LIPID Metabolites And Pathways Strategy

NAME

ChainAbbrev - Methods for processing chain abbreviations

SYNOPSIS

use ChainAbbrev;

use ChainAbbrev qw(:all);

DESCRIPTION

ChainAbbrev module provides these methods:

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

SEE ALSO

LMAPSStr.pm, ChainStr.pm

COPYRIGHT

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

LICENSE

Modified BSD License