Class RotatableBondsCountDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class RotatableBondsCountDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial
Returns a single value named nRotBParameters for this descriptor: Name Default Description includeTerminals false True if terminal bonds are included excludeAmides false True if amide C-N bonds should be excluded - Author:
- mfe4
- Dictionary pointer(s):
- rotatableBondsCount in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:rotatableBondsCount]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- bond count, rotatable, descriptor
- Created on:
- 2004-11-03
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Constructor Summary
Constructors Constructor Description RotatableBondsCountDescriptor()
Constructor for the RotatableBondsCountDescriptor object
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.IDescriptorResult
getDescriptorResultType()
Returns the specific type of the DescriptorResult object.String[]
getParameterNames()
Gets the parameterNames attribute of the RotatableBondsCountDescriptor objectObject[]
getParameters()
Gets the parameters attribute of the RotatableBondsCountDescriptor objectObject
getParameterType(String name)
Gets the parameterType attribute of the RotatableBondsCountDescriptor objectDescriptorSpecification
getSpecification()
Gets the specification attribute of the RotatableBondsCountDescriptor objectvoid
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.void
setParameters(Object[] params)
Sets the parameters attribute of the RotatableBondsCountDescriptor object-
Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
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Method Detail
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getSpecification
public DescriptorSpecification getSpecification()
Gets the specification attribute of the RotatableBondsCountDescriptor object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
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setParameters
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the RotatableBondsCountDescriptor object- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- a boolean true means that terminal atoms must be included in the count- Throws:
CDKException
- Description of the Exception- See Also:
IDescriptor.getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the RotatableBondsCountDescriptor object- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
IDescriptor.setParameters(java.lang.Object[])
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getDescriptorNames
public String[] 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
public DescriptorValue calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container. If the boolean parameter is set to true, terminal bonds are included.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
ac
- AtomContainer- Returns:
- number of rotatable bonds
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getDescriptorResultType
public IDescriptorResult 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
public String[] getParameterNames()
Gets the parameterNames attribute of the RotatableBondsCountDescriptor object- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
public Object getParameterType(String name)
Gets the parameterType attribute of the RotatableBondsCountDescriptor object- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
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initialise
public void initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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