mutant.descriptors
Class AromaticAmineSubstituentsDescriptor
java.lang.Object
mutant.descriptors.SubstituentsDescriptor
mutant.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.)
- the functional amino group is always in position 1, additional amino groups are treated as substituents;
- 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).
- 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
- when the numbering can go in two opposite directions, the substituent position with highest steric hindrance is given the lowest substitution number
- 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;
- 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 |
protected static java.lang.String |
AromAmine
|
protected static java.lang.String |
H
|
protected MoleculesFile |
lookup
|
protected static java.lang.String |
MR
|
protected static java.lang.String |
N
|
protected static java.lang.String |
R
|
protected int[] |
reverse_numbers
|
Method Summary |
static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer |
aromaticAmine(java.lang.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,
java.lang.String mark)
|
protected double[] |
getAminoGroupOrder(org.openscience.cdk.interfaces.IAtomContainerSet substituents,
java.lang.String mark)
If more than one amino group is present, the -N with lowest steric hindrance ( 1. |
protected org.openscience.cdk.interfaces.IMolecule |
getAminoGroupSubstituents(org.openscience.cdk.interfaces.IAtomContainer ac,
int natom)
|
org.openscience.cdk.qsar.DescriptorSpecification |
getSpecification()
|
protected void |
iterateSubstituents(org.openscience.cdk.interfaces.IAtomContainerSet substituents,
java.lang.String mark,
mutant.descriptors.ISubstituentAction<java.lang.Double> action,
double[] positions)
|
java.lang.String |
select(java.util.Hashtable<java.lang.String,org.openscience.cdk.interfaces.IAtomContainerSet> substituents)
|
Methods inherited from class mutant.descriptors.SubstituentsDescriptor |
getDescriptorNames, getDescriptorResultType, getParameterNames, getParameters, getParameterType, getRingQuery, setDescriptorNames, setParameterNames, setParameters, setRingQuery, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
AromAmine
protected static java.lang.String AromAmine
MR
protected static java.lang.String MR
H
protected static java.lang.String H
N
protected static java.lang.String N
R
protected static java.lang.String R
lookup
protected MoleculesFile lookup
reverse_numbers
protected int[] reverse_numbers
AromaticAmineSubstituentsDescriptor
public AromaticAmineSubstituentsDescriptor()
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,
java.lang.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.IMolecule getAminoGroupSubstituents(org.openscience.cdk.interfaces.IAtomContainer ac,
int natom)
throws org.openscience.cdk.exception.CDKException
- Throws:
org.openscience.cdk.exception.CDKException
select
public java.lang.String select(java.util.Hashtable<java.lang.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,
java.lang.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,
java.lang.String mark,
mutant.descriptors.ISubstituentAction<java.lang.Double> action,
double[] positions)
aromaticAmine
public static org.openscience.cdk.isomorphism.matchers.QueryAtomContainer aromaticAmine(java.lang.String mark)
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