NAME
    STStr - Sterol (ST) structure generation methods

SYNOPSIS
    use STStr;

    use STStr qw(:all);

DESCRIPTION
    STStr module provides these methods:

        ExpandSTCmpdAbbrevs - Expand ST abbreviation
        GenerateCmpdOntologyData - Generate ontology data
        GenerateCmpdOntologySDDataLines - Generate ontology data lines for
                                          SD file
        GenerateSTStrData - Generate structure data
        GenerateSDFile - Generate SD file
        IsSTAbbrevSupported - Is it a supported ST abbreviation
        IsSTSubstituentsNameSupported - Is it a supported ST substituent name
        IsSTDoubleBondsAbbrevOkay - Is it a valid ST double bond abbreviation
        IsSTSubstituentsAbbrevOkay - Is it a valid ST substituent abbreviation
        IsWildCardInSTAbbrev - Does ST abbreviatio contains a wild card
        ParseSTAbrev - Parse ST abbreviation
        ParseSTDoubleBondAbbrev - Parse ST double bond abbreviation
        ParseSTSubstituentAbbrev - Parse ST substituent abbreviation
        SetupSTCmpdAbbrevTemplateDataMap - Setup template structure data map
        ValidateSTAbbrev - Validate ST abbreviation

METHODS
    ExpandSTCmpdAbbrevs
            $ExpandedAbbrevArrayRef = ExpandSTCmpdAbbrevs($CmpdAbbrev);

        Return a reference to an array containing complete ST abbreviations.
        Wild card characters in ST abbreviation name are expanded to
        generate fully qualified ST abbreviations.

    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.

    GenerateSTStrData
            ($AtomLinesArrayRef, $BondLinesArrayRef) =
               GenerateSTStrData($CmpdDataRef);

        Return array references containing atom and bond data lines for SD
        file. Appropriate atom and bond data lines are generated using
        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.

    IsSTAbbrevSupported
            $Status = IsSTAbbrevSupported($Abbrev);

        Return 1 or 0 based on whether ST abbreviation is supported.

    IsSTSubstituentsNameSupported
            $Status = IsSTSubstituentsNameSupported($SubstituentAbbrev);

        Return 1 or 0 based on whether ST substituent abbreviation is
        supported.

    IsSTDoubleBondsAbbrevOkay
            $Status = IsSTDoubleBondsAbbrevOkay($STAbbrev, $STType,
               $SubstituentsAbbrev, $DoubleBondsAbbrev);

        Return 1 or 0 based on whether ST double bond abbreviation is valid.

    IsSTSubstituentsAbbrevOkay
            $Status = IsSTSubstituentsAbbrevOkay($STAbbrev, $STType,
               $SubstituentsAbbrev, $DoubleBondsAbbrev);

        Return 1 or 0 based on whether ST substituent abbreviation is valid.

    IsWildCardInSTAbbrev
            $Status = IsSTAbbrevSupported($Abbrev);

        Return 1 or 0 based on whether ST abbreviation contains wild card.

    ParseSTAbbrev
            ($STType,  $SubstituentsAbbrev, $DoubleBondsAbbrev) =
                ParseSTAbrev($Abbrev);

        Parse ST abbreviation and return these values: STType,
        SubstituentsAbbrev, and DoubleBondsAbbrev.

    ParseSTDoubleBondAbbrev
            ($BondPos1, $BondPos1) = ParseSTDoubleBondAbbrev($Abbrev);

        Parse ST double bond abbreviation and return these values: BondPos1
        and BondPos2.

    ParseSTSubstituentAbbrev
            ($SubstituentPos, $SubstituentAbbrev, $StereoChemistry) =
               ParseSTSubstituentAbbrev($Abbrev);

        Parse ST substituents abbreviation and return these values:
        SubstituentPos, SubstituentAbbrev, and SubstituentStereoChemistry.

    SetupSTCmpdAbbrevTemplateDataMap
            $AbbrevTemplateDataMapRef =
               SetupSTCmpdAbbrevTemplateDataMap($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.

    ValidateSTAbbrev
            $Status = ValidateSTAbbrev($Abbrev);

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

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    ChainStr.pm, LMAPSStr.pm

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

LICENSE
    Modified BSD License

