org.openscience.cdk.qsar.descriptors.molecular
Class KierHallSmartsDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class KierHallSmartsDescriptor
extends java.lang.Object
implements IMolecularDescriptor

A fragment count descriptor that uses e-state fragments.

Traditionally the e-state descriptors identify the relevant fragments and then evaluate the actual e-state value. However it has been shown in [Butina, D. , Performance of Kier-Hall E-state Descriptors in Quantitative Structure Activity Relationship (QSAR) Studies of Multifunctional Molecules , Molecules, 2004, 9:1004-1009] that simply using the counts of the e-state fragments can lead to QSAR models that exhibit similar performance to those built using the actual e-state indices.

Atom typing and aromaticity perception should be performed prior to calling this descriptor. The atom type definitions are taken from [Hall, L.H. and Kier, L.B. , Electrotopological State Indices for Atom Types: A Novel Combination of Electronic, Topological, and Valence State Information, Journal of Chemical Information and Computer Science, 1995, 35:1039-1045]. The SMARTS definitions were obtained from RDKit.

The descriptor returns an integer array result of 79 values with the following names (see here for the corresponding chemical groups).

Serial	Name	Pattern
0	khs.sLi	[LiD1]-*
1	khs.ssBe	[BeD2](-*)-*
2	khs.ssssBe	[BeD4](-*)(-*)(-*)-*
3	khs.ssBH	[BD2H](-*)-*
4	khs.sssB	[BD3](-*)(-*)-*
5	khs.ssssB	[BD4](-*)(-*)(-*)-*
6	khs.sCH3	[CD1H3]-*
7	khs.dCH2	[CD1H2]=*
8	khs.ssCH2	[CD2H2](-*)-*
9	khs.tCH	[CD1H]#*
10	khs.dsCH	[CD2H](=*)-*
11	khs.aaCH	[C,c;D2H](:*):*
12	khs.sssCH	[CD3H](-*)(-*)-*
13	khs.ddC	[CD2H0](=*)=*
14	khs.tsC	[CD2H0](#*)-*
15	khs.dssC	[CD3H0](=*)(-*)-*
16	khs.aasC	[C,c;D3H0](:*)(:*)-*
17	khs.aaaC	[C,c;D3H0](:*)(:*):*
18	khs.ssssC	[CD4H0](-*)(-*)(-*)-*
19	khs.sNH3	[ND1H3]-*
20	khs.sNH2	[ND1H2]-*
21	khs.ssNH2	[ND2H2](-*)-*
22	khs.dNH	[ND1H]=*
23	khs.ssNH	[ND2H](-*)-*
24	khs.aaNH	[N,nD2H](:*):*
25	khs.tN	[ND1H0]#*
26	khs.sssNH	[ND3H](-*)(-*)-*
27	khs.dsN	[ND2H0](=*)-*
28	khs.aaN	[N,nD2H0](:*):*
29	khs.sssN	[ND3H0](-*)(-*)-*
30	khs.ddsN	[ND3H0](~[OD1H0])(~[OD1H0])-,:*
31	khs.aasN	[N,nD3H0](:*)(:*)-,:*
32	khs.ssssN	[ND4H0](-*)(-*)(-*)-*
33	khs.sOH	[OD1H]-*
34	khs.dO	[OD1H0]=*
35	khs.ssO	[OD2H0](-*)-*
36	khs.aaO	[O,oD2H0](:*):*
37	khs.sF	[FD1]-*
38	khs.sSiH3	[SiD1H3]-*
39	khs.ssSiH2	[SiD2H2](-*)-*
40	khs.sssSiH	[SiD3H1](-*)(-*)-*
41	khs.ssssSi	[SiD4H0](-*)(-*)(-*)-*
42	khs.sPH2	[PD1H2]-*
43	khs.ssPH	[PD2H1](-*)-*
44	khs.sssP	[PD3H0](-*)(-*)-*
45	khs.dsssP	[PD4H0](=*)(-*)(-*)-*
46	khs.sssssP	[PD5H0](-*)(-*)(-*)(-*)-*
47	khs.sSH	[SD1H1]-*
48	khs.dS	[SD1H0]=*
49	khs.ssS	[SD2H0](-*)-*
50	khs.aaS	[S,sD2H0](:*):*
51	khs.dssS	[SD3H0](=*)(-*)-*
52	khs.ddssS	[SD4H0](~[OD1H0])(~[OD1H0])(-*)-*
53	khs.sCl	[ClD1]-*
54	khs.sGeH3	[GeD1H3](-*)
55	khs.ssGeH2	[GeD2H2](-*)-*
56	khs.sssGeH	[GeD3H1](-*)(-*)-*
57	khs.ssssGe	[GeD4H0](-*)(-*)(-*)-*
58	khs.sAsH2	[AsD1H2]-*
59	khs.ssAsH	[AsD2H1](-*)-*
60	khs.sssAs	[AsD3H0](-*)(-*)-*
61	khs.sssdAs	[AsD4H0](=*)(-*)(-*)-*
62	khs.sssssAs	[AsD5H0](-*)(-*)(-*)(-*)-*
63	khs.sSeH	[SeD1H1]-*
64	khs.dSe	[SeD1H0]=*
65	khs.ssSe	[SeD2H0](-*)-*
66	khs.aaSe	[SeD2H0](:*):*
67	khs.dssSe	[SeD3H0](=*)(-*)-*
68	khs.ddssSe	[SeD4H0](=*)(=*)(-*)-*
69	khs.sBr	[BrD1]-*
70	khs.sSnH3	[SnD1H3]-*
71	khs.ssSnH2	[SnD2H2](-*)-*
72	khs.sssSnH	[SnD3H1](-*)(-*)-*
73	khs.ssssSn	[SnD4H0](-*)(-*)(-*)-*
74	khs.sI	[ID1]-*
75	khs.sPbH3	[PbD1H3]-*
76	khs.ssPbH2	[PbD2H2](-*)-*
77	khs.sssPbH	[PbD3H1](-*)(-*)-*
78	khs.ssssPb	[PbD4H0](-*)(-*)(-*)-*

