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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) 2015 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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