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3 <title>MayaChemTools:Documentation:PDBFileUtil.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./YYLexer.html" title="YYLexer.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./PeriodicTable.html" title="PeriodicTable.html">Next</a></td><td width="34%" align="middle"><strong>PDBFileUtil.pm</strong></td><td width="33%" align="right"><a href="././code/PDBFileUtil.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/PDBFileUtil.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/PDBFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/PDBFileUtil.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/PDBFileUtil.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>PDBFileUtil</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use PDBFileUtil ;</p>
26 <p>use PDBFileUtil qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>PDBFileUtil</strong> module provides the following functions:</p>
31 <p> <a href="#generateatomorhetatmrecordline">GenerateAtomOrHetatmRecordLine</a>, <a href="#generateatomrecordline">GenerateAtomRecordLine</a>, <a href="#generateconectrecordline">GenerateConectRecordLine</a>
32 , <a href="#generateendrecordline">GenerateEndRecordLine</a>, <a href="#generateheaderrecordline">GenerateHeaderRecordLine</a>, <a href="#generateheaderrecordtimestamp">GenerateHeaderRecordTimeStamp</a>
33 , <a href="#generatehetatmrecordline">GenerateHetatmRecordLine</a>, <a href="#generateterrecordline">GenerateTerRecordLine</a>, <a href="#getallresidues">GetAllResidues</a>
34 , <a href="#getchainsandresidues">GetChainsAndResidues</a>, <a href="#getconectrecordlines">GetConectRecordLines</a>, <a href="#getexperimentaltechnique">GetExperimentalTechnique</a>
35 , <a href="#getexperimentaltechniqueresolution">GetExperimentalTechniqueResolution</a>, <a href="#getminmaxcoords">GetMinMaxCoords</a>, <a href="#getpdbrecordtype">GetPDBRecordType</a>
36 , <a href="#getrecordtypescount">GetRecordTypesCount</a>, <a href="#isatomrecordtype">IsAtomRecordType</a>, <a href="#isconectrecordtype">IsConectRecordType</a>, <a href="#isendmdlrecordtype">IsEndmdlRecordType</a>
37 , <a href="#isheaderrecordtype">IsHeaderRecordType</a>, <a href="#ishetatmrecordtype">IsHetatmRecordType</a>, <a href="#ismasterrecordtype">IsMasterRecordType</a>, <a href="#ismodelrecordtype">IsModelRecordType</a>
38 , <a href="#ispdbfile">IsPDBFile</a>, <a href="#isseqresrecordtype">IsSeqresRecordType</a>, <a href="#isterrecordtype">IsTerRecordType</a>, <a href="#parseatomorhetatmrecordline">ParseAtomOrHetatmRecordLine</a>
39 , <a href="#parseatomrecordline">ParseAtomRecordLine</a>, <a href="#parseconectrecordline">ParseConectRecordLine</a>, <a href="#parseexpdtarecordline">ParseExpdtaRecordLine</a>
40 , <a href="#parseheaderrecordline">ParseHeaderRecordLine</a>, <a href="#parsehetatmrecordline">ParseHetatmRecordLine</a>, <a href="#parsemasterrecordline">ParseMasterRecordLine</a>
41 , <a href="#parseremark2resolutionrecordline">ParseRemark2ResolutionRecordLine</a>, <a href="#parseseqresrecordline">ParseSeqresRecordLine</a>, <a href="#parseterrecordline">ParseTerRecordLine</a>
42 , <a href="#readpdbfile">ReadPDBFile</a>
43 </p><p>
44 </p>
45 <h2>METHODS</h2>
46 <dl>
47 <dt><strong><a name="generateatomorhetatmrecordline" class="item"><strong>GenerateAtomOrHetatmRecordLine</strong></a></strong></dt>
48 <dd>
49 <div class="OptionsBox">
50 $RecordLine = GenerateAtomOrHetatmRecordLine($RecordType,
51 $AtomNumber, $AtomName, $AlternateLocation, $ResidueName,
52 $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z,
53 $Occupancy, $TemperatureFactor, $SegmentID,
54 $ElementSymbol, $AtomCharge);</div>
55 <p>Returns ATOM or HETATM record line.</p>
56 </dd>
57 <dt><strong><a name="generateatomrecordline" class="item"><strong>GenerateAtomRecordLine</strong></a></strong></dt>
58 <dd>
59 <div class="OptionsBox">
60 $RecordLine = GenerateAtomRecordLine($AtomNumber,
61 $AtomName, $AlternateLocation, $ResidueName, $ChainID,
62 $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
