>
> SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance
> ());
> System.out.println(SmartsPattern.create("c1ccccc1")
> .matches(smipar.parseSmiles("C1=CC=CC=C1")));
Too many carbons in the SMILES...
On 7 June 2017 at 21:11, John Mayfield <[email protected]> wrote:
> You don't need to do any of this.
>
> - From your wording, it sounds like you store aromatic bonds in molfiles,
> do not do this. ChemAxon know this is bad, they should warn on write (like
> everyone else). Yes I know people use it but two wrongs don't make a right.
>
> - SINGLE_OR_DOUBLE is defunct do not use it... will get round to
> deprecating that at some point. If you must...do it:
> *if (bond.isAromatic() && bond.getOrder() == IBond.Order.UNSET)*
>
> - High level SMARTS matching automatically sets the aromaticity to be
> correct (Daylight's - which incidentally you're not using here anyways :-D):
>
> SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
> System.out.println(SmartsPattern.create("c1ccccc1")
> .matches(smipar.parseSmiles("C1=CC=CC=CC1")));
>
>
>
> John
>
> On 7 June 2017 at 20:58, Yannick .Djoumbou <[email protected]> wrote:
>
>> Thanks John,
>>
>> Because of the variety of sources from molecules, including the ones
>> generated by JChem (which handles aromatic bonds differently from most), I
>> decided to add a function that preprocesses molecules. here is the code.
>> Please let me know if this is OK.
>>
>> I basically percieve the atoms, ckeck the bonds, and make sure that the
>> aromatic bonds (which are represented in ChemAxon with 4 - query bonds) are
>> set appropriately. I then aromatize the structure (as I want to run them
>> against SMIRKS/SMARTS patterns that might include various representations
>> of rings). Subsequently, I convert implicit hydrogens to explicit
>> hydrogens and generate coordinates for the new atoms.
>>
>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
>> Aromaticity aromaticity = new Aromaticity( ElectronDonation.cdk(),
>> Cycles.cdkAromaticSet());
>> for (IBond bond : molecule.bonds()) {
>> if (bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE)) {
>> bond.setFlag(CDKConstants.ISAROMATIC, true);
>> bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
>> bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);
>> }
>> }
>> aromaticity.apply(molecule);
>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>> StructureDiagramGenerator sdg = new StructureDiagramGenerator();
>> sdg.setMolecule(molecule);
>> sdg.generateCoordinates();
>> IAtomContainer layedOutMol = sdg.getMolecule();
>> return layedOutMol
>>
>> Thanks,
>> Yannick
>>
>>
>>
>>
>>
>> On Wed, Jun 7, 2017 at 1:43 PM, John Mayfield <
>> [email protected]> wrote:
>>
>>> I tried MarvinSketch before I posted that and all the same there too..
>>> let me know if you still think there is a problem.
>>>
>>> On 7 June 2017 at 18:13, Yannick .Djoumbou <[email protected]> wrote:
>>>
>>>> Hi John,
>>>>
>>>> Thank you the fast response. I am using another viewer, which could
>>>> have brought the confusion. This just means the issue in my code might come
>>>> from somewhere else.
>>>>
>>>> Thanks,
>>>> Yannick
>>>>
>>>> On Tue, Jun 6, 2017 at 3:25 AM, John Mayfield <
>>>> [email protected]> wrote:
>>>>
>>>>> Hi Yannick,
>>>>>
>>>>> Please, please, please don't "add hydrogens" like this! The hydrogens
>>>>> are already there and don't need to be added - this is just wasted effort
>>>>> and worst of all the atom typing *might* change your structures
>>>>> valence!! If for some reason you want to make hydrogens explicit just call
>>>>> this method directly:
>>>>>
>>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>>>>>
>>>>>
>>>>> Anyways why do you think the stereochemistry is different? All your
>>>>> SMILES are the same and the stereochemistry is preserved correctly - paste
>>>>> them in here to see: https://cdkdepict-openche
>>>>> m.rhcloud.com/depict.html
>>>>>
>>>>>
>>>>> [image: Inline images 1]
>>>>>
>>>>
>>>>
>>>
>>
>
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