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NAME

PDBFileUtil

SYNOPSIS

use PDBFileUtil ;

use PDBFileUtil qw(:all);

DESCRIPTION

PDBFileUtil module provides the following functions:

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

METHODS

GenerateAtomOrHetatmRecordLine
$RecordLine = GenerateAtomOrHetatmRecordLine($RecordType, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge);

Returns ATOM or HETATM record line.

GenerateAtomRecordLine
$RecordLine = GenerateAtomRecordLine($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge);

Returns ATOM record line.

GenerateConectRecordLine
$RecordLine = GenerateConectRecordLine($AtomNum, $BondedAtomNum1, $BondedAtomNum2, $BondedAtomNum3, $BondedAtomNum4, $HBondedAtomNum1, $HBondedAtomNum2, $SaltBridgedAtomNum1, $HBondedAtomNum3, $HBondedAtomNum4, $SaltBridgedAtomNum2);

Returns CONECT record line.

GenerateHeaderRecordLine
$RecordLine = GenerateHeaderRecordLine($IDCode, [$Classification, $Date]);

Returns HEADER record line.

GenerateHeaderRecordTimeStamp
$Date = GenerateHeaderRecordTimeStamp();

Returns PDB header time stamp.

GenerateHetatmRecordLine
$RecordLine = GenerateHetatmRecordLine($AtomNumber, $AtomName,
$AlternateLocation, $ResidueName, $ChainID, $ResidueNumber,
$InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor,
$SegmentID, $ElementSymbol, $AtomCharge);

Returns HETATM record line.

GenerateEndRecordLine
$RecordLine = GenerateEndRecordLine();

Returns END record line.

GenerateTerRecordLine
$RecordLine = GenerateTerRecordLine($SerialNumber, [$ResidueName, $ChainID, $ResidueNumber, $InsertionCode]);

Returns TER record line.

GetAllResidues
$ResiduesDataRef = GetAllResidues($PDBRecordLinesRef);

Gets residue information using ATOM/HETATM records and returns a reference to a hash with following key/value pairs:

$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

ATOM/HETATM records after the first ENDMDL records are simply ingnored.

GetChainsAndResidues
$ChainsDataRef = GetChainsAndResidues($PDBRecordLinesRef, [$RecordsSource, $GetChainResiduesBeyondTERFlag, $GetRecordLinesFlag]);

Gets chains and residue information using ATOM/HETATM or SEQRES records and returns a reference to a hash with these keys:

$ChainsDataRef->{ChainIDs} - List of chain IDs with 'None' 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

Chains and residue data can be extacted using either ATOM/HETATM records or SEQRES records. ATOM/HETATM records after the first ENDMDL records are simply ingnored.

GetConectRecordLines
$ConectRecordLinesRef = GetConectRecordLines($PDBRecordLinesRef, $AtomNumbersMapRef);

Collects CONECT 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 CONECT record lines.

GetExperimentalTechnique
$ExperimentalTechnique = GetExperimentalTechnique($PDBRecordLinesRef);

Returns ExperimentalTechnique value retrieved from EXPDATA record line.

GetExperimentalTechniqueResolution
($Resolution, $ResolutionUnits) = GetExperimentalTechniqueResolution( $PDBRecordLinesRef);

Returns Resolution and ResolutionUnits values from REMARK 2 RESOLUTION record line.

GetMinMaxCoords
($XMin, $YMin, $ZMin, $XMax, $YMax, $ZMax) = GetMinMaxCoords($PDBRecordLinesRef);

Returns minimum and maximum XYZ coordinates for ATOM/HETATM records.

GetPDBRecordType
$RecordType = GetPDBRecordType($RecordLine);

Returns type of RecordLine.

GetRecordTypesCount
$RecordTypeDataRef = GetRecordTypesCount($PDBRecordLinesRef, [$SpecifiedRecordType, $GetRecordLinesFlag]);

Counts the number of each record type or a $SpecifiedRecordType and returns a reference to data type with following key/value pairs:

$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.
IsAtomRecordType
$Status = IsAtomRecordType($RecordLine);

Returns 1 or 0 based on whether it's a ATOM record line.

