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NAME

GPStr - Glycerolipids (GP) structure generation methods

SYNOPSIS

use GPStr;

use GPStr qw(:all);

DESCRIPTION

GPStr module provides these methods:

GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateGPChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
GetGPTemplatesData - Get templates data
GetGPSupportedHeadGroupMap - Get supported headgroups data
GetGPTemplateID - Get templates ID
IsGPChainsAbbrevSupported - Is it a supported GP abbreviation
ParseGPAbbrev - Parse GP abbreviation
ProcessGPCmpdAbbrevs - Process GP abbreviation
SetupGPCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateGPAbbrev - Validate GP abbreviation

METHODS

GenerateCmpdOntologyData
$DataHashRef = GenerateCmpdOntologyData($CmpDataRef);

Return a reference to a hash containing ontology data with hash keys and values corresponding to property names and values.

GenerateCmpdOntologySDDataLines
$DataLinesArrayRef = GenerateCmpdOntologySDDataLines($CmpdDataRef);

Return a reference to an array containing ontology data lines suitable for generate SD file data block.

GenerateGPChainStrData
($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateGPChainStrData($ChainType, $CmpdDataRef);

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.

GenerateSDFile
GenerateSDFile($SDFileName, $CmdAbbrevsRef);

Generate a SD file for compound abbreviations. Structure data for specified abbreviation is generated sequentially and written to SD file.

GetGPTemplatesData
$TemplatesDataRef = GetGPTemplatesData();

Return a reference to a hash containing GP templates data

GetGPSupportedHeadGroupMap
$SupportedHeadGroupDataRef = GetGPSupportedHeadGroupMap();

Return a reference to a hash containing supported head groups data.

GetGPTemplateID
$HeadGroupID = GetGPTemplateID($HeadGroupAbbrev, $ChainsAbbrev);

Return a supported template ID for compound abbreviation.

IsGPChainsAbbrevSupported
$Status = IsGPChainsAbbrevSupported($Abbrev, $PrintWarning);

Return 1 or 0 based on whether GP abbreviated is supported. For unsupported GP abbreviations, a warning is printed unless PrintWarning flag is set.

ParseGPAbbrev
($HeadGroup, $ChainsAbbrev, $AbbrevModifier) = ParseGPAbbrev($Abbrev);

Parse GP abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.

ProcessGPCmpdAbbrevs
ProcessGPCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev, $WriteSDFile, $SDFileName);

Process specified GP abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.

SetupGPCmpdAbbrevTemplateDataMap
$AbbrevTemplateDataMapRef = SetupGPCmpdAbbrevTemplateDataMap($Abbrev);

Return a reference to a hash containing template data for compound abbreviation. The template data is used to generate SD file for compound abbreviation.

ValidateGPAbbrev
$Status = ValidateGPAbbrev($Abbrev);

Return 1 or 0 based on whether a GP abbreviation is valid.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

SEE ALSO

ChainAbbrev.pmChainStr.pmLMAPSStr.pm

COPYRIGHT

Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.

LICENSE

Modified BSD License