- 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,
$AtomNumbersMapRef);
-
Collects CONECT record lines for specific atom number, modified specified data to exclude any atom
number not present in the list of specified atom numbers and returns a reference to list of
CONECT record lines.
- GetMinMaxCoords
-
($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.
- 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.
- 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.
Copyright (C) 2004-2012 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.
