diff mayachemtools/docs/modules/txt/PDBFileUtil.txt @ 0:73ae111cf86f draft

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+++ b/mayachemtools/docs/modules/txt/PDBFileUtil.txt	Wed Jan 20 11:55:01 2016 -0500
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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 <[e-mail]>
+
+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.
+