Author:

Rajarshi Guha

Belongs to the set:

qsar-descriptors

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

kierHallSmarts in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:kierHallSmarts]

Source code:

revision 11645

Constructor Summary

KierHallSmartsDescriptor()

Method Summary

DescriptorValue	calculate(IAtomContainer atomContainer) This method calculates occurrences of the Kier & Hall E-state fragments.
java.lang.String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
java.lang.String[]	getParameterNames() Gets the parameterNames attribute of the descriptor.
java.lang.Object[]	getParameters() Gets the parameters attribute of the descriptor.
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the descriptor.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the descriptor.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

KierHallSmartsDescriptor

public KierHallSmartsDescriptor()

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Returns a Map 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 interface IDescriptor

Returns:

An object containing the descriptor specification

setParameters

public void setParameters(java.lang.Object[] params)
                   throws CDKException

Sets the parameters attribute of the descriptor.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - if any parameters are specified

See Also:

getParameters()

getParameters

public java.lang.Object[] getParameters()

Gets the parameters attribute of the descriptor.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

getDescriptorNames

@TestMethod(value="testNamesConsistency")
public java.lang.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 decsriptor (e.g., the CPSA descriptor).

Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element

Specified by:

getDescriptorNames in interface IDescriptor

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

calculate

public DescriptorValue calculate(IAtomContainer atomContainer)

This method calculates occurrences of the Kier & Hall E-state fragments.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - The molecule for which this descriptor is to be calculated

Returns:

Counts of the fragments

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 the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

getParameterNames

public java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the descriptor.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public java.lang.Object getParameterType(java.lang.String name)

Gets the parameterType attribute of the descriptor.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object whose class is that of the parameter requested