[Cdk-user] CDK 2.0 Release

[John Mayfield]

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

[Rajarshi Guha]

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 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 University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: -0001-7542-0286
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
> 
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-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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[Cdk-user] Third CDK paper is out

[Egon Willighagen]

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 University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: -0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

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

[John Mayfield]

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]
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[Cdk-user] CDK - issue with stereochemistry

[Yannick .Djoumbou]

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. The resulting structure serves as input for
another function.

 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);

CDKHydrogenAdder.getInstance(molecule
.getBuilder()).addImplicitHydrogens(molecule);

AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);


Unfortunately, the stereochemistry in structure that results from this code
is messed up. This is what I get in return:

Mol2: [H][C@@]1(O[H])[C@@](C(O[H])([H])[H])(O[C@
@]([H])(OC2(C(C(C3(C(C(C(=O)OC3(C2([H])[H])[H])([H])[H])([H])[H])[H])([H])[H])([H])[H])[H])[C@
]([H])(O[H])[C@]1(O[H])[H])[H]

But what I think should be returned is

Mol3: [H]OC([H])([H])[C@@]1([H])O[C@
@]([H])(OC2([H])C([H])([H])C([H])([H])C3([H])C([H])([H])C([H])([H])C(=O)OC3([H])C2([H])[H])[C@
]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

Is there a reason for the change of stereochemical information? How to fix
the code in order to obtain the Mol3 structure?


Thank you so much for your help.

Best,

Yannick
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