Class MDEDescriptor
- java.lang.Object
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- org.openscience.cdk.qsar.AbstractMolecularDescriptor
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- org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
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- All Implemented Interfaces:
IDescriptor
,IMolecularDescriptor
public class MDEDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Calculates the Molecular Distance Edge descriptor described in [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38]. This class evaluates the 10 MDE descriptors described by Liu et al. and in addition it calculates variants where O and N are considered (as found in the DEDGE routine from ADAPT).Table 1 - Description of the different MDE descriptors generated MDEC-11 molecular distance edge between all primary carbons MDEC-12 molecular distance edge between all primary and secondary carbons MDEC-13 molecular distance edge between all primary and tertiary carbons MDEC-14 molecular distance edge between all primary and quaternary carbons MDEC-22 molecular distance edge between all secondary carbons MDEC-23 molecular distance edge between all secondary and tertiary carbons MDEC-24 molecular distance edge between all secondary and quaternary carbons MDEC-33 molecular distance edge between all tertiary carbons MDEC-34 molecular distance edge between all tertiary and quaternary carbons MDEC-44 molecular distance edge between all quaternary carbons MDEO-11 molecular distance edge between all primary oxygens MDEO-12 molecular distance edge between all primary and secondary oxygens MDEO-22 molecular distance edge between all secondary oxygens MDEN-11 molecular distance edge between all primary nitrogens MDEN-12 molecular distance edge between all primary and secondary nitrogens MDEN-13 molecular distance edge between all primary and tertiary niroqens MDEN-22 molecular distance edge between all secondary nitroqens MDEN-23 molecular distance edge between all secondary and tertiary nitrogens MDEN-33 molecular distance edge between all tertiary nitrogens - Author:
- Rajarshi Guha
- Dictionary pointer(s):
- mde in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:mde]
- Source code:
- main
- Belongs to CDK module:
- qsarmolecular
- Created on:
- 2006-09-18
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Field Summary
Fields Modifier and Type Field Description static int
MDEC11
static int
MDEC12
static int
MDEC13
static int
MDEC14
static int
MDEC22
static int
MDEC23
static int
MDEC24
static int
MDEC33
static int
MDEC34
static int
MDEC44
static int
MDEN11
static int
MDEN12
static int
MDEN13
static int
MDEN22
static int
MDEN23
static int
MDEN33
static int
MDEO11
static int
MDEO12
static int
MDEO22
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Constructor Summary
Constructors Constructor Description MDEDescriptor()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DescriptorValue
calculate(IAtomContainer container)
Calculate the weight of specified element type in the suppliedIAtomContainer
.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 WeightDescriptor object.Object[]
getParameters()
Gets the parameters attribute of the WeightDescriptor object.Object
getParameterType(String name)
Gets the parameterType attribute of the WeightDescriptor object.DescriptorSpecification
getSpecification()
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 WeightDescriptor 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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Field Detail
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MDEC11
public static final int MDEC11
- See Also:
- Constant Field Values
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MDEC12
public static final int MDEC12
- See Also:
- Constant Field Values
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MDEC13
public static final int MDEC13
- See Also:
- Constant Field Values
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MDEC14
public static final int MDEC14
- See Also:
- Constant Field Values
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MDEC22
public static final int MDEC22
- See Also:
- Constant Field Values
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MDEC23
public static final int MDEC23
- See Also:
- Constant Field Values
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MDEC24
public static final int MDEC24
- See Also:
- Constant Field Values
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MDEC33
public static final int MDEC33
- See Also:
- Constant Field Values
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MDEC34
public static final int MDEC34
- See Also:
- Constant Field Values
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MDEC44
public static final int MDEC44
- See Also:
- Constant Field Values
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MDEO11
public static final int MDEO11
- See Also:
- Constant Field Values
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MDEO12
public static final int MDEO12
- See Also:
- Constant Field Values
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MDEO22
public static final int MDEO22
- See Also:
- Constant Field Values
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MDEN11
public static final int MDEN11
- See Also:
- Constant Field Values
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MDEN12
public static final int MDEN12
- See Also:
- Constant Field Values
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MDEN13
public static final int MDEN13
- See Also:
- Constant Field Values
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MDEN22
public static final int MDEN22
- See Also:
- Constant Field Values
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MDEN23
public static final int MDEN23
- See Also:
- Constant Field Values
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MDEN33
public static final int MDEN33
- See Also:
- Constant Field Values
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Method Detail
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getSpecification
public DescriptorSpecification 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
public void setParameters(Object[] params) throws CDKException
Sets the parameters attribute of the WeightDescriptor object.- Specified by:
setParameters
in interfaceIDescriptor
- Parameters:
params
- The new parameters value- Throws:
CDKException
- if more than 1 parameter is specified or if the parameter is not of type String- See Also:
getParameters()
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getParameters
public Object[] getParameters()
Gets the parameters attribute of the WeightDescriptor 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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calculate
public DescriptorValue calculate(IAtomContainer container)
Calculate the weight of specified element type in the suppliedIAtomContainer
.- Specified by:
calculate
in interfaceIMolecularDescriptor
- Parameters:
container
- The AtomContainer for which this descriptor is to be calculated. If 'H' is specified as the element symbol make sure that the AtomContainer has hydrogens.- Returns:
- The total weight of atoms of the specified element type
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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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getParameterNames
public String[] getParameterNames()
Gets the parameterNames attribute of the WeightDescriptor 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 WeightDescriptor object.- Specified by:
getParameterType
in interfaceIDescriptor
- Parameters:
name
- Description of the Parameter- Returns:
- An Object whose class is that of the parameter requested
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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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