Egon, John, I think I found the issue.
See:
https://sourceforge.net/p/cdk/bugs/1300/
Best Regards,
Joos
2013/5/30 John May <[email protected]>
> Hi Joos,
>
> Nope that does look like a bug. Could you post this as a bug report on
> sourceforge so we can track it easier.
>
> It seems to be a problem with the aromatic flag of the generate
>
> *new SmilesGenerator(false):*
> [H]C1=N[N-]C(=N1)N3C(=C([H])C(C=2N=C(C([H])([H])C([H])([H])C([H])([H])OC([H])([H])[H])SC=2([H]))=C3C([H])([H])[H])C([H])([H])[H]
> *new SmilesGenerator(true):*
> [H]c1n[[nH]-]c(n1)n3c(c([H])c(c2nc(C([H])([H])C([H])([H])C([H])([H])OC([H])([H])[H])sc2([H]))c3C([H])([H])[H])C([H])([H])[H]
>
>
> Thanks,
> J
>
> On 30 May 2013, at 08:35, Joos Kiener <[email protected]> wrote:
>
> 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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