NAME
ChainStr - Fatty Acyls (FA), Glycerolipids (GL) and Glycerophospholipids (GP) structure data generation methods
SYNOPSIS
use ChainStr;
use ChainStr qw(:all);
DESCRIPTION
ChainStr module provides these methods:
GenerateAtomBlockLines - Generate SD file atom data lines
GenerateBondBlockLines - Generate SD file bond data lines
GenerateChainStrData - Generate structure data for chains
GenerateCmpdCountsLine - Generate SD file count data line
IsAnySubstituentSpecifiedWithStereoChemistry - Check stereochemistry of substituents
SetupTemplateDataMap - Set up template data for a compound abbreviation
METHODS
- AssignSubstituentStereoChemistry
-
AssignSubstituentStereoChemistry($CmpdAbbrevTemplateDataMapRef, $CmdDataLinesRef);
Assign stereochemistry to substituents using structure and stereochemistry data available via $CmpdAbbrevTemplateDataMapRef and $CmdDataLinesRef. And add new lines to existing structure data using $CmdDataLinesRef.
- GenerateAtomBlockLines
-
$AtomDataLines = GenerateAtomBlockLines($CmpdAbbrevTemplateDataMapRef, $Sn1AtomLinesRef, $Sn2AtomLinesRef, $Sn3AtomLinesRef);
Return atom data lines suitable for writing to SD file. Atom data for all approrpriate chains is merged into a single string using new line character as delimiter.
- GenerateBondBlockLines
-
$BondDataLines = GenerateBondBlockLines($CmpdAbbrevTemplateDataMapRef, $Sn1BondLinesRef, $Sn2AtomLinesRef, $Sn3AtomLinesRef);
Return bond data lines suitable for writing to SD file. Bond data for all approrpriate chains is merged into a single string using new line character as delimiter.
- GenerateChainStrData
-
($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateChainStrData($ChainType, $CmpdAbbrevTemplateDataMapRef);
Return array references containing atom and bond data lines for SD file. Appropriate atom and bond data lines are generated using chain type and abbreviation template data.
- GenerateCmpdCountsLine
-
$RetValue = GenerateCmpdCountsLine($CmpdAbbrevTemplateDataMapRef);
Return a formatted count data line for SD file.
- IsAnySubstituentSpecifiedWithStereoChemistry
-
$Status = IsAnySubstituentSpecifiedWithStereoChemistry( $CmpdAbbrevTemplateDataMapRef);
Return 1 or 0 based on whether stereochemistry is specifed for any substituent.
- SetupTemplateDataMap
-
SetupTemplateDataMap($TemplateType, $AbbrevTemplateDataMapRef, $TemplateData);
Setup compound abbreviation template data using a supported template.
AUTHOR
CONTRIBUTOR
SEE ALSO
FAStr.pm, GLStr.pm, GPStr.pm, LMAPSStr.pm, SPStr.pm,
COPYRIGHT
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
LICENSE
Modified BSD License