Class TPSADescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
Calculation of topological polar surface area based on fragment
contributions (TPSA) [Ertl, P. et. al.. J. Med. Chem.. 2000. 43].
This descriptor works properly with AtomContainers whose atoms contain either explicit hydrogens or
implicit hydrogens.
Returns a single value named TopoPSA
Name | Default | Description |
checkAromaticity | false | If true, it will check aromaticity |
- Author:
- mfe4, ulif
- Dictionary pointer(s):
- tpsa in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:tpsa]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- TPSA, total polar surface area, descriptor
- Created on:
- 2004-11-03
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtomContainer atomContainer) Calculates the TPSA for an atom container.String[]
Returns an array of names for each descriptor value calculated.Returns the specific type of the DescriptorResult object.String[]
Gets the parameterNames attribute of the TPSADescriptor object.Object[]
Gets the parameters attribute of the TPSADescriptor object.getParameterType
(String name) Gets the parameterType attribute of the TPSADescriptor object.Gets the specification attribute of the TPSADescriptor object.void
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) Sets the parameters attribute of the TPSADescriptor object.Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
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Constructor Details
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TPSADescriptor
public TPSADescriptor()Constructor for the TPSADescriptor object.
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Method Details
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getSpecification
Gets the specification attribute of the TPSADescriptor object.- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
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setParameters
Sets the parameters attribute of the TPSADescriptor object. The descriptor takes a Boolean parameter to indicate whether the descriptor routine should check for aromaticity (TRUE) or not (FALSE).- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The parameter value (TRUE or FALSE)- Throws:
CDKException
- if the supplied parameter is not of type Boolean- See Also:
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getParameters
Gets the parameters attribute of the TPSADescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameter value. For this descriptor it returns a Boolean indicating whether aromaticity was to be checked or not
- See Also:
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getDescriptorNames
Description copied from interface:IDescriptor
Returns an array of names for each descriptor value calculated. Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value. In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the descriptor (e.g., the CPSA descriptor). Note that by default if a descriptor returns a single value (such asALOGPDescriptor
the return array will have a single element- Specified by:
getDescriptorNames
in interfaceIDescriptor
- Returns:
- An array of descriptor names, equal in length to the number of descriptor calculated..
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calculate
Calculates the TPSA for an atom container. Before calling this method, you may want to set the parameter indicating that aromaticity should be checked. If no parameter is specified (or if it is set to FALSE) then it is assumed that aromaticaity has already been checked. Prior to calling this method it is necessary to either add implicit or explicit hydrogens usingCDKHydrogenAdder.addImplicitHydrogens(IAtomContainer)
orAtomContainerManipulator.convertImplicitToExplicitHydrogens(IAtomContainer)
.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
atomContainer
- The AtomContainer whose TPSA is to be calculated- Returns:
- A double containing the topological surface area
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getDescriptorResultType
Returns the specific type of the DescriptorResult object. The return value from this method really indicates what type of result will be obtained from theDescriptorValue
object. Note that the same result can be achieved by interrogating theDescriptorValue
object; this method allows you to do the same thing, without actually calculating the descriptor.- Specified by:
getDescriptorResultType
in interfaceIMolecularDescriptor
- Returns:
- an object that implements the
IDescriptorResult
interface indicating the actual type of values returned by the descriptor in theDescriptorValue
object
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getParameterNames
Gets the parameterNames attribute of the TPSADescriptor object.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
Gets the parameterType attribute of the TPSADescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
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initialise
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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