NAME
CLStr - Cardiolipins (CL) structure generation methods
SYNOPSIS
use CLStr;
use CLStr qw(:all);
DESCRIPTION
CLStr module provides these methods:
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateCLChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
GetCLTemplatesData - Get templates data
GetCLSupportedHeadGroupMap - Get supported headgroups data
GetCLTemplateID - Get templates ID
IsCLChainsAbbrevSupported - Is it a supported CL abbreviation
ParseCLAbbrev - Parse CL abbreviation
ProcessCLCmpdAbbrevs - Process CL abbreviation
SetupCLCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateCLAbbrev - Validate CL abbreviation
METHODS
- GenerateCmpdOntologyData
-
$DataHashRef = GenerateCmpdOntologyData($CmpDataRef);
Return a reference to a hash containing ontology data with hash keys and values corresponding to property names and values.
- GenerateCmpdOntologySDDataLines
-
$DataLinesArrayRef = GenerateCmpdOntologySDDataLines($CmpdDataRef);
Return a reference to an array containing ontology data lines suitable for generate SD file data block.
- GenerateCLChainStrData
-
($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateCLChainStrData($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.
- GetCLTemplatesData
-
$TemplatesDataRef = GetCLTemplatesData();
Return a reference to a hash containing CL templates data
- GetCLSupportedHeadGroupMap
-
$SupportedHeadGroupDataRef = GetCLSupportedHeadGroupMap();
Return a reference to a hash containing supported head groups data.
- GetCLTemplateID
-
$HeadGroupID = GetCLTemplateID($HeadGroupAbbrev, $ChainsAbbrev);
Return a supported template ID for compound abbreviation.
- IsCLChainsAbbrevSupported
-
$Status = IsCLChainsAbbrevSupported($Abbrev, $PrintWarning);
Return 1 or 0 based on whether CL abbreviated is supported. For unsupported CL abbreviations, a warning is printed unless PrintWarning flag is set.
- ParseCLAbbrev
-
($HeadGroup, $ChainsAbbrev, $AbbrevModifier) = ParseCLAbbrev($Abbrev);
Parse CL abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
- ProcessCLCmpdAbbrevs
-
ProcessCLCmpdAbbrevs($CmpdAbbrevsRef, $AllowArbitraryChainAbbrev, $WriteSDFile, $SDFileName);
Process specified CL abbreviations to generate structures and write them out either a SD file or simply report number of valid abbreviations.
- SetupCLCmpdAbbrevTemplateDataMap
-
$AbbrevTemplateDataMapRef = SetupCLCmpdAbbrevTemplateDataMap($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.
- ValidateCLAbbrev
-
$Status = ValidateCLAbbrev($Abbrev);
Return 1 or 0 based on whether a CL abbreviation is valid.
AUTHOR
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