NAME
    ChainAbbrev - Methods for processing chain abbreviations

SYNOPSIS
    use ChainAbbrev;

    use ChainAbbrev qw(:all);

DESCRIPTION
    ChainAbbrev module provides these methods:

        ChainAbbrevNameExists - Is it a supported chain abbreviation
        ExpandChainAbbrev - Expand wild cards in chain abbreviation
        GetChainAbbrevToNameMap - Get chain name
        GetChainLenAbbrevSupportedMap - Get reference to supported chain
                                        abbreviations data
        GetChainLenAbbrevDbleBondGeometyDataMap - Get reference to supported chain
                                                  double bond geometry data
        GetSubstituentsAbbrevToNameMap - Get substituents name
        GetSupportedChainLenList - Get supported chain lengths
        IsAlkylChainAbbrev - Is it a alkyl chain abbreviation
        IsAlkenylChainAbbrev - Is it a alkenyl chain abbreviation
        IsChainAbbrevOkay - Is it a valid chain abbreviation
        IsWildCardInChainAbbrev - Does chain abbreviation contains a wild card
        ParseChainAbbrev - Parse chain abbreviation
        ParseSubstituentAbbrev - Parse substituent abbreviation

METHODS
    ChainAbbrevNameExists
            $Status = ChainAbbrevNameExists($ChainAbbrev);

        Return 1 or 0 based on whether it's a supported chain name.

    ExpandChainAbbrev
            $AbbrevArrayRef = ExpandChainAbbrev($Abbrev);

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

    GetChainAbbrevToNameMap
            $AbbrevNameHashRef = GetChainAbbrevToNameMap();

        Return a reference to hash with chain abbreviation/name as key/value
        pair.

    GetChainLenAbbrevSupportedMap
            $ChainLenHashRef = GetChainLenAbbrevSupportedMap();

        Return a reference to hash with supported chain length as hash key.

    GetChainLenAbbrevDbleBondGeometyDataMap
            $ChainLenDblBondHashRef = GetChainLenAbbrevDbleBondGeometyDataMap();

        Return a reference to hash containing information about chain
        length, number of double bonds and geometry of double bonds.

    GetSubstituentsAbbrevToNameMap
            $AbbrevNameHashRef = GetSubstituentsAbbrevToNameMap();

        Return a reference to hash with substituents abbreviation/name as
        key/value pair.

    GetSupportedChainLenList
            $ChainLengthListRef = GetSupportedChainLenList();

        Return a reference to a sorted list containing supported chain
        lengths.

    IsAlkylChainAbbrev
            $Status = IsAlkylChainAbbrev($ChainAbbrev);

        Return 1 or 0 based on whether it's a alkyl chain abbreviation.

    IsAlkenylChainAbbrev
            $Status = IsAlkenylChainAbbrev($ChainAbbrev);

        Return 1 or 0 based on whether it's a alkenyl chain abbreviation.

    IsChainAbbrevOkay
            $Status = IsChainAbbrevOkay($ChainAbbrev);

        Return 1 or 0 based on whether chain abbreviation is valid.

    IsWildCardInChainAbbrev
            $Status = IsWildCardInChainAbbrev($ChainAbbrev);

        Return 1 or 0 based on whether chain abbreviation contains any wild
        card character.

    ParseChainAbbrev
            ($ChainLength, $DoubleBondCount, $DoubleBondGeometry) =
                ParseChainAbbrev($ChainAbbrev);

        Parse chain abbreviation and return these values: chain length,
        number of double bonds, and geometry of double bonds.

    ParseSubstituentAbbrev
            ($Pos, $Name, $StereoChemistry) =
                ParseSubstituentAbbrev($SubstituentAbbrev);

        Parse substituent abbreviation and return these values: position of
        the substituent on the chain, name, and stereochemistry of the
        substituent.

AUTHOR
    Manish Sud

CONTRIBUTOR
    Eoin Fahy

SEE ALSO
    LMAPSStr.pm, ChainStr.pm

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

