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124 .\" ========================================================================
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125 .\"
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126 .IX Title "PDBFILEUTIL 1"
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127 .TH PDBFILEUTIL 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 PDBFileUtil
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use PDBFileUtil ;
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137 .PP
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138 use PDBFileUtil qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBPDBFileUtil\fR module provides the following functions:
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142 .PP
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143 GenerateAtomOrHetatmRecordLine, GenerateAtomRecordLine, GenerateConectRecordLine,
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144 GenerateEndRecordLine, GenerateHeaderRecordLine, GenerateHeaderRecordTimeStamp,
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145 GenerateHetatmRecordLine, GenerateTerRecordLine, GetAllResidues,
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146 GetChainsAndResidues, GetConectRecordLines, GetExperimentalTechnique,
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147 GetExperimentalTechniqueResolution, GetMinMaxCoords, GetPDBRecordType,
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148 GetRecordTypesCount, IsAtomRecordType, IsConectRecordType, IsEndmdlRecordType,
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149 IsHeaderRecordType, IsHetatmRecordType, IsMasterRecordType, IsModelRecordType,
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150 IsPDBFile, IsSeqresRecordType, IsTerRecordType, ParseAtomOrHetatmRecordLine,
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151 ParseAtomRecordLine, ParseConectRecordLine, ParseExpdtaRecordLine,
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152 ParseHeaderRecordLine, ParseHetatmRecordLine, ParseMasterRecordLine,
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153 ParseRemark2ResolutionRecordLine, ParseSeqresRecordLine, ParseTerRecordLine,
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154 ReadPDBFile
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155 .SH "METHODS"
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156 .IX Header "METHODS"
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157 .IP "\fBGenerateAtomOrHetatmRecordLine\fR" 4
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158 .IX Item "GenerateAtomOrHetatmRecordLine"
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159 .Vb 5
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160 \& $RecordLine = GenerateAtomOrHetatmRecordLine($RecordType,
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161 \& $AtomNumber, $AtomName, $AlternateLocation, $ResidueName,
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162 \& $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z,
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163 \& $Occupancy, $TemperatureFactor, $SegmentID,
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164 \& $ElementSymbol, $AtomCharge);
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165 .Ve
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166 .Sp
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167 Returns \s-1ATOM\s0 or \s-1HETATM\s0 record line.
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168 .IP "\fBGenerateAtomRecordLine\fR" 4
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169 .IX Item "GenerateAtomRecordLine"
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170 .Vb 4
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171 \& $RecordLine = GenerateAtomRecordLine($AtomNumber,
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172 \& $AtomName, $AlternateLocation, $ResidueName, $ChainID,
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173 \& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
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174 \& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge);
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175 .Ve
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176 .Sp
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177 Returns \s-1ATOM\s0 record line.
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178 .IP "\fBGenerateConectRecordLine\fR" 4
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179 .IX Item "GenerateConectRecordLine"
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180 .Vb 4
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181 \& $RecordLine = GenerateConectRecordLine($AtomNum, $BondedAtomNum1,
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182 \& $BondedAtomNum2, $BondedAtomNum3, $BondedAtomNum4,
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183 \& $HBondedAtomNum1, $HBondedAtomNum2, $SaltBridgedAtomNum1,
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184 \& $HBondedAtomNum3, $HBondedAtomNum4, $SaltBridgedAtomNum2);
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185 .Ve
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186 .Sp
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187 Returns \s-1CONECT\s0 record line.
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188 .IP "\fBGenerateHeaderRecordLine\fR" 4
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189 .IX Item "GenerateHeaderRecordLine"
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190 .Vb 2
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191 \& $RecordLine = GenerateHeaderRecordLine($IDCode, [$Classification,
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192 \& $Date]);
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193 .Ve
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194 .Sp
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195 Returns \s-1HEADER\s0 record line.
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196 .IP "\fBGenerateHeaderRecordTimeStamp\fR" 4
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197 .IX Item "GenerateHeaderRecordTimeStamp"
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198 .Vb 1
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199 \& $Date = GenerateHeaderRecordTimeStamp();
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200 .Ve
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201 .Sp
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202 Returns \s-1PDB\s0 header time stamp.
