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
Assign stereochemistry to substituents using structure and stereochemistry data available via $CmpdAbbrevTemplateDataMapRef and $CmdDataLinesRef. And add new lines to existing structure data using $CmdDataLinesRef.
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.
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.
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.
Return a formatted count data line for SD file.
Return 1 or 0 based on whether stereochemistry is specifed for any substituent.
Setup compound abbreviation template data using a supported template.
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