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NAME
FAStr - Fatty Acyls (FA) structure generation methods
SYNOPSIS
use FAStr;
use FAStr qw(:all);
DESCRIPTION
FAStr module provides these methods:
GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateFAChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
IsFAAbbrevSupported - Is it a supported FA abbreviation
ParseFAAbrev - Parse FA abbreviation
SetupFACmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateFAAbbrev - Validate FA abbreviation
METHODS
- ExpandFACmpdAbbrevs
-
$ExpandedAbbrevArrayRef = ExpandFACmpdAbbrevs($CmpdAbbrev);
-
Return a reference to an array containing complete FA abbreviations. Wild card characters in FA abbreviation name are expanded to generate fully qualified FA 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.
- GenerateFAChainStrData
-
($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateFAChainStrData($ChainType, $CmpdDataRef);
-
Return array references containing atom and bond data lines for SD file. Appropriate atom and bond data lines are generated using chain type and abbreviation template data.
- GenerateSDFile
-
GenerateSDFile($SDFileName, $CmdAbbrevsRef);
-
Generate a SD file for compound abbreviations. Structure data for specified abbreviation is generated sequentially and written to SD file.
- IsFAAbbrevSupported
-
$Status = IsFAAbbrevSupported($Abbrev, $PrintWarning);
-
Return 1 or 0 based on whether FA abbreviated is supported. For unsupported FA abbreviations, a warning is printed unless PrintWarning flag is set.
- ParseFAAbrev
-
($ChainAbbrev, $AbbrevModifier) = ParseFAAbrev($Abbrev);
-
Parse FA abbreviation and return these values: ChainsAbbrev and AbbrevModifier.
- SetupFACmpdAbbrevTemplateDataMap
-
$AbbrevTemplateDataMapRef = SetupFACmpdAbbrevTemplateDataMap($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.
- ValidateFAAbbrev
-
$Status = ValidateFAAbbrev($Abbrev);
-
Return 1 or 0 based on whether a FA abbreviation is valid.
AUTHOR
CONTRIBUTOR
SEE ALSO
ChainAbbrev.pm, ChainStr.pm, LMAPSStr.pm
COPYRIGHT
Copyright (C) 2006-2008. The Regents of the University of California. All Rights Reserved.
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