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
        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
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    ChainStr.pm

COPYRIGHT
    Copyright (C) 2006-2012. The Regents of the University of California.
    All Rights Reserved.

LICENSE
    Modified BSD License