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203 .IP "\fBGenerateHetatmRecordLine\fR" 4
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204 .IX Item "GenerateHetatmRecordLine"
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205 .Vb 4
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206 \& $RecordLine = GenerateHetatmRecordLine($AtomNumber, $AtomName,
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207 \& $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber,
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208 \& $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor,
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209 \& $SegmentID, $ElementSymbol, $AtomCharge);
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210 .Ve
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211 .Sp
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212 Returns \s-1HETATM\s0 record line.
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213 .IP "\fBGenerateEndRecordLine\fR" 4
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214 .IX Item "GenerateEndRecordLine"
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215 .Vb 1
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216 \& $RecordLine = GenerateEndRecordLine();
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217 .Ve
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218 .Sp
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219 Returns \s-1END\s0 record line.
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220 .IP "\fBGenerateTerRecordLine\fR" 4
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221 .IX Item "GenerateTerRecordLine"
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222 .Vb 2
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223 \& $RecordLine = GenerateTerRecordLine($SerialNumber, [$ResidueName,
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224 \& $ChainID, $ResidueNumber, $InsertionCode]);
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225 .Ve
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226 .Sp
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227 Returns \s-1TER\s0 record line.
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228 .IP "\fBGetAllResidues\fR" 4
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229 .IX Item "GetAllResidues"
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230 .Vb 1
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231 \& $ResiduesDataRef = GetAllResidues($PDBRecordLinesRef);
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232 .Ve
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233 .Sp
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234 Gets residue information using \s-1ATOM/HETATM\s0 records and returns a reference to a hash with
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235 following key/value pairs:
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236 .Sp
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237 .Vb 9
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238 \& $ResiduesDataRef\->{ResidueNames} \- Array of all the residues
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239 \& $ResiduesDataRef\->{ResidueCount}{$ResidueName} \- Count of residues
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240 \& $ResiduesDataRef\->{AtomResidueNames}} \- Array of all ATOM residues
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241 \& $ResiduesDataRef\->{AtomResidueCount}{$ResidueName} \- Count of
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242 \& residues in ATOM records
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243 \& $ResiduesDataRef\->{HetatomResidueNames} \- List of all HETATM
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244 \& residues
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245 \& $ResiduesDataRef\->{HetatmResidueCount}{$ResidueName} \- Count of
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246 \& residues HETATM records
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247 .Ve
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248 .Sp
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249 \&\s-1ATOM/HETATM\s0 records after the first \s-1ENDMDL\s0 records are simply ingnored.
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250 .IP "\fBGetChainsAndResidues\fR" 4
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251 .IX Item "GetChainsAndResidues"
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252 .Vb 3
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253 \& $ChainsDataRef = GetChainsAndResidues($PDBRecordLinesRef,
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254 \& [$RecordsSource, $GetChainResiduesBeyondTERFlag,
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255 \& $GetRecordLinesFlag]);
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256 .Ve
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257 .Sp
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258 Gets chains and residue information using \s-1ATOM/HETATM\s0 or \s-1SEQRES\s0 records and returns a reference to a
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259 hash with these keys:
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260 .Sp
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261 .Vb 6
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262 \& $ChainsDataRef\->{ChainIDs} \- List of chain IDs with \*(AqNone\*(Aq for
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263 \& no IDs
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264 \& $ChainsDataRef\->{Residues}{$ChainID} \- List of residues in order
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265 \& of their appearance in a chain
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266 \& $ChainsDataRef\->{ResidueCount}{$ChainID}{$ResidueName} \- Count of
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267 \& residues in a chain
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268 .Ve
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269 .Sp
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270 Chains and residue data can be extacted using either \s-1ATOM/HETATM\s0 records or \s-1SEQRES\s0 records.
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271 \&\s-1ATOM/HETATM\s0 records after the first \s-1ENDMDL\s0 records are simply ingnored.
