[Rdkit-discuss] Check molecules

Hi, is there a function to check molecule structures, whether it actually is a possible structure. E.g. because of wrong assignment of aromaticity. And if not, to reassign aromaticity. regards --

Re: [Rdkit-discuss] Generation of stereo-isomers

result_sdf.append(mol2) > > else: > if not find_only: # return ALL mols > result_sdf.append(mol) > > return result_sdf, racemic_molids > > Please also have a look at this post > http://sourceforge.net/p/rdkit/mailm

[Rdkit-discuss] Generation of stereo-isomers

Hi, is it possible with RDKit to generate all stereoisomers of a given compound? If not, is anyone working on it? If not, how difficult would it be / what would be the best way to implement such a function. best regards Soren

Re: [Rdkit-discuss] Molecule objects conformation

...@gmail.com] Sent: Monday, March 30, 2015 10:00 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Molecule objects conformation Hi Soren, On Mon, Mar 30, 2015 at 11:37 PM, Soren Wacker swac...@ucalgary.camailto:swac...@ucalgary.ca wrote: I am wondering how RDKit handles molecule

[Rdkit-discuss] Molecule objects conformation

Hi, I am wondering how RDKit handles molecule conformations and stereo-isomers. E.G. when I generate a chiral molecule from a smiles string, where chirality is not explicated. Does RDKit generate a random conformation, or no specific conformation in the first place? kind regards Soren

[Rdkit-discuss] https://sourceforge.net

Hi, rdkit has moved to github, but there is still the repository on sourceforge.net. However, if you google 'rdkit bugs' the sourceforge page comes up first. I find that confusing. Is there a reason to keep the sourceforge.net stuff? If not, why don't you remove the sourceforge repository? kind

Re: [Rdkit-discuss] Wired dependencies.

Hi, OK, this issue is solved. Now, everything (anaconda, rdkit, ipython notebook jupiter) runs fine. I documented the installation process. In case anyone is interested here is my installation script. I did not run it a last time, but it should be at least a good start to install and run

[Rdkit-discuss] Identify and repair broken molecules

Hi, when generating molecules from smiles and drawing them sometimes show little red squares around certain atoms. I guess, this means that the connectivity is wrong. Is there a way to identify and potentially repair these molecules in rdkit? Thanks Soren

Re: [Rdkit-discuss] Wired dependencies.

in the environment. Thanks Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: Soren Wacker [swac

Re: [Rdkit-discuss] Wired dependencies.

Yes, sorry, I did not mention that. But I did that, too. Soren -- Dr. Soren Wacker Centre For Molecular Simulations, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca

[Rdkit-discuss] Wired dependencies.

Hi, I am using conda and rdkit, so installed https://github.com/rdkit/conda-rdkit with conda build boost conda build rdkit The installation seems to be successfull, at least in part, since I can import and use rdkit. However, I noticed some strange behaviour: When I activate a conda

Re: [Rdkit-discuss] Chem.Draw darker colors

but how? Soren From: Greg Landrum [greg.land...@gmail.com] Sent: Wednesday, February 11, 2015 10:27 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Chem.Draw darker colors My other answer about using the DrawingOptions object applies

Re: [Rdkit-discuss] RDKit YYDEBUG Redefined error

Hi, I printed some moecules with the Draw module of rdkit and generated some useful figures. I noticed that for some elements the contrast to white is very low. Therefore, I suggest to change the default colors to the darker versions. E.g. darkyellow instead of yellow for sulfur and darkcyan

[Rdkit-discuss] Draw molecules black and white.

Hi, I am looking for a keyword to draw molecules black and white or greyscale e.g. Draw.MolsToImage(...,keyword?) is there something like this? regards Soren -- Dive into the World of Parallel Programming. The Go

Re: [Rdkit-discuss] Molecular descriptors / Fragments

: Friday, January 30, 2015 11:35 PM To: Soren Wacker Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Molecular descriptors / Fragments Hi Soren, The functions should definitely still be there. In [1]: from rdkit import rdBase In [2]: rdBase.rdkitVersion Out[2]: '2014.09.2' In [3]: from rdkit import

[Rdkit-discuss] Molecular descriptors / Fragments

Hi, I installed RDKit python -c 'from rdkit import rdBase; print rdBase.rdkitVersion' 2014.09.2 with conda. Before, I used molecular descriptors as explained here: http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html For example, Descriptors.fr_Al_COO However, in the

[Rdkit-discuss] rdkit.version()

Hi, I would like to find out the currently installed version on my System. However, I cannot find a version string in RDKit. Something like rdkit.version() would be nice. Is there something like this implemented?? kind regards Soren From: James Davidson

Re: [Rdkit-discuss] [Rdkit-devel] 2014.03 (Q1 2014) RDKit release

I would appreciate RPMs for Fedora. best -- Dr. Soeren Wacker Centre For Molecular Simulation, BI # 547 The University of Calgary 2500 University Drive (NW) Calgary, Alberta Canada, T2N 1N4 Tel.: ++1 (403) 210 7860 Email: swac...@ucalgary.ca From: GALLY Jose

[Rdkit-discuss] change behaviour of mailing list

Hi, I don't find a propties or options for the mailing list. Is it possible to get the mails forwarded and not combined in one email as attachments? best Soren -- Start Your Social Network Today - Download eXo Platform