Class ProtonTotalPartialChargeDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
- All Implemented Interfaces:
IAtomicDescriptor
,IDescriptor
public class ProtonTotalPartialChargeDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor
The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).
This descriptor has no parameters. The result of this descriptor is a vector of 5 values, corresponding
to a maximum of four protons for any given atom. If an atom has fewer than four protons, the remaining values
are set to Double.NaN. Also note that the values for the neighbors are not returned in a particular order
(though the order is fixed for multiple runs for the same atom).
- Author:
- mfe4
- Dictionary pointer(s):
- protonPartialCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:protonPartialCharge]
- Source code:
- main
- Belongs to CDK module:
- qsaratomic
- Created on:
- 2004-11-03
-
Constructor Summary
ConstructorsConstructorDescriptionConstructor for the ProtonTotalPartialChargeDescriptor object -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtom atom, IAtomContainer ac) The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.String[]
Returns an array of names for each descriptor value calculated.String[]
Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor objectObject[]
Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor objectgetParameterType
(String name) Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor objectGets the specification attribute of the ProtonTotalPartialChargeDescriptor objectvoid
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) This descriptor does not have any parameter to be set.Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor
cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise
-
Constructor Details
-
ProtonTotalPartialChargeDescriptor
public ProtonTotalPartialChargeDescriptor()Constructor for the ProtonTotalPartialChargeDescriptor object
-
-
Method Details
-
getSpecification
Gets the specification attribute of the ProtonTotalPartialChargeDescriptor object- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- The specification value
-
setParameters
This descriptor does not have any parameter to be set.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- An array of Object containing the parameters for this descriptor- Throws:
CDKException
- if invalid number of type of parameters are passed to it- See Also:
-
getParameters
Gets the parameters attribute of the ProtonTotalPartialChargeDescriptor object- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
-
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..
-
calculate
The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili 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 requestedac
- AtomContainer- Returns:
- an array of doubles with partial charges of [heavy, proton_1 ... proton_n]
-
getParameterNames
Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor object- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
-
getParameterType
Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor object- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- An Object of class equal to that of the parameter being requested
-
initialise
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
-