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272 .IP "\fBGetConectRecordLines\fR" 4
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273 .IX Item "GetConectRecordLines"
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274 .Vb 2
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275 \& $ConectRecordLinesRef = GetConectRecordLines($PDBRecordLinesRef,
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276 \& $AtomNumbersMapRef);
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277 .Ve
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278 .Sp
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279 Collects \s-1CONECT\s0 record lines for specific atom number, modified specified data to exclude any atom
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280 number not present in the list of specified atom numbers and returns a reference to list of
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281 \&\s-1CONECT\s0 record lines.
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282 .IP "\fBGetExperimentalTechnique\fR" 4
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283 .IX Item "GetExperimentalTechnique"
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284 .Vb 1
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285 \& $ExperimentalTechnique = GetExperimentalTechnique($PDBRecordLinesRef);
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286 .Ve
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287 .Sp
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288 Returns \fIExperimentalTechnique\fR value retrieved from \s-1EXPDATA\s0 record line.
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289 .IP "\fBGetExperimentalTechniqueResolution\fR" 4
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290 .IX Item "GetExperimentalTechniqueResolution"
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291 .Vb 2
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292 \& ($Resolution, $ResolutionUnits) = GetExperimentalTechniqueResolution(
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293 \& $PDBRecordLinesRef);
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294 .Ve
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295 .Sp
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296 Returns \fIResolution\fR and \fIResolutionUnits\fR values from \s-1REMARK\s0 2 \s-1RESOLUTION\s0
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297 record line.
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298 .IP "\fBGetMinMaxCoords\fR" 4
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299 .IX Item "GetMinMaxCoords"
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300 .Vb 2
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301 \& ($XMin, $YMin, $ZMin, $XMax, $YMax, $ZMax) =
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302 \& GetMinMaxCoords($PDBRecordLinesRef);
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303 .Ve
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304 .Sp
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305 Returns minimum and maximum \s-1XYZ\s0 coordinates for \s-1ATOM/HETATM\s0 records.
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306 .IP "\fBGetPDBRecordType\fR" 4
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307 .IX Item "GetPDBRecordType"
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308 .Vb 1
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309 \& $RecordType = GetPDBRecordType($RecordLine);
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310 .Ve
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311 .Sp
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312 Returns type of \fIRecordLine\fR.
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313 .IP "\fBGetRecordTypesCount\fR" 4
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314 .IX Item "GetRecordTypesCount"
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315 .Vb 2
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316 \& $RecordTypeDataRef = GetRecordTypesCount($PDBRecordLinesRef,
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317 \& [$SpecifiedRecordType, $GetRecordLinesFlag]);
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318 .Ve
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319 .Sp
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320 Counts the number of each record type or a \f(CW$SpecifiedRecordType\fR and returns a reference to data
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321 type with following key/value pairs:
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322 .Sp
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323 .Vb 5
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324 \& $RecordTypeDataRef\->{RecordTypes} \- An array of unique record types
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325 \& in order of their presence in the file
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326 \& $RecordTypeDataRef\->{Count}{$RecordType} \- Count of each record type
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327 \& $RecordTypeDataRef\->{Lines}{$RecordType} \- Optional lines data for a
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328 \& specific record type.
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329 .Ve
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330 .IP "\fBIsAtomRecordType\fR" 4
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331 .IX Item "IsAtomRecordType"
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332 .Vb 1
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333 \& $Status = IsAtomRecordType($RecordLine);
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334 .Ve
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335 .Sp
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336 Returns 1 or 0 based on whether it's a \s-1ATOM\s0 record line.
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337 .IP "\fBIsConectRecordType\fR" 4
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338 .IX Item "IsConectRecordType"
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339 .Vb 1
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340 \& $Status = IsAtomConectType($RecordLine);
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341 .Ve
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342 .Sp
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343 Returns 1 or 0 based on whether it's a \s-1CONECT\s0 record line.
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344 .IP "\fBIsEndmdlRecordType\fR" 4
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345 .IX Item "IsEndmdlRecordType"
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346 .Vb 1
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347 \& $Status = IsEndmdlRecordType($RecordLine);
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348 .Ve
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349 .Sp
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350 Returns 1 or 0 based on whether it's a \s-1ENDMDL\s0 a record line.
