NAME

LMAPSStr - Glycerolipids (GL) structure generation methods

SYNOPSIS

use LMAPSStr;

use LMAPSStr qw(:all);

DESCRIPTION

LMAPSStr module provides these methods:

GenerateCmpdAtomLine - Generate SD file atom data line
GenerateCmpdBondLine - Generate SD file bond data line
GenerateCmpdCountsLine - Generate SD file count data line
GenerateCmpdMiscInfoLine - Generate SD file misc data line
ParseCmpdAtomLine - Parse SD file atom data line
ParseCmpdBondLine - Parse SD file bond data line
ParseCmpdCountsLine - Parse SD file count data line
RoundToNextInteger - Round up to next integer
SetupCmpdAbbrevs - Setup lipid abbreviations
SetupSDFileName - Setup SD file name
StandardizeStereochemistrySpec - Standardize stereochemistry
StandardizeStereochemistrySpec - Standardize ring stereochemistry

METHODS

GenerateCmpdAtomLine: $Line = GenerateCmpdAtomLine($AtomX, $AtomY, $AtomZ, $AtomSymbol);

Return a formatted atom data line for SD file.
GenerateCmpdBondLine: $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum, $BondType, [$BondStereo]);

Return a formatted bond data line for SD file.
GenerateCmpdCountsLine: $Line = GenerateCmpdCountsLine($AtomCount, $BondCount, [$ChiralFlag, $PropertyCount, $Version]);

Return a formatted count data line for SD file.
GenerateCmpdMiscInfoLine: $Line = GenerateCmpdMiscInfoLine();

Return a formatted miscellaneous data line for SD file. In addition to a time stamp, LipdMAPS name is used as the program name.
ParseCmpdAtomLine: ($AtomX, $AtomY, $AtomZ, $AtomSymbol) = ParseCmpdAtomLine($Line);

Parse SD file atom data line and return a list with these values: atom coordinates and element symbol.
ParseCmpdBondLine: ($FirstAtomNum, $SecondAtomNum, $BondType, $BondStereo) = ParseCmpdBondLine($Line);

Parse SD file atom bond data line and return a list containing these values: bond atom numbers and bond type.
ParseCmpdCountsLine: ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) = ParseCmpdCountsLine($Line);

Parse SD file count data line and return a list containing these values: atom/bond count and other miscellaneous count information.
RoundToNextInteger: $IntegerValue = RoundToNextInteger($Number);

Return an integer by rounding the number off to next integer.
SetupCmpdAbbrevs: $AbbrebArrayRef = SetupCmpdAbbrevs($CmdLineOptionsRef);

Return a reference to an array containing specified compound abbreviations by parsing command line arguments or processing files containing specified abbreviations.
SetupSDFileName: $SDFilename = SetupSDFileName($LipidCategory, $CmdLineOptionsRef);

Return a SD file name by processing a specified -r, --root option or using default values.
StandardizeStereochemistrySpec: $StandardizeSpec = StandardizeStereochemistrySpec($StereochemistrySpec);

Return a standardize stereochemistry specification containg R/S instead of a/b or alpha/beta.
StandardizeRingStereochemistrySpec: $StandardizeSpec = StandardizeRingStereochemistrySpec($StereochemistrySpec);

Return a standardize stereochemistry specification containg alpha/beta instead of a/b or alpha/beta.

AUTHOR

Manish Sud

CONTRIBUTOR

Eoin Fahy

COPYRIGHT

LICENSE

Modified BSD License