MayaChemTools:Documentation:SDFileUtil.pm

Previous TOC Next

SDFileUtil.pm

Code | PDF | PDFGreen | PDFA4 | PDFA4Green

NAME

SDFileUtil

SYNOPSIS

use SDFileUtil ;

use SDFileUtil qw(:all);

DESCRIPTION

SDFileUtil module provides the following functions:

GenerateCmpdAtomLine, GenerateCmpdBondLine, GenerateCmpdChargePropertyLines , GenerateCmpdCommentsLine, GenerateCmpdCountsLine , GenerateCmpdDataHeaderLabelsAndValuesLines, GenerateCmpdIsotopePropertyLines , GenerateCmpdMiscInfoLine, GenerateCmpdMolNameLine , GenerateCmpdRadicalPropertyLines, GenerateEmptyCtabBlockLines , GenerateMiscLineDateStamp, GetAllAndCommonCmpdDataHeaderLabels , GetCmpdDataHeaderLabels, GetCmpdDataHeaderLabelsAndValues, GetCmpdFragments , GetCtabLinesCount, GetUnknownAtoms, InternalBondOrderToMDLBondType , InternalBondTypeToMDLBondStereo, InternalChargeToMDLCharge , InternalSpinMultiplicityToMDLRadical, MDLBondStereoToInternalBondType , MDLBondTypeToInternalBondOrder, MDLChargeToInternalCharge , MDLRadicalToInternalSpinMultiplicity, ParseCmpdAtomLine, ParseCmpdBondLine , ParseCmpdChargePropertyLine, ParseCmpdCommentsLine, ParseCmpdCountsLine , ParseCmpdIsotopePropertyLine, ParseCmpdMiscInfoLine, ParseCmpdMolNameLine , ParseCmpdRadicalPropertyLine, ReadCmpdString, WashCmpd