63 $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge);</div>
64 <p>Returns ATOM record line.</p>
65 </dd>
66 <dt><strong><a name="generateconectrecordline" class="item"><strong>GenerateConectRecordLine</strong></a></strong></dt>
67 <dd>
68 <div class="OptionsBox">
69 $RecordLine = GenerateConectRecordLine($AtomNum, $BondedAtomNum1,
70 $BondedAtomNum2, $BondedAtomNum3, $BondedAtomNum4,
71 $HBondedAtomNum1, $HBondedAtomNum2, $SaltBridgedAtomNum1,
72 $HBondedAtomNum3, $HBondedAtomNum4, $SaltBridgedAtomNum2);</div>
73 <p>Returns CONECT record line.</p>
74 </dd>
75 <dt><strong><a name="generateheaderrecordline" class="item"><strong>GenerateHeaderRecordLine</strong></a></strong></dt>
76 <dd>
77 <div class="OptionsBox">
78 $RecordLine = GenerateHeaderRecordLine($IDCode, [$Classification,
79 $Date]);</div>
80 <p>Returns HEADER record line.</p>
81 </dd>
82 <dt><strong><a name="generateheaderrecordtimestamp" class="item"><strong>GenerateHeaderRecordTimeStamp</strong></a></strong></dt>
83 <dd>
84 <div class="OptionsBox">
85 $Date = GenerateHeaderRecordTimeStamp();</div>
86 <p>Returns PDB header time stamp.</p>
87 </dd>
88 <dt><strong><a name="generatehetatmrecordline" class="item"><strong>GenerateHetatmRecordLine</strong></a></strong></dt>
89 <dd>
90 <div class="OptionsBox">
91 $RecordLine = GenerateHetatmRecordLine($AtomNumber, $AtomName,
92 <br/> $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber,
93 <br/> $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor,
94 <br/> $SegmentID, $ElementSymbol, $AtomCharge);</div>
95 <p>Returns HETATM record line.</p>
96 </dd>
97 <dt><strong><a name="generateendrecordline" class="item"><strong>GenerateEndRecordLine</strong></a></strong></dt>
98 <dd>
99 <div class="OptionsBox">
100 $RecordLine = GenerateEndRecordLine();</div>
101 <p>Returns END record line.</p>
102 </dd>
103 <dt><strong><a name="generateterrecordline" class="item"><strong>GenerateTerRecordLine</strong></a></strong></dt>
104 <dd>
105 <div class="OptionsBox">
106 $RecordLine = GenerateTerRecordLine($SerialNumber, [$ResidueName,
107 $ChainID, $ResidueNumber, $InsertionCode]);</div>
108 <p>Returns TER record line.</p>
109 </dd>
110 <dt><strong><a name="getallresidues" class="item"><strong>GetAllResidues</strong></a></strong></dt>
111 <dd>
112 <div class="OptionsBox">
113 $ResiduesDataRef = GetAllResidues($PDBRecordLinesRef);</div>
114 <p>Gets residue information using ATOM/HETATM records and returns a reference to a hash with
115 following key/value pairs:</p>
116 <div class="OptionsBox">
117 $ResiduesDataRef-&gt;{ResidueNames} - Array of all the residues
118 <br/> $ResiduesDataRef-&gt;{ResidueCount}{$ResidueName} - Count of residues
119 <br/> $ResiduesDataRef-&gt;{AtomResidueNames}} - Array of all ATOM residues
120 <br/> $ResiduesDataRef-&gt;{AtomResidueCount}{$ResidueName} - Count of
121 residues in ATOM records
122 <br/> $ResiduesDataRef-&gt;{HetatomResidueNames} - List of all HETATM
123 residues
124 <br/> $ResiduesDataRef-&gt;{HetatmResidueCount}{$ResidueName} - Count of
125 residues HETATM records</div>
126 <p>ATOM/HETATM records after the first ENDMDL records are simply ingnored.</p>
127 </dd>
128 <dt><strong><a name="getchainsandresidues" class="item"><strong>GetChainsAndResidues</strong></a></strong></dt>
129 <dd>
130 <div class="OptionsBox">
131 $ChainsDataRef = GetChainsAndResidues($PDBRecordLinesRef,
132 [$RecordsSource, $GetChainResiduesBeyondTERFlag,
133 $GetRecordLinesFlag]);</div>
134 <p>Gets chains and residue information using ATOM/HETATM or SEQRES records and returns a reference to a
135 hash with these keys:</p>
136 <div class="OptionsBox">
137 $ChainsDataRef-&gt;{ChainIDs} - List of chain IDs with 'None' for
138 no IDs
139 <br/> $ChainsDataRef-&gt;{Residues}{$ChainID} - List of residues in order
140 of their appearance in a chain
141 <br/> $ChainsDataRef-&gt;{ResidueCount}{$ChainID}{$ResidueName} - Count of
142 residues in a chain</div>
143 <p>Chains and residue data can be extacted using either ATOM/HETATM records or SEQRES records.
