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
GetChainLenAbbrevDbleBondGeometryDataMap - Get reference to supported double bond geometry data
GetChainLengthAndMultipleBondCount - Get chain length and number of double and triple bonds
GetChainLenToNamePrefixMap - Get chain name prefix
GetCountToNamePrefixMap - Get count prefix
GetSubstituentsAbbrevToNameMap - Get substituents name
GetSubstituentBondOrder - Get substituent bond order
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
IsDoubleBondsAbbrevOkay - Is it a valid double bond abbreviation
IsRingsAbbrevOkay - Is it a valid ring abbreviation
IsSubstituentsAbbrevOkay - Is it a valid substituent abbreviation
IsWildCardInChainAbbrev - Does chain abbreviation contains a wild card
ParseChainAbbrev - Parse chain abbreviation
ParseRingAbbrev - Parse ring abbreviation
ParseSubstituentAbbrev - Parse substituent abbreviation
SetupChainSubstituentsName - Set up substituent name

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.
GetChainLenAbbrevDbleBondGeometryDataMap: $ChainLenDblBondHashRef = GetChainLenAbbrevDbleBondGeometryDataMap();

Return a reference to hash containing information about chain length, number of double bonds and geometry of double bonds.
GetChainLengthAndMultipleBondCount: ($ChainLength, $DoubleBondCount, $TripleBondCount) = GetChainLengthAndMultipleBondCount($ChainAbbrev);

Parse chain abbreviation and return these values: chain length; number of double and triple bonds.
GetChainLenToNamePrefixMap: $ChainNameHashRef = GetChainLenToNamePrefixMap();

Return a reference to hash with chain length/name prefix as key/value pair.
GetCountToNamePrefixMap: $CountHashRef = GetCountToNamePrefixMap();

Return a reference to hash with count/name prefix as key/value pair.
GetSubstituentsAbbrevToNameMap: $AbbrevNameHashRef = GetSubstituentsAbbrevToNameMap();

Return a reference to hash with substituents abbreviation/name as key/value pair.
GetSubstituentBondOrder: $BondOrder = GetSubstituentBondOrder($SubstituentAbbrev);

Return bond order for a sustituent.
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.
IsDoubleBondsAbbrevOkay: $Status = IsDoubleBondsAbbrevOkay($ChainAbbrev, $ChainLength, $DoubleBondCount, $DoubleBondGeometry);

Return 1 or 0 based on whether chain abbreviation contains a valid multiple bond specification.
IsRingsAbbrevOkay: $Status = IsRingsAbbrevOkay($ChainAbbrev, $ChainLength, $Rings);

Return 1 or 0 based on whether chain abbreviation contains a valid ring specification.
IsSubstituentsAbbrevOkay: $Status = IsSubstituentsAbbrevOkay($ChainAbbrev, $ChainLength, $DoubleBondCount, $DoubleBondGeometry, $Substituents);

Return 1 or 0 based on whether chain abbreviation contains a valid substituents specification.
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.
ParseRingAbbrev: ($Pos, $StereoChemistry) = ParseRingAbbrev($ChainAbbrev);

Parse chain abbreviation and return these values: ring position and stereochemistry specificaton at the ring.
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.
SetupChainSubstituentsName: $SubstituentsName = SetupChainSubstituentsName( $CmpdAbbrevTemplateDataMapRef, $ChainIndex);

Return systematic name for substituents after ordering and grouping substituents by their position.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License