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

COPYRIGHT

LICENSE

Modified BSD License