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-openchem.rhcloud.com/depict.html
>>>>
>>>>
>>>> [image: Inline images 1]
>>>>
>>>
>>>
>>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Cdk-user mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/cdk-user