IsConectRecordType
$Status = IsAtomConectType($RecordLine);

Returns 1 or 0 based on whether it's a CONECT record line.

IsEndmdlRecordType
$Status = IsEndmdlRecordType($RecordLine);

Returns 1 or 0 based on whether it's a ENDMDL a record line.

IsHeaderRecordType
$Status = IsHeaderRecordType($RecordLine);

Returns 1 or 0 based on whether it's a HEADER a record line.

IsHetatmRecordType
$Status = IsHetatmRecordType($RecordLine);

Returns 1 or 0 based on whether it's a HETATM a record line.

IsMasterRecordType
$Status = IsMasterRecordType($RecordLine);

Returns 1 or 0 based on whether it's a MASTER a record line.

IsModelRecordType
$Status = IsModelRecordType($RecordLine);

Returns 1 or 0 based on whether it's a MODEL record line.

IsPDBFile
$Status = IsPDBFile($PDBFile);

Returns 1 or 0 based on whether it's a PDB file.

IsSeqresRecordType
$Status = IsSeqresRecordType($RecordLine);

Returns 1 or 0 based on whether it's SEQRES a record line.

IsTerRecordType
$Status = IsTerRecordType($RecordLine);

Returns 1 or 0 based on whether it's a TER record line.

ParseAtomOrHetatmRecordLine
($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseAtomOrHetatmRecordLine($RecordLine);

Parses ATOM or HETATM record line.

ParseAtomRecordLine
($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseAtomRecordLine($RecordLine);

Parses ATOM record line.

ParseConectRecordLine
($AtomNum, $BondedAtomNum1, $BondedAtomNum2, $BondedAtomNum3, $BondedAtomNum4, $HBondedAtomNum1, $HBondedAtomNum2, $SaltBridgedAtomNum1, $HBondedAtomNum3, $HBondedAtomNum4, $SaltBridgedAtomNum2) = ParseConectRecordLine($RecordLine);

Parses CONECT record line.

ParseExpdtaRecordLine
($ContinuationNum, $ExperimentalTechnique) = ParseExpdtaRecordLine($Line);

Parses EXPDTA record line.

ParseHeaderRecordLine
($Classification, $DepositionDate, $IDCode) = ParseHeaderRecordLine($RecordLine);

Parses HEADER record line

ParseHetatmRecordLine
($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseHetatmRecordLine($RecordLine);

Parses HETATM record line.

ParseMasterRecordLine
($NumOfRemarkRecords, $NumOfHetRecords, $NumOfHelixRecords, $NumOfSheetRecords, $NumOfTurnRecords, $NumOfSiteRecords, $NumOfTransformationsRecords, $NumOfAtomAndHetatmRecords, $NumOfTerRecords, $NumOfConectRecords, $NumOfSeqresRecords) = ParseMasterRecordLine($RecordLine);

Parses MASTER ecord line.

ParseRemark2ResolutionRecordLine
($Resolution, $ResolutionUnits) = ParseRemark2ResolutionRecordLine( $RecordLine);

Parses REMARK 2 RESOLUTION record line.

ParseSeqresRecordLine
($RecordSerialNumber, $ChainID, $NumOfResidues, $ResidueNames) = ParseSeqresRecordLine($RecordLine);

Parses SEQRES record line.

ParseTerRecordLine
($SerialNumber, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode) = ParseTerRecordLine($RecordLine);

Parses TER record line.

ReadPDBFile
$PDBRecordLinesRef = ReadPDBFile($PDBFile);

Reads PDB file and returns reference to record lines.

AUTHOR

Manish Sud

SEE ALSO

FileUtil.pm, SequenceFileUtil.pm, TextUtil.pm

COPYRIGHT

Copyright (C) 2019 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

 

 

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