NAME
LMStr - LIPID MAPS arbitrary structure generation methods
SYNOPSIS
use LMStr;
use LMStr qw(:all);
DESCRIPTION
LMStr module provides these methods:
GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateLMChainStrData - Generate chain structure data
GenerateSDFile - Generate SD file
GetLMTemplatesData - Get templates data
GetLMSupportedHeadGroupMap - Get supported headgroups data
GetLMTemplateID - Get templates ID
IsLMChainsAbbrevSupported - Is it a supported abbreviation
ParseLMAbbrev - Parse abbreviation
SetupLMCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateLMAbbrev - Validate abbreviation
METHODS
- ExpandLMCmpdAbbrevs
-
$ExpandedAbbrevArrayRef = ExpandLMCmpdAbbrevs($CmpdAbbrev);
Return a reference to an array containing complete LM abbreviations. Wild card characters in LM abbreviation name are expanded to generate fully qualified LM abbreviations.
- 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.
- GenerateLMChainStrData
-
($AtomLinesArrayRef, $BondLinesArrayRef) =
GenerateLMChainStrData($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.
- GetLMTemplatesData
-
$TemplatesDataRef = GetLMTemplatesData();
Return a reference to a hash containing LM templates data
- GetLMSupportedHeadGroupMap
-
$SupportedHeadGroupDataRef = GetLMSupportedHeadGroupMap();
Return a reference to a hash containing supported head groups data.
- GetLMTemplateID
-
$HeadGroupID = GetLMTemplateID($HeadGroupAbbrev, $ChainsAbbrev);
Return a supported template ID for compound abbreviation.
- IsLMChainsAbbrevSupported
-
$Status = IsLMChainsAbbrevSupported($Abbrev, $PrintWarning);
Return 1 or 0 based on whether LM abbreviated is supported. For unsupported LM abbreviations, a warning is printed unless PrintWarning flag is set.
- ParseLMAbbrev
-
($HeadGroup, $ChainsAbbrev, $AbbrevModifier) =
ParseLMAbbrev($Abbrev);
Parse LM abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
- SetupLMCmpdAbbrevTemplateDataMap
-
$AbbrevTemplateDataMapRef =
SetupLMCmpdAbbrevTemplateDataMap($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.
- ValidateLMAbbrev
-
$Status = ValidateLMAbbrev($Abbrev);
Return 1 or 0 based on whether a LM abbreviation is valid.
AUTHOR
Return a reference to an array containing complete LM abbreviations. Wild card characters in LM abbreviation name are expanded to generate fully qualified LM 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 a reference to a hash containing LM templates data
Return a reference to a hash containing supported head groups data.
Return a supported template ID for compound abbreviation.
Return 1 or 0 based on whether LM abbreviated is supported. For unsupported LM abbreviations, a warning is printed unless PrintWarning flag is set.
Parse LM abbreviation and return these values: HeadGroup, ChainsAbbrev, AbbrevModifier.
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 LM 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