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NAME
SPStr - Sphingolipids (SP) structure generation methods
SYNOPSIS
use SPStr;
use SPStr qw(:all);
DESCRIPTION
SPStr module provides these methods:
GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateSPChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
GetSPTemplatesData - Get templates data
GetSPSupportedHeadGroupMap - Get supported headgroups data
GetSPTemplateID - Get templates ID
IsSPChainsAbbrevSupported - Is it a supported SP abbreviation
ParseSPAbbrev - Parse SP abbreviation
SetupSPCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateSPAbbrev - Validate SP abbreviation
METHODS
- ExpandSPCmpdAbbrevs
-
$ExpandedAbbrevArrayRef = ExpandSPCmpdAbbrevs($CmpdAbbrev);
-
Return a reference to an array containing complete SP abbreviations. Wild card characters in SP abbreviation name are expanded to generate fully qualified SP abbreviations.
- 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.
- GenerateSPChainStrData
-
($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateSPChainStrData($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.
- GetSPTemplatesData
-
$TemplatesDataRef = GetSPTemplatesData();
-
Return a reference to a hash containing SP templates data
- GetSPSupportedHeadGroupMap
-
$SupportedHeadGroupDataRef = GetSPSupportedHeadGroupMap();
-
Return a reference to a hash containing supported head groups data.
- GetSPTemplateID
-
$HeadGroupID = GetSPTemplateID($HeadGroupAbbrev, $ChainsAbbrev);
-
Return a supported template ID for compound abbreviation.
- IsSPChainsAbbrevSupported
-
$Status = IsSPChainsAbbrevSupported($Abbrev, $PrintWarning);
-
Return 1 or 0 based on whether SP abbreviated is supported. For unsupported SP abbreviations, a warning is printed unless PrintWarning flag is set.
- ParseSPAbbrev
-
($HeadGroup, $ChainsAbbrev, $AbbrevModifier) = ParseSPAbbrev($Abbrev);
-
Parse SP abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
- SetupSPCmpdAbbrevTemplateDataMap
-
$AbbrevTemplateDataMapRef = SetupSPCmpdAbbrevTemplateDataMap($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.
- ValidateSPAbbrev
-
$Status = ValidateSPAbbrev($Abbrev);
-
Return 1 or 0 based on whether a SP abbreviation is valid.
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COPYRIGHT
Copyright (C) 2006-2008. The Regents of the University of California. All Rights Reserved.
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