uk.ac.cam.ch.wwmm.opsin

Class NameToStructure

java.lang.Object

uk.ac.cam.ch.wwmm.opsin.NameToStructure

public class NameToStructure
extends java.lang.Object

The "master" class, to turn a name into a structure.

Author:

ptc24, dl387

Method Summary

Modifier and Type	Method and Description
static NameToStructure	getInstance()
static ParseRules	getOpsinParser() Returns an OPSIN parser This can be used to determine whether a word can be interpreted as being part of a chemical name.
static java.lang.String	getVersion() Returns the version of the OPSIN library
static void	main(java.lang.String[] args) Run OPSIN as a command-line application.
OpsinResult	parseChemicalName(java.lang.String name) Parses a chemical name, returning an OpsinResult which represents the molecule.
OpsinResult	parseChemicalName(java.lang.String name, NameToStructureConfig n2sConfig) Parses a chemical name, returning an OpsinResult which represents the molecule.
java.lang.String	parseToCML(java.lang.String name) Convenience method for converting a name to CML with OPSIN's default options
java.lang.String	parseToSmiles(java.lang.String name) Convenience method for converting a name to SMILES with OPSIN's default options

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static NameToStructure getInstance()

getVersion

public static java.lang.String getVersion()

Returns the version of the OPSIN library

Returns:

Version number String

parseToCML

public java.lang.String parseToCML(java.lang.String name)

Convenience method for converting a name to CML with OPSIN's default options

Parameters:

name - The chemical name to parse.

Returns:

A CML element, containing the parsed molecule, or null if the name was uninterpretable.

parseToSmiles

public java.lang.String parseToSmiles(java.lang.String name)

Convenience method for converting a name to SMILES with OPSIN's default options

Parameters:

name - The chemical name to parse.

Returns:

A SMILES string describing the parsed molecule, or null if the name was uninterpretable.

parseChemicalName

public OpsinResult parseChemicalName(java.lang.String name)

Parses a chemical name, returning an OpsinResult which represents the molecule. This object contains in the status whether the name was parsed successfully A message which may contain additional information if the status was warning/failure The OpsinResult has methods to generate a SMILES or CML representation For InChI, the OpsinResult should be given to the NameToInchi class

Parameters:

name - The chemical name to parse.

Returns:

OpsinResult

parseChemicalName

public OpsinResult parseChemicalName(java.lang.String name,
                                     NameToStructureConfig n2sConfig)

Parses a chemical name, returning an OpsinResult which represents the molecule. This object contains in the status whether the name was parsed successfully A message which may contain additional information if the status was warning/failure CML and SMILES representations may be retrieved directly from the object InChI may be generate using NameToInchi

Parameters:

name - The chemical name to parse.

n2sConfig - Options to control how OPSIN interprets the name.

Returns:

OpsinResult

getOpsinParser

public static ParseRules getOpsinParser()

Returns an OPSIN parser This can be used to determine whether a word can be interpreted as being part of a chemical name. Just because a word can be split into tokens does not mean the word constitutes a valid chemical name e.g. ester is interpretable but is not in itself a chemical name

Returns:

Opsin parser for recognition/parsing of a chemical word

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Run OPSIN as a command-line application.

Parameters:

args -

Throws:

java.lang.Exception