LIPID Metabolites And Pathways Strategy

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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
SetupTemplateDataMap - Set up template data for a compound abbreviation

METHODS

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.

SetupTemplateDataMap
SetupTemplateDataMap($TemplateType, $AbbrevTemplateDataMapRef, $TemplateData);

Setup compound abbreviation template data using a supported template.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

SEE ALSO

GLStr.pm, GPStr.pm

COPYRIGHT

Copyright (C) 2006. The Regents of the University of California. All Rights Reserved.