Class MDEDescriptor
java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
- All Implemented Interfaces:
IDescriptor
,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).
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
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculate
(IAtomContainer container) Calculate the weight of specified element type in 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 WeightDescriptor object.Object[]
Gets the parameters attribute of the WeightDescriptor object.getParameterType
(String name) Gets the parameterType attribute of the WeightDescriptor 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 WeightDescriptor 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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Field Details
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MDEC11
public static final int MDEC11- See Also:
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MDEC12
public static final int MDEC12- See Also:
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MDEC13
public static final int MDEC13- See Also:
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MDEC14
public static final int MDEC14- See Also:
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MDEC22
public static final int MDEC22- See Also:
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MDEC23
public static final int MDEC23- See Also:
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MDEC24
public static final int MDEC24- See Also:
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MDEC33
public static final int MDEC33- See Also:
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MDEC34
public static final int MDEC34- See Also:
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MDEC44
public static final int MDEC44- See Also:
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MDEO11
public static final int MDEO11- See Also:
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MDEO12
public static final int MDEO12- See Also:
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MDEO22
public static final int MDEO22- See Also:
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MDEN11
public static final int MDEN11- See Also:
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MDEN12
public static final int MDEN12- See Also:
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MDEN13
public static final int MDEN13- See Also:
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MDEN22
public static final int MDEN22- See Also:
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MDEN23
public static final int MDEN23- See Also:
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MDEN33
public static final int MDEN33- See Also:
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Constructor Details
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MDEDescriptor
public MDEDescriptor()
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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 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:
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getParameters
Gets the parameters attribute of the WeightDescriptor object.- Specified by:
getParameters
in interfaceIDescriptor
- Returns:
- The parameters value
- See Also:
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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
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
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 WeightDescriptor object.- Specified by:
getParameterNames
in interfaceIDescriptor
- Returns:
- The parameterNames value
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getParameterType
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
Default implementation of initialise allows optional override.- Specified by:
initialise
in interfaceIDescriptor
- Parameters:
builder
- chem object build
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