|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:PDBFileUtil.pm</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
13 <div class="DocNav">
|
|
|
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./YYLexer.html" title="YYLexer.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/PDBFileUtil.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/PDBFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/PDBFileUtil.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/PDBFileUtil.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
|
|
|
16 </table>
|
|
|
17 </div>
|
|
|
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->{ResidueNames} - Array of all the residues
|
|
|
118 <br/> $ResiduesDataRef->{ResidueCount}{$ResidueName} - Count of residues
|
|
|
119 <br/> $ResiduesDataRef->{AtomResidueNames}} - Array of all ATOM residues
|
|
|
120 <br/> $ResiduesDataRef->{AtomResidueCount}{$ResidueName} - Count of
|
|
|
121 residues in ATOM records
|
|
|
122 <br/> $ResiduesDataRef->{HetatomResidueNames} - List of all HETATM
|
|
|
123 residues
|
|
|
124 <br/> $ResiduesDataRef->{HetatmResidueCount}{$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->{ChainIDs} - List of chain IDs with 'None' for
|
|
|
138 no IDs
|
|
|
139 <br/> $ChainsDataRef->{Residues}{$ChainID} - List of residues in order
|
|
|
140 of their appearance in a chain
|
|
|
141 <br/> $ChainsDataRef->{ResidueCount}{$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->{RecordTypes} - An array of unique record types
|
|
|
191 in order of their presence in the file
|
|
|
192 <br/> $RecordTypeDataRef->{Count}{$RecordType} - Count of each record type
|
|
|
193 <br/> $RecordTypeDataRef->{Lines}{$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>, <a href="./SequenceFileUtil.html">SequenceFileUtil.pm</a>, <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> </p><p> </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> <a href="./index.html" title="Table of Contents">TOC</a> <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>
|
|
|
363 </table>
|
|
|
364 </div>
|
|
|
365 <br />
|
|
|
366 <center>
|
|
|
367 <img src="../../images/h2o2.png">
|
|
|
368 </center>
|
|
|
369 </body>
|
|
|
370 </html>
|
