NAME
ChainAbbrev - Methods for processing chain abbreviations
SYNOPSIS
use ChainAbbrev;
use ChainAbbrev qw(:all);
DESCRIPTION
ChainAbbrev module provides these methods:
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
Return 1 or 0 based on whether it's a supported chain name.
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.
Return a reference to hash with chain abbreviation/name as key/value pair.
Return a reference to hash with supported chain length as hash key.
Return a reference to hash containing information about chain length, number of double bonds and geometry of double bonds.
Parse chain abbreviation and return these values: chain length; number of double and triple bonds.
Return a reference to hash with chain length/name prefix as key/value pair.
Return a reference to hash with count/name prefix as key/value pair.
Return a reference to hash with substituents abbreviation/name as key/value pair.
Return bond order for a sustituent.
Return a reference to a sorted list containing supported chain lengths.
Return 1 or 0 based on whether it's a alkyl chain abbreviation.
Return 1 or 0 based on whether it's a alkenyl chain abbreviation.
Return 1 or 0 based on whether chain abbreviation is valid.
Return 1 or 0 based on whether chain abbreviation contains a valid multiple bond specification.
Return 1 or 0 based on whether chain abbreviation contains a valid ring specification.
Return 1 or 0 based on whether chain abbreviation contains a valid substituents specification.
Return 1 or 0 based on whether chain abbreviation contains any wild card character.
Parse chain abbreviation and return these values: chain length, number of double bonds, and geometry of double bonds.
Parse chain abbreviation and return these values: ring position and stereochemistry specificaton at the ring.
Parse substituent abbreviation and return these values: position of the substituent on the chain, name, and stereochemistry of the substituent.
Return systematic name for substituents after ordering and grouping substituents by their position.
CONTRIBUTOR
SEE ALSO
LMAPSStr.pm, ChainStr.pm, 
COPYRIGHT
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
LICENSE
Modified BSD License