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| author | deepakjadmin |
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| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
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NAME SDFileUtil SYNOPSIS use SDFileUtil ; use SDFileUtil qw(:all); DESCRIPTION SDFileUtil module provides the following functions: GenerateCmpdAtomAliasPropertyLines, GenerateCmpdAtomLine, GenerateCmpdBondLine, GenerateCmpdChargePropertyLines, GenerateCmpdCommentsLine, GenerateCmpdCountsLine, GenerateCmpdDataHeaderLabelsAndValuesLines, GenerateCmpdIsotopePropertyLines, GenerateCmpdMiscInfoLine, GenerateCmpdMolNameLine, GenerateCmpdRadicalPropertyLines, GenerateEmptyCtabBlockLines, GenerateMiscLineDateStamp, GetAllAndCommonCmpdDataHeaderLabels, GetCmpdDataHeaderLabels, GetCmpdDataHeaderLabelsAndValues, GetCmpdFragments, GetCtabLinesCount, GetInvalidAtomNumbers, GetUnknownAtoms, InternalBondOrderToMDLBondType, InternalBondStereochemistryToMDLBondStereo, InternalChargeToMDLCharge, InternalSpinMultiplicityToMDLRadical, IsCmpd2D, IsCmpd3D, MDLBondStereoToInternalBondStereochemistry, MDLBondTypeToInternalBondOrder, MDLChargeToInternalCharge, MDLRadicalToInternalSpinMultiplicity, ParseCmpdAtomAliasPropertyLine, ParseCmpdAtomLine, ParseCmpdBondLine, ParseCmpdChargePropertyLine, ParseCmpdCommentsLine, ParseCmpdCountsLine, ParseCmpdIsotopePropertyLine, ParseCmpdMiscInfoLine, ParseCmpdMolNameLine, ParseCmpdRadicalPropertyLine, ReadCmpdString, RemoveCmpdDataHeaderLabelAndValue, WashCmpd METHODS GenerateCmpdAtomAliasPropertyLines @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef); Returns a formatted atom alias property lines corresponding to successive pairs of atom number and alias values specified by a refernce to an array. Two lines are generate for each atom number and alias value pairs: First line - A <AtomNum>; Second line:<AtomAlias>. 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 $CtabLinesCount = GetCtabLinesCount(\@CmpdLines); Returns number of lines present between the 4th line and the line containg "M END". GetInvalidAtomNumbers ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) = GetInvalidAtomNumbers(\@CmpdLines); Returns a list of values containing information about invalid atom numbers present in block or atom property lines. GetUnknownAtoms ($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 InternalBondStereochemistryToMDLBondStereo $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo( $InternalBondStereo); Returns value of *MDLBondStereo* corresponding to *InternalBondStereo* using following mapping: InternalBondStereo MDLBondStereo Up 1 UpOrDown 4 Down 6 CisOrTrans 3 Other 0 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. IsCmpd2D $Status = IsCmpd2D(); Returns 1 or 0 based on whether z-coordinate of any atom is non-zero. IsCmpd3D $Status = IsCmpd3D(); Returns 1 or 0 based on whether z-coordinate of any atom is non-zero. MDLBondStereoToInternalBondStereochemistry $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry( $MDLBondStereo); Returns value of *InternalBondStereo* corresponding to *MDLBondStereo* using mapping shown for InternalBondStereochemistryToMDLBondStereo 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. ParseCmpdAtomAliasPropertyLine @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine( $CurrentLine, $NexLine); Parses atom alias propery lines in CTAB generic properties block and returns an array with successive pairs of values corresponding to atom number and its alias. ParseCmpdAtomLine ($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. RemoveCmpdDataHeaderLabelAndValue $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString, $DataHeaderLabel); Returns a NewCmpdString after removing *DataHeaderLabel* along with its value from *CmpdString*. 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 <msud@san.rr.com> SEE ALSO 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.