NAME

STStr - Sterol (ST) structure generation methods

SYNOPSIS

use STStr;

use STStr qw(:all);

DESCRIPTION

STStr module provides these methods:

ExpandSTCmpdAbbrevs - Expand ST abbreviation
GenerateCmpdOntologyData - Generate ontology data
GenerateCmpdOntologySDDataLines - Generate ontology data lines for SD file
GenerateSTStrData - Generate structure data
GenerateSDFile - Generate SD file
IsSTAbbrevSupported - Is it a supported ST abbreviation
IsSTSubstituentsNameSupported - Is it a supported ST substituent name
IsSTDoubleBondsAbbrevOkay - Is it a valid ST double bond abbreviation
IsSTSubstituentsAbbrevOkay - Is it a valid ST substituent abbreviation
IsWildCardInSTAbbrev - Does ST abbreviatio contains a wild card
ParseSTAbrev - Parse ST abbreviation
ParseSTDoubleBondAbbrev - Parse ST double bond abbreviation
ParseSTSubstituentAbbrev - Parse ST substituent abbreviation
SetupSTCmpdAbbrevTemplateDataMap - Setup template structure data map
ValidateSTAbbrev - Validate ST abbreviation

METHODS

ExpandSTCmpdAbbrevs: $ExpandedAbbrevArrayRef = ExpandSTCmpdAbbrevs($CmpdAbbrev);

Return a reference to an array containing complete ST abbreviations. Wild card characters in ST abbreviation name are expanded to generate fully qualified ST 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.
GenerateSTStrData: ($AtomLinesArrayRef, $BondLinesArrayRef) = GenerateSTStrData($CmpdDataRef);

Return array references containing atom and bond data lines for SD file. Appropriate atom and bond data lines are generated using 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.
IsSTAbbrevSupported: $Status = IsSTAbbrevSupported($Abbrev);

Return 1 or 0 based on whether ST abbreviation is supported.
IsSTSubstituentsNameSupported: $Status = IsSTSubstituentsNameSupported($SubstituentAbbrev);

Return 1 or 0 based on whether ST substituent abbreviation is supported.
IsSTDoubleBondsAbbrevOkay: $Status = IsSTDoubleBondsAbbrevOkay($STAbbrev, $STType, $SubstituentsAbbrev, $DoubleBondsAbbrev);

Return 1 or 0 based on whether ST double bond abbreviation is valid.
IsSTSubstituentsAbbrevOkay: $Status = IsSTSubstituentsAbbrevOkay($STAbbrev, $STType, $SubstituentsAbbrev, $DoubleBondsAbbrev);

Return 1 or 0 based on whether ST substituent abbreviation is valid.
IsWildCardInSTAbbrev: $Status = IsSTAbbrevSupported($Abbrev);

Return 1 or 0 based on whether ST abbreviation contains wild card.
ParseSTAbbrev: ($STType, $SubstituentsAbbrev, $DoubleBondsAbbrev) = ParseSTAbrev($Abbrev);

Parse ST abbreviation and return these values: STType, SubstituentsAbbrev, and DoubleBondsAbbrev.
ParseSTDoubleBondAbbrev: ($BondPos1, $BondPos1) = ParseSTDoubleBondAbbrev($Abbrev);

Parse ST double bond abbreviation and return these values: BondPos1 and BondPos2.
ParseSTSubstituentAbbrev: ($SubstituentPos, $SubstituentAbbrev, $StereoChemistry) = ParseSTSubstituentAbbrev($Abbrev);

Parse ST substituents abbreviation and return these values: SubstituentPos, SubstituentAbbrev, and SubstituentStereoChemistry.
SetupSTCmpdAbbrevTemplateDataMap: $AbbrevTemplateDataMapRef = SetupSTCmpdAbbrevTemplateDataMap($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.
ValidateSTAbbrev: $Status = ValidateSTAbbrev($Abbrev);

Return 1 or 0 based on whether a ST abbreviation is valid.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License