305 $CurrentLine, $NexLine);</div>
306 <p>Parses atom alias propery lines in CTAB generic properties block and returns an array
307 with successive pairs of values corresponding to atom number and its alias.</p>
308 </dd>
309 <dt><strong><a name="parsecmpdatomline" class="item"><strong>ParseCmpdAtomLine</strong></a></strong></dt>
310 <dd>
311 <div class="OptionsBox">
312 ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge,
313 $StereoParity) = ParseCmpdAtomLine($AtomDataLine);</div>
314 <p>Parses compound data line containing atom information and returns a list
315 of values.</p>
316 </dd>
317 <dt><strong><a name="parsecmpdbondline" class="item"><strong>ParseCmpdBondLine</strong></a></strong></dt>
318 <dd>
319 <div class="OptionsBox">
320 ($FirstAtomNum, $SecondAtomNum, $BondType) =
321 ParseCmpdBondLine($BondDataLine);</div>
322 <p>Parses compound data line containing bond information and returns a list of
323 values.</p>
324 </dd>
325 <dt><strong><a name="parsecmpdcommentsline" class="item"><strong>ParseCmpdCommentsLine</strong></a></strong></dt>
326 <dd>
327 <div class="OptionsBox">
328 $Comments = ParseCmpdCommentsLine($CommentsDataLine);</div>
329 <p>Returns the comment string.</p>
330 </dd>
331 <dt><strong><a name="parsecmpdchargepropertyline" class="item"><strong>ParseCmpdChargePropertyLine</strong></a></strong></dt>
332 <dd>
333 <div class="OptionsBox">
334 @AtomNumAndValuePairs = ParseCmpdChargePropertyLine(
335 $ChargeDataLine);</div>
336 <p>Parses charge propery line in CTAB generic properties block and returns an array
337 with successive pairs of values corresponding to atom number and its charge.</p>
338 </dd>
339 <dt><strong><a name="parsecmpdcountsline" class="item"><strong>ParseCmpdCountsLine</strong></a></strong></dt>
340 <dd>
341 <div class="OptionsBox">
342 ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) =
343 ParseCmpdCountsLine(\@CountDataLines);</div>
344 <p>Returns a list of values containing count information.</p>
345 </dd>
346 <dt><strong><a name="parsecmpdmiscinfoline" class="item"><strong>ParseCmpdMiscInfoLine</strong></a></strong></dt>
347 <dd>
348 <div class="OptionsBox">
349 ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2,
350 $Energy, $RegistryNum) = ParseCmpdMiscInfoLine($Line);</div>
351 <p>Returns a list of values containing miscellaneous information.</p>
352 </dd>
353 <dt><strong><a name="parsecmpdisotopepropertyline" class="item"><strong>ParseCmpdIsotopePropertyLine</strong></a></strong></dt>
354 <dd>
355 <div class="OptionsBox">
356 @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine(
357 $IsotopeDataLine);</div>
358 <p>Parses isotopic propery line in CTAB generic properties block and returns an array
359 with successive pairs of values corresponding to atom number and absolute mass of
360 atom isotope.</p>
361 </dd>
362 <dt><strong><a name="parsecmpdmolnameline" class="item"><strong>ParseCmpdMolNameLine</strong></a></strong></dt>
363 <dd>
364 <div class="OptionsBox">
365 $MolName = ParseCmpdMolNameLine($Line);</div>
366 <p>Returns a string containing molecule name.</p>
367 </dd>
368 <dt><strong><a name="parsecmpdradicalpropertyline" class="item"><strong>ParseCmpdRadicalPropertyLine</strong></a></strong></dt>
369 <dd>
370 <div class="OptionsBox">
371 @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine(
372 $RadicalDataLine);</div>
373 <p>Parses radical propery line in CTAB generic properties block and returns an array
374 with successive pairs of values corresponding to atom number and radical number
375 value.</p>
376 </dd>
377 <dt><strong><a name="removecmpddataheaderlabelandvalue" class="item"><strong>RemoveCmpdDataHeaderLabelAndValue</strong></a></strong></dt>
378 <dd>
379 <div class="OptionsBox">
380 $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString,
381 $DataHeaderLabel);</div>
382 <p>Returns a <strong>NewCmpdString</strong> after removing <em>DataHeaderLabel</em> along with its
383 value from <em>CmpdString</em>.</p>
384 </dd>
385 <dt><strong><a name="readcmpdstring" class="item"><strong>ReadCmpdString</strong></a></strong></dt>
386 <dd>
387 <div class="OptionsBox">
388 $CmpdString = ReadCmpdString(\*SDFILEHANDLE);</div>
389 <p>Returns a string containing all the data lines for the next available compound
390 in an already open file indicated by SDFILEHANDLE. A NULL string is returned
391 on EOF.</p>
392 </dd>
393 <dt><strong><a name="washcmpd" class="item"><strong>WashCmpd</strong></a></strong></dt>
394 <dd>
395 <div class="OptionsBox">
396 ($FragmentCount, $Fragments, $WashedCmpdString) =
397 WashCmpd(\@CmpdLines);</div>
398 <p>Figures out the number of disconnected fragments and return their values along
399 with the atom numbers in a string delimited by new line character. Fragment data
400 in <strong>FragmentString</strong> is sorted on based on its size.</p>
401 </dd>
402 </dl>
403 <p>
404 </p>
405 <h2>AUTHOR</h2>
406 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
407 <p>
408 </p>
409 <h2>SEE ALSO</h2>
410 <p><a href="./TextUtil.html">TextUtil.pm</a>
411 </p>
412 <p>
413 </p>
414 <h2>COPYRIGHT</h2>
415 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
416 <p>This file is part of MayaChemTools.</p>
417 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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