Class DistanceToAtomDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
This class returns the 3D distance between two atoms. Only works with 3D coordinates, which must be calculated beforehand.
Name | Default | Description |
focusPosition | 0 | The position of the second atom |
- Author:
- mfe4
- Dictionary pointer(s):
- distanceToAtom in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:distanceToAtom]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2004-11-13
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Constructor Summary
ConstructorsConstructorDescriptionConstructor for the DistanceToAtomDescriptor object -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtom atom, IAtomContainer container) This method calculate the 3D distance between two atoms.String[]
Returns an array of names for each descriptor value calculated.String[]
Gets the parameterNames attribute of the DistanceToAtomDescriptor objectObject[]
Gets the parameters attribute of the DistanceToAtomDescriptor objectgetParameterType
(String name) Gets the parameterType attribute of the DistanceToAtomDescriptor objectGets the specification attribute of the DistanceToAtomDescriptor objectvoid
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) Sets the parameters attribute of the DistanceToAtomDescriptor objectMethods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
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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DistanceToAtomDescriptor
public DistanceToAtomDescriptor()Constructor for the DistanceToAtomDescriptor object
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Method Details
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getSpecification
Gets the specification attribute of the DistanceToAtomDescriptor object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
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setParameters
Sets the parameters attribute of the DistanceToAtomDescriptor object- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The parameter is the position to focus- Throws:
CDKException
- Description of the Exception- See Also:
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getParameters
Gets the parameters attribute of the DistanceToAtomDescriptor 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
This method calculate the 3D distance between two atoms.- Specified by:
calculate
in interfaceIAtomicDescriptor
- Parameters:
atom
- The IAtom for which the DescriptorValue is requestedcontainer
- Parameter is the atom container.- Returns:
- The number of bonds on the shortest path between two atoms
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getParameterNames
Gets the parameterNames attribute of the DistanceToAtomDescriptor object- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
Gets the parameterType attribute of the DistanceToAtomDescriptor 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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