144 ATOM/HETATM records after the first ENDMDL records are simply ingnored.</p>
145 </dd>
146 <dt><strong><a name="getconectrecordlines" class="item"><strong>GetConectRecordLines</strong></a></strong></dt>
147 <dd>
148 <div class="OptionsBox">
149 $ConectRecordLinesRef = GetConectRecordLines($PDBRecordLinesRef,
150 $AtomNumbersMapRef);</div>
151 <p>Collects CONECT record lines for specific atom number, modified specified data to exclude any atom
152 number not present in the list of specified atom numbers and returns a reference to list of
153 CONECT record lines.</p>
154 </dd>
155 <dt><strong><a name="getexperimentaltechnique" class="item"><strong>GetExperimentalTechnique</strong></a></strong></dt>
156 <dd>
157 <div class="OptionsBox">
158 $ExperimentalTechnique = GetExperimentalTechnique($PDBRecordLinesRef);</div>
159 <p>Returns <em>ExperimentalTechnique</em> value retrieved from EXPDATA record line.</p>
160 </dd>
161 <dt><strong><a name="getexperimentaltechniqueresolution" class="item"><strong>GetExperimentalTechniqueResolution</strong></a></strong></dt>
162 <dd>
163 <div class="OptionsBox">
164 ($Resolution, $ResolutionUnits) = GetExperimentalTechniqueResolution(
165 $PDBRecordLinesRef);</div>
166 <p>Returns <em>Resolution</em> and <em>ResolutionUnits</em> values from REMARK 2 RESOLUTION
167 record line.</p>
168 </dd>
169 <dt><strong><a name="getminmaxcoords" class="item"><strong>GetMinMaxCoords</strong></a></strong></dt>
170 <dd>
171 <div class="OptionsBox">
172 ($XMin, $YMin, $ZMin, $XMax, $YMax, $ZMax) =
173 GetMinMaxCoords($PDBRecordLinesRef);</div>
174 <p>Returns minimum and maximum XYZ coordinates for ATOM/HETATM records.</p>
175 </dd>
176 <dt><strong><a name="getpdbrecordtype" class="item"><strong>GetPDBRecordType</strong></a></strong></dt>
177 <dd>
178 <div class="OptionsBox">
179 $RecordType = GetPDBRecordType($RecordLine);</div>
180 <p>Returns type of <em>RecordLine</em>.</p>
181 </dd>
182 <dt><strong><a name="getrecordtypescount" class="item"><strong>GetRecordTypesCount</strong></a></strong></dt>
183 <dd>
184 <div class="OptionsBox">
185 $RecordTypeDataRef = GetRecordTypesCount($PDBRecordLinesRef,
186 [$SpecifiedRecordType, $GetRecordLinesFlag]);</div>
187 <p>Counts the number of each record type or a $SpecifiedRecordType and returns a reference to data
188 type with following key/value pairs:</p>
189 <div class="OptionsBox">
190 $RecordTypeDataRef-&gt;{RecordTypes} - An array of unique record types
191 in order of their presence in the file
192 <br/> $RecordTypeDataRef-&gt;{Count}{$RecordType} - Count of each record type
193 <br/> $RecordTypeDataRef-&gt;{Lines}{$RecordType} - Optional lines data for a
194 specific record type.</div>
195 </dd>
196 <dt><strong><a name="isatomrecordtype" class="item"><strong>IsAtomRecordType</strong></a></strong></dt>
197 <dd>
198 <div class="OptionsBox">
199 $Status = IsAtomRecordType($RecordLine);</div>
200 <p>Returns 1 or 0 based on whether it's a ATOM record line.</p>
201 </dd>
202 <dt><strong><a name="isconectrecordtype" class="item"><strong>IsConectRecordType</strong></a></strong></dt>
203 <dd>
204 <div class="OptionsBox">
205 $Status = IsAtomConectType($RecordLine);</div>
206 <p>Returns 1 or 0 based on whether it's a CONECT record line.</p>
207 </dd>
208 <dt><strong><a name="isendmdlrecordtype" class="item"><strong>IsEndmdlRecordType</strong></a></strong></dt>
209 <dd>
210 <div class="OptionsBox">
211 $Status = IsEndmdlRecordType($RecordLine);</div>
212 <p>Returns 1 or 0 based on whether it's a ENDMDL a record line.</p>
213 </dd>
