public class BCUTDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
The descriptor is based on a weighted version of the Burden matrix (Burden, F.R.. J. Chem. Inf. Comput. Sci.. 1989. 29, Burden, F.R.. Quant. Struct .-Act. Relat.. 1997. 16) which takes into account both the connectivity as well as atomic properties of a molecule. The weights are a variety of atom properties placed along the diagonal of the Burden matrix. Currently three weighting schemes are employed
By default, the descriptor will return the highest and lowest eigenvalues for the three classes of descriptor in a single ArrayList (in the order shown above). However it is also possible to supply a parameter list indicating how many of the highest and lowest eigenvalues (for each class of descriptor) are required. The descriptor works with the hydrogen depleted molecule. A side effect of specifying the number of highest and lowest eigenvalues is that it is possible to get two copies of all the eigenvalues. That is, if a molecule has 5 heavy atoms, then specifying the 5 highest eigenvalues returns all of them, and specifying the 5 lowest eigenvalues returns all of them, resulting in two copies of all the eigenvalues.
Note that it is possible to specify an arbitrarily large number of eigenvalues to be returned. However if the number (i.e., nhigh or nlow) is larger than the number of heavy atoms, the remaining eignevalues will be NaN. Given the above description, if the aim is to gt all the eigenvalues for a molecule, you should set nlow to 0 and specify the number of heavy atoms (or some large number) for nhigh (or vice versa).
Name | Default | Description |
nhigh | 1 | The number of highest eigenvalue |
nlow | 1 | The number of lowest eigenvalue |
checkAromaticity | true | Whether aromaticity should be checked |
Constructor and Description |
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BCUTDescriptor() |
Modifier and Type | Method and Description |
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DescriptorValue |
calculate(IAtomContainer container)
Calculates the three classes of BCUT descriptors.
|
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 BCUTDescriptor object.
|
Object[] |
getParameters()
Gets the parameters attribute of the BCUTDescriptor object.
|
Object |
getParameterType(String name)
Gets the parameterType attribute of the BCUTDescriptor object.
|
DescriptorSpecification |
getSpecification()
Returns a
IImplementationSpecification which specifies which descriptor
is implemented by this class. |
void |
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.
|
void |
setParameters(Object[] params)
Sets the parameters attribute of the BCUTDescriptor object.
|
clone
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
initialise
public DescriptorSpecification getSpecification()
IDescriptor
IImplementationSpecification
which specifies which descriptor
is implemented by this class.
These fields are used in the map:
getSpecification
in interface IDescriptor
public void setParameters(Object[] params) throws CDKException
setParameters
in interface IDescriptor
params
- The new parameter values. This descriptor takes 3 parameters: number of highest
eigenvalues and number of lowest eigenvalues. If 0 is specified for either (the default)
then all calculated eigenvalues are returned. The third parameter checkAromaticity is a boolean.
If checkAromaticity is true, the method check the aromaticity, if false, means that the aromaticity has
already been checked.CDKException
- if the parameters are of the wrong typegetParameters()
public Object[] getParameters()
getParameters
in interface IDescriptor
setParameters(java.lang.Object[])
public String[] getDescriptorNames()
IDescriptor
ALOGPDescriptor
the return array will have a single elementgetDescriptorNames
in interface IDescriptor
public String[] getParameterNames()
getParameterNames
in interface IDescriptor
public Object getParameterType(String name)
getParameterType
in interface IDescriptor
name
- Description of the Parameter (can be either 'nhigh' or 'nlow' or checkAromaticity)public DescriptorValue calculate(IAtomContainer container)
calculate
in interface IMolecularDescriptor
container
- Parameter is the atom container.public IDescriptorResult getDescriptorResultType()
DescriptorValue
object. Note that the same result
can be achieved by interrogating the DescriptorValue
object; this method
allows you to do the same thing, without actually calculating the descriptor.getDescriptorResultType
in interface IMolecularDescriptor
IDescriptorResult
interface indicating
the actual type of values returned by the descriptor in the DescriptorValue
objectpublic void initialise(IChemObjectBuilder builder)
initialise
in interface IDescriptor
builder
- chem object buildCopyright © 2018. All Rights Reserved.