NAME
FAStr - Fatty Acyls (FA) structure generation methods
SYNOPSIS
use FAStr;
use FAStr qw(:all);
DESCRIPTION
FAStr module provides these methods:
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
- 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.
- ProcessFACmpdAbbrevs
-
ProcessFACmpdAbbrevs($CmpdAbbrevsRef, $WriteSDFile, $SDFileName);
Process specified FA abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
- 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
Return a reference to a hash containing ontology data with hash keys and values corresponding to property names and values.
Return a reference to an array containing ontology data lines suitable for generate SD file data block.
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.
Generate a SD file for compound abbreviations. Structure data for specified abbreviation is generated sequentially and written to SD file.
Return 1 or 0 based on whether FA abbreviated is supported. For unsupported FA abbreviations, a warning is printed unless PrintWarning flag is set.
Parse FA abbreviation and return these values: ChainsAbbrev and AbbrevModifier.
Process specified FA abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
Return a reference to a hash containing template data for compound abbreviation. The template data is used to generate SD file for compound abbreviation.
Return 1 or 0 based on whether a FA abbreviation is valid.
CONTRIBUTOR
SEE ALSO
ChainAbbrev.pm, ChainStr.pm, LMAPSStr.pm, 
COPYRIGHT
Copyright (C) 2006-2017. The Regents of the University of California. All Rights Reserved.
LICENSE
Modified BSD License