Class AminoAcidCountDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor
- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class AminoAcidCountDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
Class that returns the number of each amino acid in an atom container.
Returns 20 values with names of the form nX, where X is the short versio
of the amino acid name
Name | Default | Description |
no parameters |
- Author:
- egonw
- Dictionary pointer(s):
- aminoAcidsCount in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:aminoAcidsCount]
- Source code:
- main
- Belongs to CDK module:
- qsarprotein
- Created on:
- 2006-01-15
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Constructor Summary
ConstructorsConstructorDescriptionConstructor for the AromaticAtomsCountDescriptor object. -
Method Summary
Modifier and TypeMethodDescriptionDetermine the number of amino acids groups the suppliedIAtomContainer
.String[]
Returns an array of names for each descriptor value calculated.Returns the specific type of the DescriptorResult object.String[]
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.Object[]
Gets the parameters attribute of the AminoAcidsCountDescriptor object.getParameterType
(String name) Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.Returns aMap
which specifies which descriptor is implemented by this class.void
initialise
(IChemObjectBuilder builder) Default implementation of initialise allows optional override.void
setParameters
(Object[] params) Sets the parameters attribute of the AminoAcidsCountDescriptor object.Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone
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
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Constructor Details
-
AminoAcidCountDescriptor
public AminoAcidCountDescriptor()Constructor for the AromaticAtomsCountDescriptor object.
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Method Details
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getSpecification
Returns aMap
which specifies which descriptor is implemented by this class. These fields are used in the map:- Specification-Reference: refers to an entry in a unique dictionary
- Implementation-Title: anything
- Implementation-Identifier: a unique identifier for this version of this class
- Implementation-Vendor: CDK, JOELib, or anything else
- Specified by:
getSpecification
in interfaceIDescriptor
- Returns:
- An object containing the descriptor specification
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setParameters
Sets the parameters attribute of the AminoAcidsCountDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameters value- Throws:
CDKException
- if more than one parameter or a non-Boolean parameter is specified- See Also:
-
getParameters
Gets the parameters attribute of the AminoAcidsCountDescriptor 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..
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calculate
Determine the number of amino acids groups the suppliedIAtomContainer
.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
ac
- TheIAtomContainer
for which this descriptor is to be calculated- Returns:
- the number of aromatic atoms of this AtomContainer
- See Also:
-
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
Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
Gets the parameterType attribute of the AromaticAtomsCountDescriptor 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
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initialise
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
-