NAME
    FAStr - Fatty Acyls (FA) structure generation methods

SYNOPSIS
    use FAStr;

    use FAStr qw(:all);

DESCRIPTION
    FAStr module provides these methods:

        GenerateCmpdOntologyData - Generate ontology data
        GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
        GenerateFAChainStrData - Generate chain structure data
        GenerateSDFile - Generate SD file
        IsFAAbbrevSupported - Is it a supported FA abbreviation
        ParseFAAbrev - Parse FA abbreviation
        SetupFACmpdAbbrevTemplateDataMap - Setup template structure data map
        ValidateFAAbbrev - Validate FA abbreviation

METHODS
    GenerateCmpdOntologyData
            $DataHashRef = GenerateCmpdOntologyData($CmpdDataRef);

        Return a reference to a hash containing ontology data with hash keys
        and values corresponding to property names and values.

    GenerateCmpdOntologySDDataLines
            $DataLinesArrayRef = GenerateCmpdOntologySDDataLines($CmpDataRef);

        Return a reference to an array containing ontology data lines
        suitable for generate SD file data block.

    GenerateFAChainStrData
            ($AtomLinesArrayRef, $BondLinesArrayRef) =
               GenerateFAChainStrData($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.

    IsFAAbbrevSupported
            $Status = IsFAAbbrevSupported($Abbrev, $PrintWarning);

        Return 1 or 0 based on whether FA abbreviated is supported. For
        unsupported FA abbreviations, a warning is printed unless
        PrintWarning flag is set.

    ParseFAAbrev
            ($ChainAbbrev, $AbbrevModifier) = ParseFAAbrev($Abbrev);

        Parse FA abbreviation and return these values: ChainsAbbrev and
        AbbrevModifier.

    ProcessFACmpdAbbrevs
            ProcessFACmpdAbbrevs($CmpdAbbrevsRef, $WriteSDFile, $SDFileName);

        Process specified FA abbreviations to generate structures and write
        them out either a SD file or simply report number of valid
        abbreviations.

    SetupFACmpdAbbrevTemplateDataMap
            $AbbrevTemplateDataMapRef =
               SetupFACmpdAbbrevTemplateDataMap($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.

    ValidateFAAbbrev
            $Status = ValidateFAAbbrev($Abbrev);

        Return 1 or 0 based on whether a FA abbreviation is valid.

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    ChainAbbrev.pm, ChainStr.pm, LMAPSStr.pm

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

LICENSE
    Modified BSD License

