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diff mayachemtools/docs/modules/man3/PDBFileUtil.3 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/PDBFileUtil.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,511 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +PDBFileUtil +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use PDBFileUtil ; +.PP +use PDBFileUtil qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBPDBFileUtil\fR module provides the following functions: +.PP +GenerateAtomOrHetatmRecordLine, GenerateAtomRecordLine, GenerateConectRecordLine, +GenerateEndRecordLine, GenerateHeaderRecordLine, GenerateHeaderRecordTimeStamp, +GenerateHetatmRecordLine, GenerateTerRecordLine, GetAllResidues, +GetChainsAndResidues, GetConectRecordLines, GetExperimentalTechnique, +GetExperimentalTechniqueResolution, GetMinMaxCoords, GetPDBRecordType, +GetRecordTypesCount, IsAtomRecordType, IsConectRecordType, IsEndmdlRecordType, +IsHeaderRecordType, IsHetatmRecordType, IsMasterRecordType, IsModelRecordType, +IsPDBFile, IsSeqresRecordType, IsTerRecordType, ParseAtomOrHetatmRecordLine, +ParseAtomRecordLine, ParseConectRecordLine, ParseExpdtaRecordLine, +ParseHeaderRecordLine, ParseHetatmRecordLine, ParseMasterRecordLine, +ParseRemark2ResolutionRecordLine, ParseSeqresRecordLine, ParseTerRecordLine, +ReadPDBFile +.SH "METHODS" +.IX Header "METHODS" +.IP "\fBGenerateAtomOrHetatmRecordLine\fR" 4 +.IX Item "GenerateAtomOrHetatmRecordLine" +.Vb 5 +\& $RecordLine = GenerateAtomOrHetatmRecordLine($RecordType, +\& $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, +\& $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, +\& $Occupancy, $TemperatureFactor, $SegmentID, +\& $ElementSymbol, $AtomCharge); +.Ve +.Sp +Returns \s-1ATOM\s0 or \s-1HETATM\s0 record line. +.IP "\fBGenerateAtomRecordLine\fR" 4 +.IX Item "GenerateAtomRecordLine" +.Vb 4 +\& $RecordLine = GenerateAtomRecordLine($AtomNumber, +\& $AtomName, $AlternateLocation, $ResidueName, $ChainID, +\& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, +\& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge); +.Ve +.Sp +Returns \s-1ATOM\s0 record line. +.IP "\fBGenerateConectRecordLine\fR" 4 +.IX Item "GenerateConectRecordLine" +.Vb 4 +\& $RecordLine = GenerateConectRecordLine($AtomNum, $BondedAtomNum1, +\& $BondedAtomNum2, $BondedAtomNum3, $BondedAtomNum4, +\& $HBondedAtomNum1, $HBondedAtomNum2, $SaltBridgedAtomNum1, +\& $HBondedAtomNum3, $HBondedAtomNum4, $SaltBridgedAtomNum2); +.Ve +.Sp +Returns \s-1CONECT\s0 record line. +.IP "\fBGenerateHeaderRecordLine\fR" 4 +.IX Item "GenerateHeaderRecordLine" +.Vb 2 +\& $RecordLine = GenerateHeaderRecordLine($IDCode, [$Classification, +\& $Date]); +.Ve +.Sp +Returns \s-1HEADER\s0 record line. +.IP "\fBGenerateHeaderRecordTimeStamp\fR" 4 +.IX Item "GenerateHeaderRecordTimeStamp" +.Vb 1 +\& $Date = GenerateHeaderRecordTimeStamp(); +.Ve +.Sp +Returns \s-1PDB\s0 header time stamp. +.IP "\fBGenerateHetatmRecordLine\fR" 4 +.IX Item "GenerateHetatmRecordLine" +.Vb 4 +\& $RecordLine = GenerateHetatmRecordLine($AtomNumber, $AtomName, +\& $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, +\& $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, +\& $SegmentID, $ElementSymbol, $AtomCharge); +.Ve +.Sp +Returns \s-1HETATM\s0 record line. +.IP "\fBGenerateEndRecordLine\fR" 4 +.IX Item "GenerateEndRecordLine" +.Vb 1 +\& $RecordLine = GenerateEndRecordLine(); +.Ve +.Sp +Returns \s-1END\s0 record line. +.IP "\fBGenerateTerRecordLine\fR" 4 +.IX Item "GenerateTerRecordLine" +.Vb 2 +\& $RecordLine = GenerateTerRecordLine($SerialNumber, [$ResidueName, +\& $ChainID, $ResidueNumber, $InsertionCode]); +.Ve +.Sp +Returns \s-1TER\s0 record line. +.IP "\fBGetAllResidues\fR" 4 +.IX Item "GetAllResidues" +.Vb 1 +\& $ResiduesDataRef = GetAllResidues($PDBRecordLinesRef); +.Ve +.Sp +Gets residue information using \s-1ATOM/HETATM\s0 records and returns a reference to a hash with +following key/value pairs: +.Sp +.Vb 9 +\& $ResiduesDataRef\->{ResidueNames} \- Array of all the residues +\& $ResiduesDataRef\->{ResidueCount}{$ResidueName} \- Count of residues +\& $ResiduesDataRef\->{AtomResidueNames}} \- Array of all ATOM residues +\& $ResiduesDataRef\->{AtomResidueCount}{$ResidueName} \- Count of +\& residues in ATOM records +\& $ResiduesDataRef\->{HetatomResidueNames} \- List of all HETATM +\& residues +\& $ResiduesDataRef\->{HetatmResidueCount}{$ResidueName} \- Count of +\& residues HETATM records +.Ve +.Sp +\&\s-1ATOM/HETATM\s0 records after the first \s-1ENDMDL\s0 records are simply ingnored. +.IP "\fBGetChainsAndResidues\fR" 4 +.IX Item "GetChainsAndResidues" +.Vb 3 +\& $ChainsDataRef = GetChainsAndResidues($PDBRecordLinesRef, +\& [$RecordsSource, $GetChainResiduesBeyondTERFlag, +\& $GetRecordLinesFlag]); +.Ve +.Sp +Gets chains and residue information using \s-1ATOM/HETATM\s0 or \s-1SEQRES\s0 records and returns a reference to a +hash with these keys: +.Sp +.Vb 6 +\& $ChainsDataRef\->{ChainIDs} \- List of chain IDs with \*(AqNone\*(Aq for +\& no IDs +\& $ChainsDataRef\->{Residues}{$ChainID} \- List of residues in order +\& of their appearance in a chain +\& $ChainsDataRef\->{ResidueCount}{$ChainID}{$ResidueName} \- Count of +\& residues in a chain +.Ve +.Sp +Chains and residue data can be extacted using either \s-1ATOM/HETATM\s0 records or \s-1SEQRES\s0 records. +\&\s-1ATOM/HETATM\s0 records after the first \s-1ENDMDL\s0 records are simply ingnored. +.IP "\fBGetConectRecordLines\fR" 4 +.IX Item "GetConectRecordLines" +.Vb 2 +\& $ConectRecordLinesRef = GetConectRecordLines($PDBRecordLinesRef, +\& $AtomNumbersMapRef); +.Ve +.Sp +Collects \s-1CONECT\s0 record lines for specific atom number, modified specified data to exclude any atom +number not present in the list of specified atom numbers and returns a reference to list of +\&\s-1CONECT\s0 record lines. +.IP "\fBGetExperimentalTechnique\fR" 4 +.IX Item "GetExperimentalTechnique" +.Vb 1 +\& $ExperimentalTechnique = GetExperimentalTechnique($PDBRecordLinesRef); +.Ve +.Sp +Returns \fIExperimentalTechnique\fR value retrieved from \s-1EXPDATA\s0 record line. +.IP "\fBGetExperimentalTechniqueResolution\fR" 4 +.IX Item "GetExperimentalTechniqueResolution" +.Vb 2 +\& ($Resolution, $ResolutionUnits) = GetExperimentalTechniqueResolution( +\& $PDBRecordLinesRef); +.Ve +.Sp +Returns \fIResolution\fR and \fIResolutionUnits\fR values from \s-1REMARK\s0 2 \s-1RESOLUTION\s0 +record line. +.IP "\fBGetMinMaxCoords\fR" 4 +.IX Item "GetMinMaxCoords" +.Vb 2 +\& ($XMin, $YMin, $ZMin, $XMax, $YMax, $ZMax) = +\& GetMinMaxCoords($PDBRecordLinesRef); +.Ve +.Sp +Returns minimum and maximum \s-1XYZ\s0 coordinates for \s-1ATOM/HETATM\s0 records. +.IP "\fBGetPDBRecordType\fR" 4 +.IX Item "GetPDBRecordType" +.Vb 1 +\& $RecordType = GetPDBRecordType($RecordLine); +.Ve +.Sp +Returns type of \fIRecordLine\fR. +.IP "\fBGetRecordTypesCount\fR" 4 +.IX Item "GetRecordTypesCount" +.Vb 2 +\& $RecordTypeDataRef = GetRecordTypesCount($PDBRecordLinesRef, +\& [$SpecifiedRecordType, $GetRecordLinesFlag]); +.Ve +.Sp +Counts the number of each record type or a \f(CW$SpecifiedRecordType\fR and returns a reference to data +type with following key/value pairs: +.Sp +.Vb 5 +\& $RecordTypeDataRef\->{RecordTypes} \- An array of unique record types +\& in order of their presence in the file +\& $RecordTypeDataRef\->{Count}{$RecordType} \- Count of each record type +\& $RecordTypeDataRef\->{Lines}{$RecordType} \- Optional lines data for a +\& specific record type. +.Ve +.IP "\fBIsAtomRecordType\fR" 4 +.IX Item "IsAtomRecordType" +.Vb 1 +\& $Status = IsAtomRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1ATOM\s0 record line. +.IP "\fBIsConectRecordType\fR" 4 +.IX Item "IsConectRecordType" +.Vb 1 +\& $Status = IsAtomConectType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1CONECT\s0 record line. +.IP "\fBIsEndmdlRecordType\fR" 4 +.IX Item "IsEndmdlRecordType" +.Vb 1 +\& $Status = IsEndmdlRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1ENDMDL\s0 a record line. +.IP "\fBIsHeaderRecordType\fR" 4 +.IX Item "IsHeaderRecordType" +.Vb 1 +\& $Status = IsHeaderRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1HEADER\s0 a record line. +.IP "\fBIsHetatmRecordType\fR" 4 +.IX Item "IsHetatmRecordType" +.Vb 1 +\& $Status = IsHetatmRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1HETATM\s0 a record line. +.IP "\fBIsMasterRecordType\fR" 4 +.IX Item "IsMasterRecordType" +.Vb 1 +\& $Status = IsMasterRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1MASTER\s0 a record line. +.IP "\fBIsModelRecordType\fR" 4 +.IX Item "IsModelRecordType" +.Vb 1 +\& $Status = IsModelRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1MODEL\s0 record line. +.IP "\fBIsPDBFile\fR" 4 +.IX Item "IsPDBFile" +.Vb 1 +\& $Status = IsPDBFile($PDBFile); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1PDB\s0 file. +.IP "\fBIsSeqresRecordType\fR" 4 +.IX Item "IsSeqresRecordType" +.Vb 1 +\& $Status = IsSeqresRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's \s-1SEQRES\s0 a record line. +.IP "\fBIsTerRecordType\fR" 4 +.IX Item "IsTerRecordType" +.Vb 1 +\& $Status = IsTerRecordType($RecordLine); +.Ve +.Sp +Returns 1 or 0 based on whether it's a \s-1TER\s0 record line. +.IP "\fBParseAtomOrHetatmRecordLine\fR" 4 +.IX Item "ParseAtomOrHetatmRecordLine" +.Vb 4 +\& ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, +\& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, +\& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = +\& ParseAtomOrHetatmRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1ATOM\s0 or \s-1HETATM\s0 record line. +.IP "\fBParseAtomRecordLine\fR" 4 +.IX Item "ParseAtomRecordLine" +.Vb 4 +\& ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, +\& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, +\& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = +\& ParseAtomRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1ATOM\s0 record line. +.IP "\fBParseConectRecordLine\fR" 4 +.IX Item "ParseConectRecordLine" +.Vb 4 +\& ($AtomNum, $BondedAtomNum1, $BondedAtomNum2, $BondedAtomNum3, +\& $BondedAtomNum4, $HBondedAtomNum1, $HBondedAtomNum2, +\& $SaltBridgedAtomNum1, $HBondedAtomNum3, $HBondedAtomNum4, +\& $SaltBridgedAtomNum2) = ParseConectRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1CONECT\s0 record line. +.IP "\fBParseExpdtaRecordLine\fR" 4 +.IX Item "ParseExpdtaRecordLine" +.Vb 1 +\& ($ContinuationNum, $ExperimentalTechnique) = ParseExpdtaRecordLine($Line); +.Ve +.Sp +Parses \s-1EXPDTA\s0 record line. +.IP "\fBParseHeaderRecordLine\fR" 4 +.IX Item "ParseHeaderRecordLine" +.Vb 1 +\& ($Classification, $DepositionDate, $IDCode) = ParseHeaderRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1HEADER\s0 record line +.IP "\fBParseHetatmRecordLine\fR" 4 +.IX Item "ParseHetatmRecordLine" +.Vb 4 +\& ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, +\& $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, +\& $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = +\& ParseHetatmRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1HETATM\s0 record line. +.IP "\fBParseMasterRecordLine\fR" 4 +.IX Item "ParseMasterRecordLine" +.Vb 5 +\& ($NumOfRemarkRecords, $NumOfHetRecords, $NumOfHelixRecords, +\& $NumOfSheetRecords, $NumOfTurnRecords, $NumOfSiteRecords, +\& $NumOfTransformationsRecords, $NumOfAtomAndHetatmRecords, +\& $NumOfTerRecords, $NumOfConectRecords, $NumOfSeqresRecords) = +\& ParseMasterRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1MASTER\s0 ecord line. +.IP "\fBParseRemark2ResolutionRecordLine\fR" 4 +.IX Item "ParseRemark2ResolutionRecordLine" +.Vb 2 +\& ($Resolution, $ResolutionUnits) = ParseRemark2ResolutionRecordLine( +\& $RecordLine); +.Ve +.Sp +Parses \s-1REMARK\s0 2 \s-1RESOLUTION\s0 record line. +.IP "\fBParseSeqresRecordLine\fR" 4 +.IX Item "ParseSeqresRecordLine" +.Vb 2 +\& ($RecordSerialNumber, $ChainID, $NumOfResidues, $ResidueNames) = +\& ParseSeqresRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1SEQRES\s0 record line. +.IP "\fBParseTerRecordLine\fR" 4 +.IX Item "ParseTerRecordLine" +.Vb 2 +\& ($SerialNumber, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode) = +\& ParseTerRecordLine($RecordLine); +.Ve +.Sp +Parses \s-1TER\s0 record line. +.IP "\fBReadPDBFile\fR" 4 +.IX Item "ReadPDBFile" +.Vb 1 +\& $PDBRecordLinesRef = ReadPDBFile($PDBFile); +.Ve +.Sp +Reads \s-1PDB\s0 file and returns reference to record lines. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +FileUtil.pm, SequenceFileUtil.pm, TextUtil.pm +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.