Re: [Rdkit-discuss] Draw.MolsToGridImage error: got multiple values for keyword argument

Hi Paolo, Your solution works perfectly.  Thank you! - Konrad From: Paolo Tosco Date: Tuesday, February 25, 2020 at 6:34 PM To: Konrad Koehler , RDKit Discuss Subject: Re: [Rdkit-discuss] Draw.MolsToGridImage error: got multiple values for keyword argument Hi Konrad, you

[Rdkit-discuss] Draw.MolsToGridImage error: got multiple values for keyword argument

Hi everyone, I am having trouble using a mol property value to define highlighted atoms when generating an image. Starting from the beginning, I have defined a variable highlight_atom_numbers as a tuple: >>> type(highlight_atom_numbers) >>> And set a mol property to this value: mo

Re: [Rdkit-discuss] Custom fingerprint in PostgreSQL: null character error; convert numpy array into bit vector

; On 5 Sep 2017, at 06:37, Greg Landrum wrote: > > I know from the subsequent post that you've moved on from this, but it's > probably worth responding here anyway: > > On Fri, Sep 1, 2017 at 9:36 AM, Konrad Koehler <mailto:konrad.koeh...@icloud.com>> wrote: &

[Rdkit-discuss] ErG: 2D Pharmacophore Similarity Searches

esults.append([smiles, name, ergtc]) sorted_results = sorted(results, key = lambda x: x[2], reverse=True) print '%s\t%s\t%.4f' % (query_smiles, query_name, 1.0) for result in sorted_results: (smiles, name, ergtc) = result print '%s\t%s\t%.4f' % (smiles, name, ergtc) > On 1 Sep 2017

[Rdkit-discuss] Custom fingerprint in PostgreSQL: null character error; convert numpy array into bit vector

Hi, I am trying to add ErG fingerprints to PostgreSQL using the following post as a guide: https://github.com/greglandrum/rdkit_blog/blob/master/notebooks/Custom%20fingerprint%20in%20PostgreSQL.ipynb

[Rdkit-discuss] kekulize AllChem.CanonSmiles error and workaround

Hi, I am having trouble canonicalizing smiles with ambiguous heteroaromatic tautomers such as imidazole. For example: >>> from rdkit import Chem >>> from rdkit.Chem import AllChem >>> smiles = ‘n1cncc1' >>> AllChem.CanonSmiles(smiles) [21:42:52] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4

[Rdkit-discuss] requested documentation update: conda rdkit installation

Just a suggestion, I believe the following page: http://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda should include a link to https://anaconda.org/rdkit/rdkit and shou

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

nD2] would, indeed, match pyridine > and pyrrole. > > Hope this helps, > Dave > > > > Cheers, > Dave > > > On Sat, May 7, 2016 at 10:34 AM, Konrad Koehler <mailto:konrad.koeh...@icloud.com>> wrote: > Hi David, > > Thanks for your help

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

the second SMARTS file above. There are > also programs for doing pharmacophore searches of large databases of > conformations using these pharmacophore definitions. > > Hope this helps, > Dave > > > On Sun, May 1, 2016 at 11:08 AM, Konrad Koehler <mailto:konrad.koeh

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

Hi Greg, Digging around a bit more, I noticed there are at least two published SMARTS definitions of hydrogen bond acceptor. The first by Gillet et al. (1998, see below) that is also found on the Daylight web site and the second by Gobbi et al. (1998). It appears that both versions are deficie

Re: [Rdkit-discuss] Gobbi hydrogen bond acceptor definition

of definitions would be welcome. They > just need to have a different name. :-) > > -greg > > > On Saturday, 30 April 2016, Konrad Koehler <mailto:konrad.koeh...@icloud.com>> wrote: > Hi All, > > The following is a relatively minor point, but IMHO, the Gobbi hydrogen b

[Rdkit-discuss] Gobbi hydrogen bond acceptor definition

Hi All, The following is a relatively minor point, but IMHO, the Gobbi hydrogen bond acceptor definition probably should be modified so that only aromatic nitrogen atoms with two and not three non-hydrogen attachments are considered as acceptors. For example, the aromatic nitrogen atom pyridin

[Rdkit-discuss] Molecular Fragments Invariant Violation: Problem solved

Hi, Problem solved (the sample script was missing a few lines of code). Sorry about that. A fully functional script is below. Best regards, Konrad = begin active_fragments.py = from rdkit import Chem from rdkit.ML.InfoTheory import InfoBitRanker from rdkit.Chem import FragmentCatalog

[Rdkit-discuss] Molecular Fragments Invariant Violation

Hi, First of all, thanks to the rdkit developers for making available this incredibly powerful package. I am trying to get an example script taken from the rdkit documentation to work, and it is generating an "Invariant Violation" error. The example script and the exact error message it gener