Package uk.ac.cam.ch.wwmm.opsin

Class OpsinResult

java.lang.Object

uk.ac.cam.ch.wwmm.opsin.OpsinResult

public class OpsinResult
extends java.lang.Object

Holds the structure OPSIN has generated from a name Additionally holds a status code for whether name interpretation was successful

Author:

dl387

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	OpsinResult.OPSIN_RESULT_STATUS	Whether parsing the chemical name was successful, encountered problems or was unsuccessful. If the result is not OpsinResult.OPSIN_RESULT_STATUS.FAILURE then a structure has been generated

Method Summary

Modifier and Type	Method	Description
java.lang.String	getChemicalName()	Returns the chemical name that this OpsinResult was generated from
java.lang.String	getCml()	Generates the CML corresponding to the molecule described by the name If name generation failed i.e.
java.lang.String	getExtendedSmiles()	Experimental function that generates the extended SMILES corresponding to the molecule described by the name If name generation failed i.e.
java.lang.String	getMessage()	Returns a message explaining why generation of a molecule from the name failed This string will be blank when no problems were encountered
java.lang.String	getPrettyPrintedCml()	Generates the CML corresponding to the molecule described by the name If name generation failed i.e.
java.lang.String	getSmiles()	Generates the SMILES corresponding to the molecule described by the name If name generation failed i.e.
java.lang.String	getSmiles(int options)	Generates the SMILES corresponding to the molecule described by the name If name generation failed i.e.
OpsinResult.OPSIN_RESULT_STATUS	getStatus()	Returns an enum indicating whether interpreting the chemical name was successful If an issue was identified but a chemical structure could be still be deduced the status is OpsinResult.OPSIN_RESULT_STATUS.WARNING
java.util.List<OpsinWarning>	getWarnings()	A list of warnings encountered when the result was OpsinResult.OPSIN_RESULT_STATUS.WARNING This list of warnings is immutable
boolean	nameAppearsToBeAmbiguous()	Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.APPEARS_AMBIGUOUS
boolean	stereochemistryIgnored()	Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.STEREOCHEMISTRY_IGNORED

Methods inherited from class java.lang.Object

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

Method Detail

getStatus

public OpsinResult.OPSIN_RESULT_STATUS getStatus()

Returns an enum indicating whether interpreting the chemical name was successful If an issue was identified but a chemical structure could be still be deduced the status is OpsinResult.OPSIN_RESULT_STATUS.WARNING

Returns:

OpsinResult.OPSIN_RESULT_STATUS status

getMessage

public java.lang.String getMessage()

Returns a message explaining why generation of a molecule from the name failed This string will be blank when no problems were encountered

Returns:

String explaining problems encountered

getChemicalName

public java.lang.String getChemicalName()

Returns the chemical name that this OpsinResult was generated from

Returns:

String containing the original chemical name

getCml

public java.lang.String getCml()

Generates the CML corresponding to the molecule described by the name If name generation failed i.e. the OPSIN_RESULT_STATUS is FAILURE then null is returned

Returns:

Chemical Markup Language as a String

getPrettyPrintedCml

public java.lang.String getPrettyPrintedCml()

Generates the CML corresponding to the molecule described by the name
If name generation failed i.e. the OPSIN_RESULT_STATUS is FAILURE then null is returned
The CML is indented

Returns:

Idented Chemical Markup Language as a String

getSmiles

public java.lang.String getSmiles()

Generates the SMILES corresponding to the molecule described by the name
If name generation failed i.e. the OPSIN_RESULT_STATUS is FAILURE then null is returned

Returns:

SMILES as a String

getSmiles

public java.lang.String getSmiles(int options)

Generates the SMILES corresponding to the molecule described by the name
If name generation failed i.e. the OPSIN_RESULT_STATUS is FAILURE then null is returned.
The options parameter is used to control the output by a set of binary flags. This is primarily used to control the output layers in ChemAxon Extended SMILES (CXSMILES).

 // only the include the enhanced stereo layers
 result.getSmiles(SmilesOptions.CXSMILES_ENHANCED_STEREO);
 // only the include the enhanced stereo and polymer layers
 result.getSmiles(SmilesOptions.CXSMILES_ENHANCED_STEREO |
                  SmilesOptions.CXSMILES_POLYMERS);
 

Parameters:

options - binary flags of SmilesOptions (default: SmilesOptions.DEFAULT))

Returns:

SMILES as a String

See Also:

SmilesOptions

getExtendedSmiles

public java.lang.String getExtendedSmiles()

Experimental function that generates the extended SMILES corresponding to the molecule described by the name If name generation failed i.e. the OPSIN_RESULT_STATUS is FAILURE then null is returned If the molecule doesn't utilise any features made possible by extended SMILES this is equivalent to getSmiles()

Returns:

Extended SMILES as a String

getWarnings

public java.util.List<OpsinWarning> getWarnings()

A list of warnings encountered when the result was OpsinResult.OPSIN_RESULT_STATUS.WARNING
This list of warnings is immutable

Returns:

A list of OpsinWarning

nameAppearsToBeAmbiguous

public boolean nameAppearsToBeAmbiguous()

Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.APPEARS_AMBIGUOUS

Returns:

true if name appears to be ambiguous

stereochemistryIgnored

public boolean stereochemistryIgnored()

Convenience method to check if one of the associated OPSIN warnings was OpsinWarning.OpsinWarningType.STEREOCHEMISTRY_IGNORED

Returns:

true if stereochemistry was ignored to interpret the name