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.\" ========================================================================
.\"
.IX Title "PDBFILEUTIL 1"
.TH PDBFILEUTIL 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  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 <[e-mail]>
.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.