Class CPSADescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class CPSADescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Calculates 29 Charged Partial Surface Area (CPSA) descriptors. The CPSA's were developed by Stanton et al. ([Stanton, D.T. and Jurs, P.C. . Analytical Chemistry. 1990. 62]) and are related to the Polar Surface Area descriptors. The original implementation was in the ADAPT software package and the definitions of the individual descriptors are presented in the following table. This class returns aDoubleArrayResult
containing the 29 descriptors in the order described in the table.A Summary of the 29 CPSA Descriptors IDescriptor Meaning PPSA-1 partial positive surface area -- sum of surface area on positive parts of molecule PPSA-2 partial positive surface area * total positive charge on the molecule PPSA-3 charge weighted partial positive surface area PNSA-1 partial negative surface area -- sum of surface area on negative parts of molecule PNSA-2 partial negative surface area * total negative charge on the molecule PNSA-3 charge weighted partial negative surface area DPSA-1 difference of PPSA-1 and PNSA-1 DPSA-2 difference of FPSA-2 and PNSA-2 DPSA-3 difference of PPSA-3 and PNSA-3 FPSA-1 PPSA-1 / total molecular surface area FFSA-2 PPSA-2 / total molecular surface area FPSA-3 PPSA-3 / total molecular surface area FNSA-1 PNSA-1 / total molecular surface area FNSA-2 PNSA-2 / total molecular surface area FNSA-3 PNSA-3 / total molecular surface area WPSA-1 PPSA-1 * total molecular surface area / 1000 WPSA-2 PPSA-2 * total molecular surface area /1000 WPSA-3 PPSA-3 * total molecular surface area / 1000 WNSA-1 PNSA-1 * total molecular surface area /1000 WNSA-2 PNSA-2 * total molecular surface area / 1000 WNSA-3 PNSA-3 * total molecular surface area / 1000 RPCG relative positive charge -- most positive charge / total positive charge RNCG relative negative charge -- most negative charge / total negative charge RPCS relative positive charge surface area -- most positive surface area * RPCG RNCS relative negative charge surface area -- most negative surface area * RNCG THSA sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2 TPSA sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2 RHSA THSA / total molecular surface area RPSA TPSA / total molecular surface area NumericalSurface
) and obtains partial charges using the Gasteiger-Marsilli algorithm (seeGasteigerMarsiliPartialCharges
). However, a comparison of the values calculated by the two implementations indicates that they are qualitatively the same.Parameters for this descriptor: Name Default Description no parameters - Author:
- Rajarshi Guha
- Dictionary pointer(s):
- CPSA in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:CPSA]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Created on:
- 2005-05-16
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Constructor Summary
Constructors Constructor Description CPSADescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.String[]
getDescriptorNames()
Returns an array of names for each descriptor value calculated.IDescriptorResult
getDescriptorResultType()
Returns the specific type of the DescriptorResult object.String[]
getParameterNames()
Gets the parameterNames attribute of the CPSADescriptor object.Object[]
getParameters()
Gets the parameters attribute of the CPSADescriptor object.Object
getParameterType(String name)
Gets the parameterType attribute of the CPSADescriptor object.DescriptorSpecification
getSpecification()
Returns aIImplementationSpecification
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 CPSADescriptor object.-
Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone
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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()
Description copied from interface:IDescriptor
Returns aIImplementationSpecification
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
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the CPSADescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameters value- Throws:
CDKException
- Description of the Exception- See Also:
getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the CPSADescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
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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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the CPSADescriptor 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 CPSADescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- The parameterType value
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calculate
public DescriptorValue calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
atomContainer
- Parameter is the atom container.- Returns:
- An ArrayList containing 29 elements in the order described above
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getDescriptorResultType
public IDescriptorResult 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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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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