NAME

LMStr - LIPID MAPS arbitrary structure generation methods

SYNOPSIS

use LMStr;

use LMStr qw(:all);

DESCRIPTION

LMStr module provides these methods:

ExpandLMCmpdAbbrevs - Expand abbreviation
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

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License