Hi all,
SMILESGenerator creates invalid smiles (SmilesParser can't read it anymore)
for ZINC58167940.
The generated smiles is:
O=C(Nc1cccc(c1)c2nnn[[nH]-]2)C4Oc3ccc(cc3C4)Cl
SMILES Generation is done like this:
AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(mol);
mol = (IAtomContainer)
AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
SmilesGenerator generator = new SmilesGenerator(true);
String smiles = generator.createSMILES(mol);
After reading the molfile:
IAtomContainer mol = (IAtomContainer) molReader.read((ChemObject) new
AtomContainer(20, 20, 0, 0));
logger.debug("Perceiving Atom Types and configuring unset properties...");
AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(mol);
boolean isAromatic = CDKHueckelAromaticityDetector.detectAromaticity(mol);
mol.setFlag(CDKConstants.ISAROMATIC, isAromatic);
CDKHydrogenAdder hydrogenAdder =
CDKHydrogenAdder.getInstance(mol.getBuilder());
hydrogenAdder.addImplicitHydrogens(mol);
My question is:
Is there an additional detection step or other tool I need to use to deal
with the charge? Or is it a bug?
Best Regards,
Joos
Molfile for ZINC58167940:
ZINC58167940
-OEChem-04211110313D
40 42 0 0 0 0 0 0 0999 V2000
0.0246 -0.4743 2.6161 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0222 -0.8880 1.1670 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0225 -2.1540 0.7107 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0191 -2.0954 -0.7070 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0170 -0.7817 -1.0547 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0133 -0.0402 0.0940 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0055 1.3500 0.1603 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0096 2.1950 -0.8912 N 0 5 0 0 0 0 0 0 0 0 0 0
-0.0129 3.4928 -0.3548 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.0001 3.3675 0.9456 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0058 2.0720 1.2586 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0136 -0.2377 -2.4601 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0190 -3.2532 -1.6368 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1276 -4.5399 -1.1841 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0667 -5.4381 -2.7260 S 0 0 0 0 0 0 0 0 0 0 0 0
-0.0865 -4.1195 -3.7600 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0919 -3.0944 -2.9474 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.1971 -4.1198 -5.2630 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2017 -4.0365 -5.8773 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0894 -4.0368 -7.4031 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3959 -3.9590 -7.9769 O 0 0 0 0 0 0 0 0 0 0 0 0
2.4037 -3.9528 -9.4058 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0025 -0.3808 2.9690 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5450 -1.2272 3.2081 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5329 0.4844 2.7195 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0253 -3.0503 1.3131 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0018 4.1830 1.6536 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0113 -0.0276 -2.7659 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5989 0.6811 -2.4954 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4507 -0.9731 -3.1355 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2235 -4.9097 -0.1739 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6840 -5.0381 -5.5913 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7867 -3.2611 -5.5841 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6886 -3.1182 -5.5490 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7913 -4.8952 -5.5561 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6025 -4.9551 -7.7314 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4999 -3.1781 -7.7243 H 0 0 0 0 0 0 0 0 0 0 0 0
3.4316 -3.8920 -9.7633 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9441 -4.8693 -9.7757 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8414 -3.0923 -9.7685 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 23 1 0 0 0 0
1 24 1 0 0 0 0
1 25 1 0 0 0 0
2 6 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
3 26 1 0 0 0 0
4 5 2 0 0 0 0
4 13 1 0 0 0 0
5 6 1 0 0 0 0
5 12 1 0 0 0 0
6 7 1 0 0 0 0
7 11 2 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
10 11 1 0 0 0 0
10 27 1 0 0 0 0
12 28 1 0 0 0 0
12 29 1 0 0 0 0
12 30 1 0 0 0 0
13 17 1 0 0 0 0
13 14 2 0 0 0 0
14 15 1 0 0 0 0
14 31 1 0 0 0 0
15 16 1 0 0 0 0
16 17 2 0 0 0 0
16 18 1 0 0 0 0
18 19 1 0 0 0 0
18 32 1 0 0 0 0
18 33 1 0 0 0 0
19 20 1 0 0 0 0
19 34 1 0 0 0 0
19 35 1 0 0 0 0
20 21 1 0 0 0 0
20 36 1 0 0 0 0
20 37 1 0 0 0 0
21 22 1 0 0 0 0
22 38 1 0 0 0 0
22 39 1 0 0 0 0
22 40 1 0 0 0 0
M CHG 1 8 -1
M END
$$$$
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