NAME
SPStr - Sphingolipids (SP) structure generation methods
SYNOPSIS
use SPStr;
use SPStr qw(:all);
DESCRIPTION
SPStr module provides these methods:
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
ProcessSPCmpdAbbrevs - Process SP abbreviation
SetupSPCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateSPAbbrev - Validate SP 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.
- 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.
- ProcessSPCmpdAbbrevs
-
ProcessSPCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev,
$WriteSDFile, $SDFileName);
Process specified SP abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
- 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.
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 SP 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 SP abbreviated is supported. For unsupported SP abbreviations, a warning is printed unless PrintWarning flag is set.
Parse SP abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
Process specified SP 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 SP abbreviation is valid.
CONTRIBUTOR
SEE ALSO
COPYRIGHT
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
LICENSE
Modified BSD License