Re: [Cdk-user] CDK - issue with stereochemistry

Hi John, Thanks for the quick response. My concern is that I would like to preprocess the structures correctly so that no matter how the molecule was originally stored and what tools was used (OpenBabel, CDK, JChem/MarVin), I return one unique representation. Afterwards the molecule is subjected

Re: [Cdk-user] CDK - issue with stereochemistry

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 wrote: > Hi John, > > Thank you the fast response. I am using another viewer, which could have > brought the

Re: [Cdk-user] CDK - issue with stereochemistry

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 wrote: > Hi Yannick, > >

Re: [Cdk-user] CDK - issue with stereochemistry

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

[Cdk-user] CDK - issue with stereochemistry

Hi all, I have an issue handling stereochemistry with CDK. I am using CDK-1.5.13. I have the following molecule: Mol 1: [H][C@@]1(O)[C@@H](CO)O[C@@]([H])(OC2CCC3CCC(=O)OC3C2)[C@ ]([H])(O)[C@H]1O I am using the following code to add implicit hydrogens and further convert them into explicit ones.