NAME
GLStr - Glycerolipids (GL) structure generation methods
SYNOPSIS
use GLStr;
use GLStr qw(:all);
DESCRIPTION
GLStr module provides these methods:
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateGLChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
IsGLAbbrevSupported - Is it a supported GL abbreviation
ParseGLAbrev - Parse GL abbreviation
ProcessGLCmpdAbbrevs - Process GL abbreviation
SetupGLCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateGLAbbrev - Validate GL abbreviation
METHODS
- ExpandGLCmpdAbbrevs
-
$ExpandedAbbrevArrayRef = ExpandGLCmpdAbbrevs($CmpdAbbrev);
Return a reference to an array containing complete GL abbreviations. Wild card characters in GL abbreviation name are expanded to generate fully qualified GL 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.
- GenerateGLChainStrData
-
($AtomLinesArrayRef, $BondLinesArrayRef) =
GenerateGLChainStrData($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.
- IsGLAbbrevSupported
-
$Status = IsGLAbbrevSupported($Abbrev, $PrintWarning);
Return 1 or 0 based on whether GL abbreviated is supported. For unsupported GL abbreviations, a warning is printed unless PrintWarning flag is set.
- ParseGLAbrev
-
($GLType, $ChainsAbbrev, $AbbrevModifier) = ParseGLAbrev($Abbrev);
Parse GL abbreviation and return these values: GLType, ChainsAbbrev, AbbrevModifier.
- ProcessGLCmpdAbbrevs
-
ProcessGLCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev,
$WriteSDFile, $SDFileName);
Process specified GL abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
- SetupGLCmpdAbbrevTemplateDataMap
-
$AbbrevTemplateDataMapRef =
SetupGLCmpdAbbrevTemplateDataMap($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.
- ValidateGLAbbrev
-
$Status = ValidateGLAbbrev($Abbrev);
Return 1 or 0 based on whether a GL abbreviation is valid.
AUTHOR
Return a reference to an array containing complete GL abbreviations. Wild card characters in GL abbreviation name are expanded to generate fully qualified GL abbreviations.
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 GL abbreviated is supported. For unsupported GL abbreviations, a warning is printed unless PrintWarning flag is set.
Parse GL abbreviation and return these values: GLType, ChainsAbbrev, AbbrevModifier.
Process specified GL 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 GL 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