214 <dt><strong><a name="isheaderrecordtype" class="item"><strong>IsHeaderRecordType</strong></a></strong></dt>
215 <dd>
216 <div class="OptionsBox">
217 $Status = IsHeaderRecordType($RecordLine);</div>
218 <p>Returns 1 or 0 based on whether it's a HEADER a record line.</p>
219 </dd>
220 <dt><strong><a name="ishetatmrecordtype" class="item"><strong>IsHetatmRecordType</strong></a></strong></dt>
221 <dd>
222 <div class="OptionsBox">
223 $Status = IsHetatmRecordType($RecordLine);</div>
224 <p>Returns 1 or 0 based on whether it's a HETATM a record line.</p>
225 </dd>
226 <dt><strong><a name="ismasterrecordtype" class="item"><strong>IsMasterRecordType</strong></a></strong></dt>
227 <dd>
228 <div class="OptionsBox">
229 $Status = IsMasterRecordType($RecordLine);</div>
230 <p>Returns 1 or 0 based on whether it's a MASTER a record line.</p>
231 </dd>
232 <dt><strong><a name="ismodelrecordtype" class="item"><strong>IsModelRecordType</strong></a></strong></dt>
233 <dd>
234 <div class="OptionsBox">
235 $Status = IsModelRecordType($RecordLine);</div>
236 <p>Returns 1 or 0 based on whether it's a MODEL record line.</p>
237 </dd>
238 <dt><strong><a name="ispdbfile" class="item"><strong>IsPDBFile</strong></a></strong></dt>
239 <dd>
240 <div class="OptionsBox">
241 $Status = IsPDBFile($PDBFile);</div>
242 <p>Returns 1 or 0 based on whether it's a PDB file.</p>
243 </dd>
244 <dt><strong><a name="isseqresrecordtype" class="item"><strong>IsSeqresRecordType</strong></a></strong></dt>
245 <dd>
246 <div class="OptionsBox">
247 $Status = IsSeqresRecordType($RecordLine);</div>
248 <p>Returns 1 or 0 based on whether it's SEQRES a record line.</p>
249 </dd>
250 <dt><strong><a name="isterrecordtype" class="item"><strong>IsTerRecordType</strong></a></strong></dt>
251 <dd>
252 <div class="OptionsBox">
253 $Status = IsTerRecordType($RecordLine);</div>
254 <p>Returns 1 or 0 based on whether it's a TER record line.</p>
255 </dd>
256 <dt><strong><a name="parseatomorhetatmrecordline" class="item"><strong>ParseAtomOrHetatmRecordLine</strong></a></strong></dt>
257 <dd>
258 <div class="OptionsBox">
259 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID,
260 $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
261 $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) =
262 ParseAtomOrHetatmRecordLine($RecordLine);</div>
263 <p>Parses ATOM or HETATM record line.</p>
264 </dd>
265 <dt><strong><a name="parseatomrecordline" class="item"><strong>ParseAtomRecordLine</strong></a></strong></dt>
266 <dd>
267 <div class="OptionsBox">
268 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID,
269 $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
270 $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) =
271 ParseAtomRecordLine($RecordLine);</div>
272 <p>Parses ATOM record line.</p>
273 </dd>
274 <dt><strong><a name="parseconectrecordline" class="item"><strong>ParseConectRecordLine</strong></a></strong></dt>
275 <dd>
276 <div class="OptionsBox">
277 ($AtomNum, $BondedAtomNum1, $BondedAtomNum2, $BondedAtomNum3,
278 $BondedAtomNum4, $HBondedAtomNum1, $HBondedAtomNum2,
279 $SaltBridgedAtomNum1, $HBondedAtomNum3, $HBondedAtomNum4,
280 $SaltBridgedAtomNum2) = ParseConectRecordLine($RecordLine);</div>
281 <p>Parses CONECT record line.</p>
282 </dd>
283 <dt><strong><a name="parseexpdtarecordline" class="item"><strong>ParseExpdtaRecordLine</strong></a></strong></dt>
284 <dd>
285 <div class="OptionsBox">
286 ($ContinuationNum, $ExperimentalTechnique) = ParseExpdtaRecordLine($Line);</div>
287 <p>Parses EXPDTA record line.</p>
288 </dd>
