Class HBondDonorCountDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class HBondDonorCountDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types. The following groups are counted as hydrogen bond donors:- Any-OH where the formal charge of the oxygen is non-negative (i.e. formal charge ≥ 0)
- Any-NH where the formal charge of the nitrogen is non-negative (i.e. formal charge ≥ 0)
This descriptor uses no parameters.
This descriptor works properly with AtomContainers whose atoms contain either implicit or explicit hydrogen atoms. It does not work with atoms that contain neither implicit nor explicit hydrogens. Returns a single value named nHBDon.
Parameters for this descriptor: Name Default Description no parameters - Author:
- ulif
- Dictionary pointer(s):
- hBondDonors in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:hBondDonors]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Created on:
- 2005-22-07
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Constructor Summary
Constructors Constructor Description HBondDonorCountDescriptor()
Constructor for the HBondDonorCountDescriptor object
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.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 of the HBondDonorCountDescriptor.Object[]
getParameters()
Gets the parameters of the HBondDonorCountDescriptor instance.Object
getParameterType(String name)
Gets the parameterType of the HBondDonorCountDescriptor.DescriptorSpecification
getSpecification()
Gets the specification attribute of the HBondDonorCountDescriptor objectvoid
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.void
setParameters(Object[] params)
Sets the parameter of this HBondDonorCountDescriptor instance.-
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 HBondDonorCountDescriptor object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
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setParameters
public void setParameters(Object[] params) throws CDKException
Sets the parameter of this HBondDonorCountDescriptor instance.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- this descriptor does not have any parameters- Throws:
CDKException
- Description of the Exception- See Also:
IDescriptor.getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters of the HBondDonorCountDescriptor instance.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- null as this descriptor does not have any parameters
- 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 atomContainer)
Calculates the number of H bond donors.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
atomContainer
- AtomContainer- Returns:
- number of H bond donors
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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 of the HBondDonorCountDescriptor.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- null as this descriptor does not have any parameters
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getParameterType
public Object getParameterType(String name)
Gets the parameterType of the HBondDonorCountDescriptor.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- null as this descriptor does not have any parameters
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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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