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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/SDFileUtil.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,577 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +SDFileUtil +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use SDFileUtil ; +.PP +use SDFileUtil qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBSDFileUtil\fR module provides the following functions: +.PP +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 +.SH "METHODS" +.IX Header "METHODS" +.IP "\fBGenerateCmpdAtomAliasPropertyLines\fR" 4 +.IX Item "GenerateCmpdAtomAliasPropertyLines" +.Vb 1 +\& @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef); +.Ve +.Sp +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>. +.IP "\fBGenerateCmpdAtomLine\fR" 4 +.IX Item "GenerateCmpdAtomLine" +.Vb 2 +\& $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY, +\& $AtomZ, [$MassDifference, $Charge, $StereoParity]); +.Ve +.Sp +Returns a formatted atom data line containing all the input values. +.IP "\fBGenerateCmpdBondLine\fR" 4 +.IX Item "GenerateCmpdBondLine" +.Vb 2 +\& $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum, +\& $BondType, [$BondStereo]); +.Ve +.Sp +Returns a formatted bond data line containing all the input values. +.IP "\fBGenerateCmpdChargePropertyLines\fR" 4 +.IX Item "GenerateCmpdChargePropertyLines" +.Vb 1 +\& @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef); +.Ve +.Sp +Returns a formatted M \s-1CHG\s0 property lines corresponding to successive pairs of +atom number and charge values specified by a refernce to an array. +.IP "\fBGenerateCmpdCommentsLine\fR" 4 +.IX Item "GenerateCmpdCommentsLine" +.Vb 1 +\& $Line = GenerateCmpdCommentsLine($Comments); +.Ve +.Sp +Returns a formatted comments data line. +.IP "\fBGenerateCmpdCountsLine\fR" 4 +.IX Item "GenerateCmpdCountsLine" +.Vb 2 +\& $Line = GenerateCmpdCountsLine($AtomCount, $BondCount, +\& $ChiralFlag, [$PropertyCount, $Version]); +.Ve +.Sp +Returns a formatted line containing all the input values. The default values of 999 +and V2000 are used for \fIPropertyCount\fR and \fIVersion\fR. +.IP "\fBGenerateCmpdDataHeaderLabelsAndValuesLines\fR" 4 +.IX Item "GenerateCmpdDataHeaderLabelsAndValuesLines" +.Vb 3 +\& @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines( +\& $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef, +\& [$SortDataLabels]); +.Ve +.Sp +Returns formatted data lines containing header label and values lines corresponding to +all data header labels in array reference \fIDataHeaderLabelsRef\fR with values in hash +reference \fIDataHeaderLabelsAndValuesRef\fR. By default, data header labels are +not sorted and correspond to the label order in array reference \fIDataHeaderLabelsRef\fR. +.IP "\fBGenerateCmpdIsotopePropertyLines\fR" 4 +.IX Item "GenerateCmpdIsotopePropertyLines" +.Vb 1 +\& @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef); +.Ve +.Sp +Returns a formatted M \s-1ISO\s0 property lines corresponding to successive pairs of +atom number and isotope values specified by a refernce to an array. +.IP "\fBGenerateCmpdMiscInfoLine\fR" 4 +.IX Item "GenerateCmpdMiscInfoLine" +.Vb 2 +\& $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial, +\& $Code]); +.Ve +.Sp +Returns a formatted line containing specified user initial, program name, date and code. +Default values are: \fIProgramName \- MayaChem; UserInitial \- \s-1NULL\s0; Code \- 2D\fR. +.IP "\fBGenerateCmpdMolNameLine\fR" 4 +.IX Item "GenerateCmpdMolNameLine" +.Vb 1 +\& $Line = GenerateCmpdMolNameLine($MolName); +.Ve +.Sp +Returns a formatted molecule name data line. +.IP "\fBGenerateCmpdRadicalPropertyLines\fR" 4 +.IX Item "GenerateCmpdRadicalPropertyLines" +.Vb 1 +\& @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef); +.Ve +.Sp +Returns a formatted M \s-1CHG\s0 property lines corresponding to successive pairs of +atom number and multiplicity values specified by a refernce to an array. +.IP "\fBGenerateEmptyCtabBlockLines\fR" 4 +.IX Item "GenerateEmptyCtabBlockLines" +.Vb 1 +\& $Lines = GenerateCmpdMiscInfoLine([$Date]); +.Ve +.Sp +Returns formatted lines representing empty \s-1CTAB\s0 block. +.IP "\fBGenerateMiscLineDateStamp\fR" 4 +.IX Item "GenerateMiscLineDateStamp" +.Vb 1 +\& $Line = GenerateMiscLineDateStamp(); +.Ve +.Sp +Returns date stamp for misc line. +.IP "\fBGetAllAndCommonCmpdDataHeaderLabels\fR" 4 +.IX Item "GetAllAndCommonCmpdDataHeaderLabels" +.Vb 3 +\& ($CmpdCount, $DataFieldLabelsArrayRef, +\& $CommonDataFieldLabelsArrayRef) = +\& GetAllAndCommonCmpdDataHeaderLabels(\e*SDFILE); +.Ve +.Sp +Returns number of comopunds, a reference to an array containing all unique data header +label and a reference to an array containing common data field labels for all compounds +in \s-1SD\s0 file. +.IP "\fBGetCmpdDataHeaderLabels\fR" 4 +.IX Item "GetCmpdDataHeaderLabels" +.Vb 1 +\& (@Labels) = GetCmpdDataHeaderLabels(\e@CmpdLines); +.Ve +.Sp +Returns an array containg data header labels for a compound +.IP "\fBGetCmpdDataHeaderLabelsAndValues\fR" 4 +.IX Item "GetCmpdDataHeaderLabelsAndValues" +.Vb 1 +\& (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\e@CmpdLines); +.Ve +.Sp +Returns a hash conating data header labes and values for a compound. +.IP "\fBGetCmpdFragments\fR" 4 +.IX Item "GetCmpdFragments" +.Vb 1 +\& ($FragmentCount, $FragmentString) = GetCmpdFragments(\e@CmpLines); +.Ve +.Sp +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 \fBFragmentString\fR is sorted on based on its size. +.IP "\fBGetCtabLinesCount\fR" 4 +.IX Item "GetCtabLinesCount" +.Vb 1 +\& $CtabLinesCount = GetCtabLinesCount(\e@CmpdLines); +.Ve +.Sp +Returns number of lines present between the 4th line and the line containg \*(L"M \s-1END\s0\*(R". +.IP "\fBGetInvalidAtomNumbers\fR" 4 +.IX Item "GetInvalidAtomNumbers" +.Vb 2 +\& ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) = +\& GetInvalidAtomNumbers(\e@CmpdLines); +.Ve +.Sp +Returns a list of values containing information about invalid atom numbers present +in block or atom property lines. +.IP "\fBGetUnknownAtoms\fR" 4 +.IX Item "GetUnknownAtoms" +.Vb 2 +\& ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) = +\& GetUnknownAtoms(\e@CmpdLines); +.Ve +.Sp +Returns a list of values containing information about atoms which contain special element +symbols not present in the periodic table. +.IP "\fBInternalBondOrderToMDLBondType\fR" 4 +.IX Item "InternalBondOrderToMDLBondType" +.Vb 1 +\& $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder); +.Ve +.Sp +Returns value of \fIMDLBondType\fR corresponding to \fIInternalBondOrder\fR. +.Sp +.Vb 1 +\& InternalBondOrder MDLBondType +\& +\& 1 1 +\& 2 2 +\& 3 3 +\& 1.5 4 +.Ve +.IP "\fBInternalBondStereochemistryToMDLBondStereo\fR" 4 +.IX Item "InternalBondStereochemistryToMDLBondStereo" +.Vb 