289 <dt><strong><a name="parseheaderrecordline" class="item"><strong>ParseHeaderRecordLine</strong></a></strong></dt>
290 <dd>
291 <div class="OptionsBox">
292 ($Classification, $DepositionDate, $IDCode) = ParseHeaderRecordLine($RecordLine);</div>
293 <p>Parses HEADER record line</p>
294 </dd>
295 <dt><strong><a name="parsehetatmrecordline" class="item"><strong>ParseHetatmRecordLine</strong></a></strong></dt>
296 <dd>
297 <div class="OptionsBox">
298 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID,
299 $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
300 $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) =
301 ParseHetatmRecordLine($RecordLine);</div>
302 <p>Parses HETATM record line.</p>
303 </dd>
304 <dt><strong><a name="parsemasterrecordline" class="item"><strong>ParseMasterRecordLine</strong></a></strong></dt>
305 <dd>
306 <div class="OptionsBox">
307 ($NumOfRemarkRecords, $NumOfHetRecords, $NumOfHelixRecords,
308 $NumOfSheetRecords, $NumOfTurnRecords, $NumOfSiteRecords,
309 $NumOfTransformationsRecords, $NumOfAtomAndHetatmRecords,
310 $NumOfTerRecords, $NumOfConectRecords, $NumOfSeqresRecords) =
311 ParseMasterRecordLine($RecordLine);</div>
312 <p>Parses MASTER ecord line.</p>
313 </dd>
314 <dt><strong><a name="parseremark2resolutionrecordline" class="item"><strong>ParseRemark2ResolutionRecordLine</strong></a></strong></dt>
315 <dd>
316 <div class="OptionsBox">
317 ($Resolution, $ResolutionUnits) = ParseRemark2ResolutionRecordLine(
318 $RecordLine);</div>
319 <p>Parses REMARK 2 RESOLUTION record line.</p>
320 </dd>
321 <dt><strong><a name="parseseqresrecordline" class="item"><strong>ParseSeqresRecordLine</strong></a></strong></dt>
322 <dd>
323 <div class="OptionsBox">
324 ($RecordSerialNumber, $ChainID, $NumOfResidues, $ResidueNames) =
325 ParseSeqresRecordLine($RecordLine);</div>
326 <p>Parses SEQRES record line.</p>
327 </dd>
328 <dt><strong><a name="parseterrecordline" class="item"><strong>ParseTerRecordLine</strong></a></strong></dt>
329 <dd>
330 <div class="OptionsBox">
331 ($SerialNumber, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode) =
332 ParseTerRecordLine($RecordLine);</div>
333 <p>Parses TER record line.</p>
334 </dd>
335 <dt><strong><a name="readpdbfile" class="item"><strong>ReadPDBFile</strong></a></strong></dt>
336 <dd>
337 <div class="OptionsBox">
338 $PDBRecordLinesRef = ReadPDBFile($PDBFile);</div>
339 <p>Reads PDB file and returns reference to record lines.</p>
340 </dd>
341 </dl>
342 <p>
343 </p>
344 <h2>AUTHOR</h2>
345 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
346 <p>
347 </p>
348 <h2>SEE ALSO</h2>
349 <p><a href="./FileUtil.html">FileUtil.pm</a>,&nbsp<a href="./SequenceFileUtil.html">SequenceFileUtil.pm</a>,&nbsp<a href="./TextUtil.html">TextUtil.pm</a>
350 </p>
351 <p>
352 </p>
353 <h2>COPYRIGHT</h2>
354 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
355 <p>This file is part of MayaChemTools.</p>
356 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
357 the terms of the GNU Lesser General Public License as published by the Free
358 Software Foundation; either version 3 of the License, or (at your option)
359 any later version.</p>
360 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
361 <table width="100%" border=0 cellpadding=0 cellspacing=2>
362 <tr align="left" valign="top"><td width="33%" align="left"><a href="./YYLexer.html" title="YYLexer.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./PeriodicTable.html" title="PeriodicTable.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>PDBFileUtil.pm</strong></td></tr>
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