[Cdk-user] CDK 2.0 Release

Hi All, Been live for almost two weeks but 2.0 is released. As always, available on Maven, GitHub, and SF. Release (GitHub Bundle Jar) Release Notes John

Re: [Cdk-user] Third CDK paper is out

congratulations to everybody, but especially to John and Egon for all their efforts on the code & the paper On Tue, Jun 6, 2017 at 12:59 PM, Egon Willighagen < egon.willigha...@gmail.com> wrote: > Hi all, > > https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0220-4 > > Thanks to

[Cdk-user] Third CDK paper is out

Hi all, https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0220-4 Thanks to everyone who contributed to the project, both (part-time) developers but also all users, for whom we are doing this. Happy reading! Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht

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.