NAME
GPStr - Glycerolipids (GP) structure generation methods
SYNOPSIS
use GPStr;
use GPStr qw(:all);
DESCRIPTION
GPStr module provides these methods:
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
Return a reference to a hash containing ontology data with hash keys and values corresponding to property names and values.
Return a reference to an array containing ontology data lines suitable for generate SD file data block.
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.
Generate a SD file for compound abbreviations. Structure data for specified abbreviation is generated sequentially and written to SD file.
Return a reference to a hash containing GP templates data
Return a reference to a hash containing supported head groups data.
Return a supported template ID for compound abbreviation.
Return 1 or 0 based on whether GP abbreviated is supported. For unsupported GP abbreviations, a warning is printed unless PrintWarning flag is set.
Parse GP abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
Process specified GP abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
Return a reference to a hash containing template data for compound abbreviation. The template data is used to generate SD file for compound abbreviation.
Return 1 or 0 based on whether a GP abbreviation is valid.
CONTRIBUTOR
SEE ALSO
ChainAbbrev.pm, ChainStr.pm, LMAPSStr.pm,
COPYRIGHT
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
LICENSE
Modified BSD License