Class PiContactDetectionDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractAtomPairDescriptor
org.openscience.cdk.qsar.descriptors.atompair.PiContactDetectionDescriptor
- All Implemented Interfaces:
IAtomPairDescriptor
,IDescriptor
public class PiContactDetectionDescriptor
extends AbstractAtomPairDescriptor
implements IAtomPairDescriptor
This class checks if two atoms have pi-contact (this is true when there is
one and the same conjugated pi-system which contains both atoms, or directly
linked neighbours of the atoms). Only conjugated systems with more than 2
atoms are considered.
Name | Default | Description |
firstAtom | 0 | The position of the first atom |
secondAtom | 0 | The position of the second atom |
checkAromaticity | false | True is the aromaticity has to be checked |
- Author:
- mfe4
- Dictionary pointer(s):
- piContact in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:piContact]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Created on:
- 2004-11-03
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Constructor Summary
ConstructorsConstructorDescriptionConstructor for the PiContactDetectionDescriptor object. -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtom first, IAtom second, IAtomContainer atomContainer) The method returns if two atoms have pi-contact.String[]
Returns an array of names for each descriptor value calculated.String[]
Gets the parameterNames attribute of the PiContactDetectionDescriptor object.Object[]
Gets the parameters attribute of the PiContactDetectionDescriptor object.getParameterType
(String name) Gets the parameterType attribute of the PiContactDetectionDescriptor object.Gets the specification attribute of the PiContactDetectionDescriptor object.void
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) Sets the parameters attribute of the PiContactDetectionDescriptor object.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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PiContactDetectionDescriptor
public PiContactDetectionDescriptor()Constructor for the PiContactDetectionDescriptor object.
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Method Details
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getSpecification
Gets the specification attribute of the PiContactDetectionDescriptor object.- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
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setParameters
Sets the parameters attribute of the PiContactDetectionDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- Parameters contains a boolean (true if is needed a checkAromaticity)- Throws:
CDKException
- Description of the Exception- See Also:
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getParameters
Gets the parameters attribute of the PiContactDetectionDescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- 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
The method returns if two atoms have pi-contact.- Specified by:
calculate
in interfaceIAtomPairDescriptor
- Parameters:
atomContainer
- AtomContainerfirst
- The firstIAtom
of the pair for which this descriptor should be calculatedsecond
- The secondIAtom
of the pair for which this descriptor should be calculated- Returns:
- true if the atoms have pi-contact
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getParameterNames
Gets the parameterNames attribute of the PiContactDetectionDescriptor object.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
Gets the parameterType attribute of the PiContactDetectionDescriptor 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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