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351 .IP "\fBIsHeaderRecordType\fR" 4
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352 .IX Item "IsHeaderRecordType"
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353 .Vb 1
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354 \& $Status = IsHeaderRecordType($RecordLine);
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355 .Ve
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356 .Sp
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357 Returns 1 or 0 based on whether it's a \s-1HEADER\s0 a record line.
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358 .IP "\fBIsHetatmRecordType\fR" 4
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359 .IX Item "IsHetatmRecordType"
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360 .Vb 1
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361 \& $Status = IsHetatmRecordType($RecordLine);
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362 .Ve
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363 .Sp
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364 Returns 1 or 0 based on whether it's a \s-1HETATM\s0 a record line.
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365 .IP "\fBIsMasterRecordType\fR" 4
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366 .IX Item "IsMasterRecordType"
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367 .Vb 1
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368 \& $Status = IsMasterRecordType($RecordLine);
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369 .Ve
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370 .Sp
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371 Returns 1 or 0 based on whether it's a \s-1MASTER\s0 a record line.
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372 .IP "\fBIsModelRecordType\fR" 4
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373 .IX Item "IsModelRecordType"
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374 .Vb 1
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375 \& $Status = IsModelRecordType($RecordLine);
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376 .Ve
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377 .Sp
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378 Returns 1 or 0 based on whether it's a \s-1MODEL\s0 record line.
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379 .IP "\fBIsPDBFile\fR" 4
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380 .IX Item "IsPDBFile"
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381 .Vb 1
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382 \& $Status = IsPDBFile($PDBFile);
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383 .Ve
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384 .Sp
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385 Returns 1 or 0 based on whether it's a \s-1PDB\s0 file.
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386 .IP "\fBIsSeqresRecordType\fR" 4
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387 .IX Item "IsSeqresRecordType"
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388 .Vb 1
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389 \& $Status = IsSeqresRecordType($RecordLine);
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390 .Ve
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391 .Sp
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392 Returns 1 or 0 based on whether it's \s-1SEQRES\s0 a record line.
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393 .IP "\fBIsTerRecordType\fR" 4
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394 .IX Item "IsTerRecordType"
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395 .Vb 1
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396 \& $Status = IsTerRecordType($RecordLine);
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397 .Ve
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398 .Sp
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399 Returns 1 or 0 based on whether it's a \s-1TER\s0 record line.
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400 .IP "\fBParseAtomOrHetatmRecordLine\fR" 4
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401 .IX Item "ParseAtomOrHetatmRecordLine"
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402 .Vb 4
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403 \& ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID,
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404 \& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
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405 \& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) =
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406 \& ParseAtomOrHetatmRecordLine($RecordLine);
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407 .Ve
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408 .Sp
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409 Parses \s-1ATOM\s0 or \s-1HETATM\s0 record line.
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410 .IP "\fBParseAtomRecordLine\fR" 4
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411 .IX Item "ParseAtomRecordLine"
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412 .Vb 4
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413 \& ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID,
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414 \& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
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415 \& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) =
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416 \& ParseAtomRecordLine($RecordLine);
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417 .Ve
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418 .Sp
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419 Parses \s-1ATOM\s0 record line.
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420 .IP "\fBParseConectRecordLine\fR" 4
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421 .IX Item "ParseConectRecordLine"
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422 .Vb 4
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423 \& ($AtomNum, $BondedAtomNum1, $BondedAtomNum2, $BondedAtomNum3,
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424 \& $BondedAtomNum4, $HBondedAtomNum1, $HBondedAtomNum2,
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425 \& $SaltBridgedAtomNum1, $HBondedAtomNum3, $HBondedAtomNum4,
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426 \& $SaltBridgedAtomNum2) = ParseConectRecordLine($RecordLine);
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427 .Ve
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428 .Sp
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429 Parses \s-1CONECT\s0 record line.
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430 .IP "\fBParseExpdtaRecordLine\fR" 4
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431 .IX Item "ParseExpdtaRecordLine"
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432 .Vb 1
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433 \& ($ContinuationNum, $ExperimentalTechnique) = ParseExpdtaRecordLine($Line);
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434 .Ve
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435 .Sp
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436 Parses \s-1EXPDTA\s0 record line.
