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[Cdk-user] HybridizationStateATMatcher
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From: Nina J. <ni...@ac...> - 2005-06-22 12:18:24
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Hi all,
I am trying to use org.openscience.cdk.atomtype.HybridizationStateATMatcher.
It works nice with recognizing carbons and hydrogens, as parametrized by
"org/openscience/cdk/config/data/hybridization_atomtypes.xml".
However, I couldn't get it to recognize most of the other atom types listed ,
for example O, P, S , hallogens and nitrogen (except Nplus.sp3). Below is the
test for oxygen with the corresponding debug log.
-- test to produce the log above --
protected Molecule getMol() {
Molecule mol = new Molecule();
Atom a1 = new Atom("C");
mol.addAtom(a1);
Atom a2 = new Atom("C");
mol.addAtom(a2);
Atom a3 = new Atom("O");
mol.addAtom(a3);
Atom a4 = new Atom("O");
mol.addAtom(a4);
Atom a5 = new Atom("H");
mol.addAtom(a5);
Atom a6 = new Atom("H");
mol.addAtom(a6);
Atom a7 = new Atom("H");
mol.addAtom(a7);
Atom a8 = new Atom("H");
mol.addAtom(a8);
Bond b1 = new Bond(a2, a1, 1.0);
mol.addBond(b1);
Bond b2 = new Bond(a3, a2, 1.0);
mol.addBond(b2);
Bond b3 = new Bond(a4, a2, 2.0);
mol.addBond(b3);
Bond b4 = new Bond(a1, a5, 1.0);
mol.addBond(b4);
Bond b5 = new Bond(a1, a6, 1.0);
mol.addBond(b5);
Bond b6 = new Bond(a1, a7, 1.0);
mol.addBond(b6);
Bond b7 = new Bond(a3, a8, 1.0);
mol.addBond(b7);
return mol;
}
public void testHybridizationStateATMatcher() {
AtomContainer mol = getMol();
HybridizationStateATMatcher h = new HybridizationStateATMatcher();
for (int i = 0; i < mol.getAtomCount(); i++) {
try {
AtomType a = h.findMatchingAtomType(mol,mol.getAtomAt(i));
assertTrue(a != null);
} catch (CDKException x) {
fail();
x.printStackTrace();
}
}
}
-- end test
-- start log
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - My ATOM TYPE C 4.0
1.0 4
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - 0ATOM TYPE 4.0 1.0
4
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - !!!!! ATOM TYPE
FOUND
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.config.AtomTypeFactory - Request for atomtype for symbol C
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.config.AtomTypeFactory - Atomtype for symbol C has this
number of types: 7
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - My ATOM TYPE C 4.0
2.0 3
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - 0ATOM TYPE 4.0 1.0
4
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - 1ATOM TYPE 4.0 2.0
3
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - !!!!! ATOM TYPE
FOUND
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.config.AtomTypeFactory - Request for atomtype for symbol O
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.config.AtomTypeFactory - Atomtype for symbol O has this
number of types: 3
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - My ATOM TYPE O 2.0
1.0 2
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - 0ATOM TYPE 2.0 2.0
0
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - 1ATOM TYPE 3.0 2.0
0
2005-06-22 14:55:47,765 [main] DEBUG
org.openscience.cdk.atomtype.HybridizationStateATMatcher - 2ATOM TYPE 1.0 1.0
0
-- end
I've noticed that most of the not-recognized-atoms do not have defined
"cdk:formalNeighbourCount" in hybridization_atomtypes.xml, which is then
assumed zero by HybridizationStateATMatcher. Naturally, only disconnected atom
can have zero neighbors count and atoms in a molecule are not matched.
Finally, I am wondering if this is a bug (which could be fixed easily by
editing hybridization_atomtypes.xml appropriately), or I am just not using
HybridizationStateATMatcher correctly.
Best regards,
Nina
--
------------------------------------------------------------------
Assoc. Prof. Dr. Nina Nikolova-Jeliazkova
* * Institute for Parallel Processing
* * Bulgarian Academy of Sciences
* IST Foundation * Acad. G. Bonchev St 25-A
* The Bulgarian NREN * 1113 Sofia, Bulgaria
* * Tel: +3592 9796616
* * ICQ: 10705013
http://www.ist.bg www: http://luna.acad.bg/nina
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