Package org.openscience.cdk.qsar.descriptors.atomic

Class PartialTChargeMMFF94Descriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.PartialTChargeMMFF94Descriptor
All Implemented Interfaces:
IAtomicDescriptor, IDescriptor
public class PartialTChargeMMFF94Descriptor extends AbstractAtomicDescriptor
The calculation of total partial charges of an heavy atom is based on MMFF94 model.
Parameters for this descriptor
Name Default Description
no parameters
Author:
Miguel Rojas
See Also:
This class is affected by these bug(s):
1628461
Dictionary pointer(s):
partialTChargeMMFF94 in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:partialTChargeMMFF94]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2006-04-11

  • Constructor Details

    • PartialTChargeMMFF94Descriptor

      public PartialTChargeMMFF94Descriptor()
      Constructor for the PartialTChargeMMFF94Descriptor object

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
      Returns:
      The specification value

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      This descriptor does not have any parameter to be set.
      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

      public Object[] getParameters()
      Gets the parameters attribute of the PartialTChargeMMFF94Descriptor object
      Returns:
      The parameters value
      See Also:

    • 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 as ALOGPDescriptor the return array will have a single element
      Returns:
      An array of descriptor names, equal in length to the number of descriptor calculated..

    • calculate

      public DescriptorValue calculate(IAtom atom, IAtomContainer org)
      The method returns partial charges assigned to an heavy atom through MMFF94 method. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
      Parameters:
      atom - The IAtom for which the DescriptorValue is requested
      org - AtomContainer
      Returns:
      partial charge of parameter atom

    • getParameterNames

      public String[] getParameterNames()
      Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor object
      Returns:
      The parameterNames value

    • getParameterType

      public Object getParameterType(String name)
      Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object
      Parameters:
      name - Description of the Parameter
      Returns:
      The parameterType value

    • initialise

      public void initialise(IChemObjectBuilder builder)
      Default implementation of initialise allows optional override.
      Specified by:
      initialise in interface IDescriptor
      Parameters:
      builder - chem object build