Class IsProtonInAromaticSystemDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractAtomicDescriptor
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- org.openscience.cdk.qsar.descriptors.atomic.IsProtonInAromaticSystemDescriptor
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- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
public class IsProtonInAromaticSystemDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor
This descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions. It is needed to use addExplicitHydrogensToSatisfyValency method.Parameters for this descriptor: Name Default Description checkAromaticity false True is the aromaticity has to be checked - Author:
- mfe4
- Dictionary pointer(s):
- isProtonInAromaticSystem in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:isProtonInAromaticSystem]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2004-11-03
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Constructor Summary
Constructors Constructor Description IsProtonInAromaticSystemDescriptor()
Constructor for the IsProtonInAromaticSystemDescriptor object
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtom atom, IAtomContainer atomContainer)
The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.String[]
getParameterNames()
Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor objectObject[]
getParameters()
Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor objectObject
getParameterType(String name)
Gets the parameterType attribute of the IsProtonInAromaticSystemDescriptor objectDescriptorSpecification
getSpecification()
Gets the specification attribute of the IsProtonInAromaticSystemDescriptor objectvoid
initialise(IChemObjectBuilder builder)
Default implementation of initialise allows optional override.void
setParameters(Object[] params)
Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object-
Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
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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 IsProtonInAromaticSystemDescriptor 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 IsProtonInAromaticSystemDescriptor object- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameters value- Throws:
CDKException
- Possible Exceptions- See Also:
IDescriptor.getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor 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(IAtom atom, IAtomContainer atomContainer)
The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.- Specified by:
calculate
in interfaceIAtomicDescriptor
- Parameters:
atom
- The IAtom for which the DescriptorValue is requestedatomContainer
- AtomContainer- Returns:
- true if the proton is bonded to an aromatic atom.
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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the IsProtonInAromaticSystemDescriptor 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 IsProtonInAromaticSystemDescriptor 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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