@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.AtomHybridizationVSEPRDescriptorTest") public class AtomHybridizationVSEPRDescriptor extends Object implements IAtomicDescriptor
This class try to find a SIMPLE WAY the molecular geometry for following from Valence Shell Electron Pair Repulsion or VSEPR model and at the same time its hybridization of atoms in a molecule.
The basic premise of the model is that the electrons are paired in a molecule and that the molecule geometry is determined only by the repulsion between the pairs. The geometry adopted by a molecule is then the one in which the repulsions are minimized.
It counts the number of electron pairs in the Lewis dot diagram which are attached to an atom. Then uses the following table.
pairs on an atom | hybridization of the atom | geometry | number for CDK.Constants |
2 | sp | linear | 1 |
3 | sp^2 | trigonal planar | 2 |
4 | sp^3 | tetrahedral | 3 |
5 | sp^3d | trigonal bipyramid | 4 |
6 | sp^3d^2 | octahedral | 5 |
7 | sp^3d^3 | pentagonal bipyramid | 6 |
8 | sp^3d^4 | square antiprim | 7 |
9 | sp^3d^5 | tricapped trigonal prism | 8 |
This table only works if the central atom is a p-block element (groups IIA through VIIIA), not a transition metal.
This descriptor uses these parameters:
Name | Default | Description |
no parameters |
Constructor and Description |
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AtomHybridizationVSEPRDescriptor()
Constructor for the AtomHybridizationVSEPRDescriptor object
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Modifier and Type | Method and Description |
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DescriptorValue |
calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
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String[] |
getDescriptorNames()
Returns an array of names for each descriptor value calculated.
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String[] |
getParameterNames()
Gets the parameterNames attribute of the AtomHybridizationVSEPRDescriptor object
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Object[] |
getParameters()
Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
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Object |
getParameterType(String name)
Gets the parameterType attribute of the AtomHybridizationVSEPRDescriptor object
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DescriptorSpecification |
getSpecification()
Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
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void |
setParameters(Object[] params)
This descriptor does have any parameter.
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public AtomHybridizationVSEPRDescriptor()
@TestMethod(value="testGetSpecification") public DescriptorSpecification getSpecification()
getSpecification
in interface IDescriptor
@TestMethod(value="testSetParameters_arrayObject") public void setParameters(Object[] params) throws CDKException
setParameters
in interface IDescriptor
params
- An array of Object containing the parameters for this descriptorCDKException
- if invalid number of type of parameters are passed to itIDescriptor.getParameters()
@TestMethod(value="testGetParameters") public Object[] getParameters()
getParameters
in interface IDescriptor
setParameters(java.lang.Object[])
@TestMethod(value="testNamesConsistency") public String[] getDescriptorNames()
IDescriptor
ALOGPDescriptor
the return array will have a single element
getDescriptorNames
in interface IDescriptor
@TestMethod(value="testCalculate_IAtomContainer") public DescriptorValue calculate(IAtom atom, IAtomContainer container)
calculate
in interface IAtomicDescriptor
atom
- The IAtom for which the DescriptorValue is requestedcontainer
- Parameter is the atom container.@TestMethod(value="testGetParameterNames") public String[] getParameterNames()
getParameterNames
in interface IDescriptor
@TestMethod(value="testGetParameterType_String") public Object getParameterType(String name)
getParameterType
in interface IDescriptor
name
- Description of the Parameter