toxtree.plugins.ames.descriptors

Class AromaticAmineSubstituentsDescriptor

java.lang.Object

toxtree.plugins.ames.descriptors.SubstituentsDescriptor

toxtree.plugins.ames.descriptors.AromaticAmineSubstituentsDescriptor

All Implemented Interfaces:

org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor

public class AromaticAmineSubstituentsDescriptor
extends SubstituentsDescriptor

returns "MR","LSTM","B1STM","B5STM" for substituents at postitions 1 to 6 (amine group at 1 position). TODO verify how substituted amine group should be treated (params of amine group + substituent, only substituent, largest substituent, average, etc.)

1. the functional amino group is always in position 1, additional amino groups are treated as substituents;
2. if more than one amino group is present, the -N with lowest steric hindrance ( 1. primary amines; 2. secondary amines; 3. tertiary amines; in increasing steric hindrance order) is considered to be the functional group;
3. if more than one amino group is present, and all of them have the same steric hindrance on the -N, the one that is considered to be the functional group is that which has a substituent in an adjacent position (ortho-substituent).
4. if two amino groups in ortho position are present and there are other substituents attached to the ring, the amino group that is considered to be the functional group is that which allow to assign the minimum position number to the substituent
5. when the numbering can go in two opposite directions, the substituent position with highest steric hindrance is given the lowest substitution number
6. in case the amino group is attached to more then one aromatic ring, the more extended aromatic system is to be considered as the one bearing the functional amino group;
7. in case the amino group is attached to more than one aromatic ring, with the aromatic systems equally extended, the ring bearing the functional amino group is chosen in such a way that the sterimol is the highest possible."

Author:

Nina Jeliazkova

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	AromAmine
protected static String	H
protected MoleculesFile	lookup
protected static String	MR
protected static String	N
protected static String	R
protected int[]	reverse_numbers

Fields inherited from class toxtree.plugins.ames.descriptors.SubstituentsDescriptor

descriptorNames, extractor, logger, paramNames

Constructor Summary

Constructors

Constructor and Description
AromaticAmineSubstituentsDescriptor()

Method Summary

Modifier and Type	Method and Description
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	aromaticAmine(String mark)
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer a)
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainerSet substituents, String mark)
protected double[]	getAminoGroupOrder(org.openscience.cdk.interfaces.IAtomContainerSet substituents, String mark) If more than one amino group is present, the -N with lowest steric hindrance ( 1.
protected org.openscience.cdk.interfaces.IAtomContainer	getAminoGroupSubstituents(org.openscience.cdk.interfaces.IAtomContainer ac, int natom)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
protected void	iterateSubstituents(org.openscience.cdk.interfaces.IAtomContainerSet substituents, String mark, toxtree.plugins.ames.descriptors.ISubstituentAction<Double> action, double[] positions)
String	select(Hashtable<String,org.openscience.cdk.interfaces.IAtomContainerSet> substituents)

Methods inherited from class toxtree.plugins.ames.descriptors.SubstituentsDescriptor

getDescriptorNames, getDescriptorResultType, getParameterNames, getParameters, getParameterType, getRingQuery, initialise, setDescriptorNames, setParameterNames, setParameters, setRingQuery, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

AromAmine

protected static String AromAmine

MR

protected static String MR

H

protected static String H

N

protected static String N

R

protected static String R

lookup

protected MoleculesFile lookup

reverse_numbers

protected int[] reverse_numbers

Constructor Detail

AromaticAmineSubstituentsDescriptor

public AromaticAmineSubstituentsDescriptor()

Method Detail

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

Overrides:

getSpecification in class SubstituentsDescriptor

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer a)

Specified by:

calculate in interface org.openscience.cdk.qsar.IMolecularDescriptor

Overrides:

calculate in class SubstituentsDescriptor

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainerSet substituents,
                                                          String mark)
                                                   throws org.openscience.cdk.exception.CDKException

Specified by:

calculate in class SubstituentsDescriptor

Throws:

org.openscience.cdk.exception.CDKException

getAminoGroupSubstituents

protected org.openscience.cdk.interfaces.IAtomContainer getAminoGroupSubstituents(org.openscience.cdk.interfaces.IAtomContainer ac,
                                                                                  int natom)
                                                                           throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

select

public String select(Hashtable<String,org.openscience.cdk.interfaces.IAtomContainerSet> substituents)
              throws org.openscience.cdk.exception.CDKException

Specified by:

select in class SubstituentsDescriptor

Throws:

org.openscience.cdk.exception.CDKException

getAminoGroupOrder

protected double[] getAminoGroupOrder(org.openscience.cdk.interfaces.IAtomContainerSet substituents,
                                      String mark)

If more than one amino group is present, the -N with lowest steric hindrance ( 1. primary amines; 2. secondary amines; 3. tertiary amines; in increasing steric hindrance order) is considered to be the functional group;
If more than one amino group is present, and all of them have the same steric hindrance on the -N, the one that is considered to be the functional group is that which has a substituent in an adjacent position (ortho-substituent).

Parameters:

substituents -

mark - the name of the property under which the substituent number is stored

Returns:

number, ordering the amino group as explained above. The number is composed as A + 1/B, where A = 10, 20 or 30 for primary, secondary or tertiary amine. B = 1 if there are no ortho substituents to amine group; B=2 if there is one ortho substituents and B=3 if there are two ortho substituents. The size of ortho substituents is not taken into account. This number effectively orders the amino groups as explained above.

iterateSubstituents

protected void iterateSubstituents(org.openscience.cdk.interfaces.IAtomContainerSet substituents,
                                   String mark,
                                   toxtree.plugins.ames.descriptors.ISubstituentAction<Double> action,
                                   double[] positions)

aromaticAmine

public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aromaticAmine(String mark)