METHODS

GenerateCmpdAtomLine: $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY, $AtomZ, [$MassDifference, $Charge, $StereoParity]);; Returns a formatted atom data line containing all the input values
GenerateCmpdBondLine: $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum, $BondType, [$BondStereo]);; Returns a formatted bond data line containing all the input values
GenerateCmpdChargePropertyLines: @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef);; Returns a formatted M CHG property lines corresponding to successive pairs of atom number and charge values specified by a refernce to an array
GenerateCmpdCommentsLine: $Line = GenerateCmpdCommentsLine($Comments);; Returns a formatted comments data line
GenerateCmpdCountsLine: $Line = GenerateCmpdCountsLine($AtomCount, $BondCount, $ChiralFlag, [$PropertyCount, $Version]);; Returns a formatted line containing all the input values. The default values of 999 and V2000 are used for PropertyCount and Version.
GenerateCmpdDataHeaderLabelsAndValuesLines: @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines( $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef, [$SortDataLabels]);; Returns formatted data lines containing header label and values lines corresponding to all data header labels in array reference DataHeaderLabelsRef with values in hash reference DataHeaderLabelsAndValuesRef. By default, data header labels are not sorted and correspond to the label order in array reference DataHeaderLabelsRef.
GenerateCmpdIsotopePropertyLines: @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef);; Returns a formatted M ISO property lines corresponding to successive pairs of atom number and isotope values specified by a refernce to an array
GenerateCmpdMiscInfoLine: $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial, $Code]);; Returns a formatted line containing specified user initial, program name, date and code. Default values are: ProgramName - MayaChem; UserInitial - NULL; Code - 2D.
GenerateCmpdMolNameLine: $Line = GenerateCmpdMolNameLine($MolName);; Returns a formatted molecule name data line
GenerateCmpdRadicalPropertyLines: @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef);; Returns a formatted M CHG property lines corresponding to successive pairs of atom number and multiplicity values specified by a refernce to an array
GenerateEmptyCtabBlockLines: $Lines = GenerateCmpdMiscInfoLine([$Date]);; Returns formatted lines representing empty CTAB block
GenerateMiscLineDateStamp: $Line = GenerateMiscLineDateStamp();; Returns date stamp for misc line.
GetAllAndCommonCmpdDataHeaderLabels: ($CmpdCount, $DataFieldLabelsArrayRef, $CommonDataFieldLabelsArrayRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);; Returns number of comopunds, a reference to an array containing all unique data header label and a reference to an array containing common data field labels for all compounds in SD file.
GetCmpdDataHeaderLabels: (@Labels) = GetCmpdDataHeaderLabels(\@CmpdLines);; Returns an array containg data header labels for a compound
GetCmpdDataHeaderLabelsAndValues: (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);; Returns a hash conating data header labes and values for a compound
GetCmpdFragments: ($FragmentCount, $FragmentString) = GetCmpdFragments(\@CmpLines);; Figures out the number of disconnected fragments and return their values along with the atom numbers in a string delimited by new line character. Fragment data in FragmentString is sorted on based on its size.
GetCtabLinesCount: $CtabLinesCount = GetCtabLinesCount(\@CmpdLines);; Returns number of lines present between the 4th line and the line containg ''M END''
GetUnknownAtoms: ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) = GetUnknownAtoms(\@CmpdLines);; Returns a list of values containing information about atoms which contain special element symbols not present in the periodic table
InternalBondOrderToMDLBondType: $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder);; Returns value of MDLBondType corresponding to InternalBondOrder; InternalBondOrder MDLBondType; 1 1 2 2 3 3 1.5 4
InternalBondTypeToMDLBondStereo: $MDLBondStereo = InternalBondTypeToMDLBondStereo($InternalBondType);; Returns value of MDLBondStereo corresponding to InternalBondType using following mapping:; InternalBondType MDLBondStereo; SingleUp 1 SingleWavy 4 SingleDown 6 DoubleCross 3
InternalChargeToMDLCharge: $MDLCharge = InternalChargeToMDLCharge($InternalCharge);; Returns value of MDLCharge corresponding to InternalCharge using following mapping:; InternalCharge MDLCharge; 3 1 2 2 1 3
-1 5
-2 6
-3 7
InternalSpinMultiplicityToMDLRadical: $MDLRadical = InternalSpinMultiplicityToMDLRadical( $InternalSpinMultiplicity);; Returns value of MDLRadical corresponding to InternalSpinMultiplicity. These value are equivalent.
MDLBondStereoToInternalBondType: $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo);; Returns value of InternalBondType corresponding to MDLBondStereo using mapping shown for InternalBondTypeToMDLBondStereo function
MDLBondTypeToInternalBondOrder: $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType);; Returns value of $InternalBondOrder corresponding to MDLBondType using mapping shown for InternalBondOrderToMDLBondType function
MDLChargeToInternalCharge: $InternalCharge = MDLChargeToInternalCharge($MDLCharge);; Returns value of $InternalCharge corresponding to MDLCharge using mapping shown for InternalChargeToMDLCharge function
MDLRadicalToInternalSpinMultiplicity: $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity( $MDLRadical);; Returns value of InternalSpinMultiplicity corresponding to MDLRadical. These value are equivalent.
ParseCmpdAtomLine: ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge, $StereoParity) = ParseCmpdAtomLine($AtomDataLine);; Parses compound data line containing atom information and returns a list of values
ParseCmpdBondLine: ($FirstAtomNum, $SecondAtomNum, $BondType) = ParseCmpdBondLine($BondDataLine);; Parses compound data line containing bond information and returns a list of values
ParseCmpdCommentsLine: $Comments = ParseCmpdCommentsLine($CommentsDataLine);; Returns the comment string
ParseCmpdChargePropertyLine: @AtomNumAndValuePairs = ParseCmpdChargePropertyLine( $ChargeDataLine);; Parses charge propery line in CTAB generic properties block and returns an array with successive pairs of values corresponding to atom number and its charge
ParseCmpdCountsLine: ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) = ParseCmpdCountsLine(\@CountDataLines);; Returns a list of values containing count information
ParseCmpdMiscInfoLine: ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2, $Energy, $RegistryNum) = ParseCmpdMiscInfoLine($Line);; Returns a list of values containing miscellaneous information.
ParseCmpdIsotopePropertyLine: @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine( $IsotopeDataLine);; Parses isotopic propery line in CTAB generic properties block and returns an array with successive pairs of values corresponding to atom number and absolute mass of atom isotope
ParseCmpdMolNameLine: $MolName = ParseCmpdMolNameLine($Line);; Returns a string containing molecule name
ParseCmpdRadicalPropertyLine: @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine( $RadicalDataLine);; Parses radical propery line in CTAB generic properties block and returns an array with successive pairs of values corresponding to atom number and radical number value
ReadCmpdString: $CmpdString = ReadCmpdString(\*SDFILEHANDLE);; Returns a string containing all the data lines for the next available compound in an already open file indicated by SDFILEHANDLE. A NULL string is returned on EOF.
WashCmpd: ($FragmentCount, $Fragments, $WashedCmpdString) = WashCmpd(\@CmpdLines);; Figures out the number of disconnected fragments and return their values along with the atom numbers in a string delimited by new line character. Fragment data in FragmentString is sorted on based on its size.

AUTHOR

Manish Sud

COPYRIGHT

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.