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437 .IP "\fBParseHeaderRecordLine\fR" 4
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438 .IX Item "ParseHeaderRecordLine"
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439 .Vb 1
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440 \& ($Classification, $DepositionDate, $IDCode) = ParseHeaderRecordLine($RecordLine);
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441 .Ve
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442 .Sp
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443 Parses \s-1HEADER\s0 record line
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444 .IP "\fBParseHetatmRecordLine\fR" 4
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445 .IX Item "ParseHetatmRecordLine"
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446 .Vb 4
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447 \& ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID,
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448 \& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy,
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449 \& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) =
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450 \& ParseHetatmRecordLine($RecordLine);
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451 .Ve
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452 .Sp
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453 Parses \s-1HETATM\s0 record line.
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454 .IP "\fBParseMasterRecordLine\fR" 4
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455 .IX Item "ParseMasterRecordLine"
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456 .Vb 5
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457 \& ($NumOfRemarkRecords, $NumOfHetRecords, $NumOfHelixRecords,
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458 \& $NumOfSheetRecords, $NumOfTurnRecords, $NumOfSiteRecords,
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459 \& $NumOfTransformationsRecords, $NumOfAtomAndHetatmRecords,
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460 \& $NumOfTerRecords, $NumOfConectRecords, $NumOfSeqresRecords) =
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461 \& ParseMasterRecordLine($RecordLine);
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462 .Ve
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463 .Sp
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|
464 Parses \s-1MASTER\s0 ecord line.
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465 .IP "\fBParseRemark2ResolutionRecordLine\fR" 4
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466 .IX Item "ParseRemark2ResolutionRecordLine"
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467 .Vb 2
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468 \& ($Resolution, $ResolutionUnits) = ParseRemark2ResolutionRecordLine(
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|
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469 \& $RecordLine);
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470 .Ve
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|
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471 .Sp
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|
472 Parses \s-1REMARK\s0 2 \s-1RESOLUTION\s0 record line.
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473 .IP "\fBParseSeqresRecordLine\fR" 4
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474 .IX Item "ParseSeqresRecordLine"
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|
|
475 .Vb 2
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476 \& ($RecordSerialNumber, $ChainID, $NumOfResidues, $ResidueNames) =
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|
|
477 \& ParseSeqresRecordLine($RecordLine);
|
|
|
478 .Ve
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|
|
479 .Sp
|
|
|
480 Parses \s-1SEQRES\s0 record line.
|
|
|
481 .IP "\fBParseTerRecordLine\fR" 4
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|
|
482 .IX Item "ParseTerRecordLine"
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|
|
483 .Vb 2
|
|
|
484 \& ($SerialNumber, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode) =
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|
|
485 \& ParseTerRecordLine($RecordLine);
|
|
|
486 .Ve
|
|
|
487 .Sp
|
|
|
488 Parses \s-1TER\s0 record line.
|
|
|
489 .IP "\fBReadPDBFile\fR" 4
|
|
|
490 .IX Item "ReadPDBFile"
|
|
|
491 .Vb 1
|
|
|
492 \& $PDBRecordLinesRef = ReadPDBFile($PDBFile);
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|
|
493 .Ve
|
|
|
494 .Sp
|
|
|
495 Reads \s-1PDB\s0 file and returns reference to record lines.
|
|
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496 .SH "AUTHOR"
|
|
|
497 .IX Header "AUTHOR"
|
|
|
498 Manish Sud <msud@san.rr.com>
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|
|
499 .SH "SEE ALSO"
|
|
|
500 .IX Header "SEE ALSO"
|
|
|
501 FileUtil.pm, SequenceFileUtil.pm, TextUtil.pm
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|
|
502 .SH "COPYRIGHT"
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|
|
503 .IX Header "COPYRIGHT"
|
|
|
504 Copyright (C) 2015 Manish Sud. All rights reserved.
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|
|
505 .PP
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|
|
506 This file is part of MayaChemTools.
|
|
|
507 .PP
|
|
|
508 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
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509 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
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510 Software Foundation; either version 3 of the License, or (at your option)
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511 any later version.
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