2 +\& $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo( +\& $InternalBondStereo); +.Ve +.Sp +Returns value of \fIMDLBondStereo\fR corresponding to \fIInternalBondStereo\fR using following +mapping: +.Sp +.Vb 1 +\& InternalBondStereo MDLBondStereo +\& +\& Up 1 +\& UpOrDown 4 +\& Down 6 +\& CisOrTrans 3 +\& Other 0 +.Ve +.IP "\fBInternalChargeToMDLCharge\fR" 4 +.IX Item "InternalChargeToMDLCharge" +.Vb 1 +\& $MDLCharge = InternalChargeToMDLCharge($InternalCharge); +.Ve +.Sp +Returns value of \fIMDLCharge\fR corresponding to \fIInternalCharge\fR using following +mapping: +.Sp +.Vb 1 +\& InternalCharge MDLCharge +\& +\& 3 1 +\& 2 2 +\& 1 3 +\& \-1 5 +\& \-2 6 +\& \-3 7 +.Ve +.IP "\fBInternalSpinMultiplicityToMDLRadical\fR" 4 +.IX Item "InternalSpinMultiplicityToMDLRadical" +.Vb 2 +\& $MDLRadical = InternalSpinMultiplicityToMDLRadical( +\& $InternalSpinMultiplicity); +.Ve +.Sp +Returns value of \fIMDLRadical\fR corresponding to \fIInternalSpinMultiplicity\fR. These +value are equivalent. +.IP "\fBMDLBondStereoToInternalBondType\fR" 4 +.IX Item "MDLBondStereoToInternalBondType" +.Vb 1 +\& $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo); +.Ve +.Sp +Returns value of \fIInternalBondType\fR corresponding to \fIMDLBondStereo\fR using +mapping shown for \fBInternalBondTypeToMDLBondStereo\fR function. +.IP "\fBIsCmpd2D\fR" 4 +.IX Item "IsCmpd2D" +.Vb 1 +\& $Status = IsCmpd2D(); +.Ve +.Sp +Returns 1 or 0 based on whether z\-coordinate of any atom is non-zero. +.IP "\fBIsCmpd3D\fR" 4 +.IX Item "IsCmpd3D" +.Vb 1 +\& $Status = IsCmpd3D(); +.Ve +.Sp +Returns 1 or 0 based on whether z\-coordinate of any atom is non-zero. +.IP "\fBMDLBondStereoToInternalBondStereochemistry\fR" 4 +.IX Item "MDLBondStereoToInternalBondStereochemistry" +.Vb 2 +\& $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry( +\& $MDLBondStereo); +.Ve +.Sp +Returns value of \fIInternalBondStereo\fR corresponding to \fIMDLBondStereo\fR using +mapping shown for \fBInternalBondStereochemistryToMDLBondStereo\fR function. +.IP "\fBMDLBondTypeToInternalBondOrder\fR" 4 +.IX Item "MDLBondTypeToInternalBondOrder" +.Vb 1 +\& $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType); +.Ve +.Sp +Returns value of \fIInternalBondOrder\fR corresponding to \fIMDLBondType\fR using +mapping shown for \fBInternalBondOrderToMDLBondType\fR function. +.IP "\fBMDLChargeToInternalCharge\fR" 4 +.IX Item "MDLChargeToInternalCharge" +.Vb 1 +\& $InternalCharge = MDLChargeToInternalCharge($MDLCharge); +.Ve +.Sp +Returns value of \fI\f(CI$InternalCharge\fI\fR corresponding to \fIMDLCharge\fR using +mapping shown for \fBInternalChargeToMDLCharge\fR function. +.IP "\fBMDLRadicalToInternalSpinMultiplicity\fR" 4 +.IX Item "MDLRadicalToInternalSpinMultiplicity" +.Vb 2 +\& $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity( +\& $MDLRadical); +.Ve +.Sp +Returns value of \fIInternalSpinMultiplicity\fR corresponding to \fIMDLRadical\fR. These +value are equivalent. +.IP "\fBParseCmpdAtomAliasPropertyLine\fR" 4 +.IX Item "ParseCmpdAtomAliasPropertyLine" +.Vb 2 +\& @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine( +\& $CurrentLine, $NexLine); +.Ve +.Sp +Parses atom alias propery lines in \s-1CTAB\s0 generic properties block and returns an array +with successive pairs of values corresponding to atom number and its alias. +.IP "\fBParseCmpdAtomLine\fR" 4 +.IX Item "ParseCmpdAtomLine" +.Vb 2 +\& ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge, +\& $StereoParity) = ParseCmpdAtomLine($AtomDataLine); +.Ve +.Sp +Parses compound data line containing atom information and returns a list +of values. +.IP "\fBParseCmpdBondLine\fR" 4 +.IX Item "ParseCmpdBondLine" +.Vb 2 +\& ($FirstAtomNum, $SecondAtomNum, $BondType) = +\& ParseCmpdBondLine($BondDataLine); +.Ve +.Sp +Parses compound data line containing bond information and returns a list of +values. +.IP "\fBParseCmpdCommentsLine\fR" 4 +.IX Item "ParseCmpdCommentsLine" +.Vb 1 +\& $Comments = ParseCmpdCommentsLine($CommentsDataLine); +.Ve +.Sp +Returns the comment string. +.IP "\fBParseCmpdChargePropertyLine\fR" 4 +.IX Item "ParseCmpdChargePropertyLine" +.Vb 2 +\& @AtomNumAndValuePairs = ParseCmpdChargePropertyLine( +\& $ChargeDataLine); +.Ve +.Sp +Parses charge propery line in \s-1CTAB\s0 generic properties block and returns an array +with successive pairs of values corresponding to atom number and its charge. +.IP "\fBParseCmpdCountsLine\fR" 4 +.IX Item "ParseCmpdCountsLine" +.Vb 2 +\& ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) = +\& ParseCmpdCountsLine(\e@CountDataLines); +.Ve +.Sp +Returns a list of values containing count information. +.IP "\fBParseCmpdMiscInfoLine\fR" 4 +.IX Item "ParseCmpdMiscInfoLine" +.Vb 2 +\& ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2, +\& $Energy, $RegistryNum) = ParseCmpdMiscInfoLine($Line); +.Ve +.Sp +Returns a list of values containing miscellaneous information. +.IP "\fBParseCmpdIsotopePropertyLine\fR" 4 +.IX Item "ParseCmpdIsotopePropertyLine" +.Vb 2 +\& @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine( +\& $IsotopeDataLine); +.Ve +.Sp +Parses isotopic propery line in \s-1CTAB\s0 generic properties block and returns an array +with successive pairs of values corresponding to atom number and absolute mass of +atom isotope. +.IP "\fBParseCmpdMolNameLine\fR" 4 +.IX Item "ParseCmpdMolNameLine" +.Vb 1 +\& $MolName = ParseCmpdMolNameLine($Line); +.Ve +.Sp +Returns a string containing molecule name. +.IP "\fBParseCmpdRadicalPropertyLine\fR" 4 +.IX Item "ParseCmpdRadicalPropertyLine" +.Vb 2 +\& @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine( +\& $RadicalDataLine); +.Ve +.Sp +Parses radical propery line in \s-1CTAB\s0 generic properties block and returns an array +with successive pairs of values corresponding to atom number and radical number +value. +.IP "\fBRemoveCmpdDataHeaderLabelAndValue\fR" 4 +.IX Item "RemoveCmpdDataHeaderLabelAndValue" +.Vb 2 +\& $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString, +\& $DataHeaderLabel); +.Ve +.Sp +Returns a \fBNewCmpdString\fR after removing \fIDataHeaderLabel\fR along with its +value from \fICmpdString\fR. +.IP "\fBReadCmpdString\fR" 4 +.IX Item "ReadCmpdString" +.Vb 1 +\& $CmpdString = ReadCmpdString(\e*SDFILEHANDLE); +.Ve +.Sp +Returns a string containing all the data lines for the next available compound +in an already open file indicated by \s-1SDFILEHANDLE\s0. A \s-1NULL\s0 string is returned +on \s-1EOF\s0. +.IP "\fBWashCmpd\fR" 4 +.IX Item "WashCmpd" +.Vb 2 +\& ($FragmentCount, $Fragments, $WashedCmpdString) = +\& WashCmpd(\e@CmpdLines); +.Ve +.Sp +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 \fBFragmentString\fR is sorted on based on its size. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +TextUtil.pm +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.