Class BCUTDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class BCUTDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Eigenvalue based descriptor noted for its utility in chemical diversity. Described by Pearlman et al. [Pearlman, R.S. and Smith, K.M.. J. Chem. Inf. Comput. Sci.. 1999. 39].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
- atomic weight
- partial charge (Gasteiger Marsilli)
- polarizability [Kang, Y.K. and Jhon, M.S.. Theoretica Chimica Acta. 1982. 61]
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).
Returns an array of values in the following orderParameters for this descriptor: Name Default Description nhigh 1 The number of highest eigenvalue nlow 1 The number of lowest eigenvalue checkAromaticity true Whether aromaticity should be checked - BCUTw-1l, BCUTw-2l ... - nhigh lowest atom weighted BCUTS
- BCUTw-1h, BCUTw-2h ... - nlow highest atom weighted BCUTS
- BCUTc-1l, BCUTc-2l ... - nhigh lowest partial charge weighted BCUTS
- BCUTc-1h, BCUTc-2h ... - nlow highest partial charge weighted BCUTS
- BCUTp-1l, BCUTp-2l ... - nhigh lowest polarizability weighted BCUTS
- BCUTp-1h, BCUTp-2h ... - nlow highest polarizability weighted BCUTS
- Author:
- Rajarshi Guha
- Dictionary pointer(s):
- BCUT in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:BCUT]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Keywords:
- BCUT, descriptor
- Created on:
- 2004-11-30
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Constructor Summary
Constructors Constructor Description BCUTDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 aIImplementationSpecification
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.-
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()
Description copied from interface:IDescriptor
Returns aIImplementationSpecification
which specifies which descriptor is implemented by this class. These fields are used in the map:- Specification-Reference: refers to an entry in a unique dictionary
- Implementation-Title: anything
- Implementation-Identifier: a unique identifier for this version of this class
- Implementation-Vendor: CDK, JOELib, or anything else
- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- An object containing the descriptor specification
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setParameters
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the BCUTDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
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.- Throws:
CDKException
- if the parameters are of the wrong type- See Also:
getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the BCUTDescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- Three element array of Integer and one boolean representing number of highest and lowest eigenvalues and the checkAromaticity flag to return respectively
- See Also:
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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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the BCUTDescriptor 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 BCUTDescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter (can be either 'nhigh' or 'nlow' or checkAromaticity)- Returns:
- The parameterType value
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calculate
public DescriptorValue calculate(IAtomContainer container)
Calculates the three classes of BCUT descriptors.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- Parameter is the atom container.- Returns:
- An ArrayList containing the descriptors. The default is to return all calculated eigenvalues of the Burden matrices in the order described above. If a parameter list was supplied, then only the specified number of highest and lowest eigenvalues (for each class of BCUT) will be returned.
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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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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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