[Rdkit-discuss] A question of GitHub Issue tracking for RDKit
yo folks, I noticed some of entries in the sourceforge bug list are not in the github list, e.g. my pet one http://sourceforge.net/p/rdkit/bugs/205/ Is there a specific reason for this? Is it OK if I move the bugs which I am interested in to GitHub? Also, is there a 'search' function in the issue list in github? Many Thanks, JP -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDkit user beginner.
Hi - welcome to the community You have a typo there GenMACCSkeys Should actually be GenMACCSKeys (ie an uppercase K in Keys) Try ipython (with the ipython notebook) then autocomplete will solve those issues for you more or less. The notebook is cool and there is some info in the mailing list on how to use it. Ciao Nik On 7/4/13 9:16 AM, segie...@sanbi.ac.za segie...@sanbi.ac.za wrote: Hi all, I just started using RDkit for chemoinformatics analysis. I tried out this code in the tutorial but got an error(please advise): The code: from rdkit import Chem from rdkit.Chem import MACCSkeys nat = Chem.SDMolSupplier(nat.sdf) fps = [MACCSkeys.GenMACCSkeys(x) for x in nat] fp = DataStructs.FingerprintSimilarity(fps[0], fps[89]) print fp The error message: Traceback (most recent call last): File rdkittest2.py, line 7, in module fps = [MACCSkeys.GenMACCSkeys(x) for x in nat] AttributeError: 'module' object has no attribute 'GenMACCSkeys' -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] random compound
Dear Greg, Could you please help me to check whether function RandomizeMol(mol) is able to generate a random compound? http://www.rdkit.org/docs/api/rdkit.Chem.Randomize-module.html#RandomizeMol If so, could you please give me more details? Thanks. On Tue, Jul 2, 2013 at 11:22 AM, Greg Landrum greg.land...@gmail.comwrote: On Tue, Jul 2, 2013 at 5:20 PM, Yingfeng Wang ywang...@gmail.com wrote: If I have the formula, is RDKit able to generate a random compound based on the given formula? It's not, but it is kind of an interesting problem to think about.[1] -greg [1] Note: this is absolutely *not* me saying that I'm going to do it. :-) -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] random compound
I'm not an expert on this, but I think this function just randomizes the order of the atoms in a molecule. Generating a random molecule for a particular molecular formula that is consistent with rules of valence is kind of tricky. If you're interested in doing this sort of thing, you may want to look at the work of Jean-Louis Reymond. http://reymond.dcb.unibe.ch/ Pat On Thu, Jul 4, 2013 at 4:31 PM, Yingfeng Wang ywang...@gmail.com wrote: This is the case I tested. from rdkit import Chem from rdkit.Chem import Randomize mymol = Chem.MolFromInchi(InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)) rmol = Chem.Randomize.RandomizeMol(mymol) Chem.MolToInchi(rmol) Finally, I got the same structure. InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14) On Thu, Jul 4, 2013 at 3:35 PM, Yingfeng Wang ywang...@gmail.com wrote: Dear Greg, Could you please help me to check whether function RandomizeMol(mol) is able to generate a random compound? http://www.rdkit.org/docs/api/rdkit.Chem.Randomize-module.html#RandomizeMol If so, could you please give me more details? Thanks. On Tue, Jul 2, 2013 at 11:22 AM, Greg Landrum greg.land...@gmail.comwrote: On Tue, Jul 2, 2013 at 5:20 PM, Yingfeng Wang ywang...@gmail.comwrote: If I have the formula, is RDKit able to generate a random compound based on the given formula? It's not, but it is kind of an interesting problem to think about.[1] -greg [1] Note: this is absolutely *not* me saying that I'm going to do it. :-) -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
