Re: [Rdkit-discuss] 64 bit Morgan Fingerpronts

Wojtek, You can use GetNonzeroelements() to convert the sparse fingerprint to a Python Dict of hash to count. Cheers, Gareth In [7]: mol = Chem.MolFromSmiles('Cn1cnc2n(C)c(=O)n(C)c(=O)c12') In [8]: fp = AllChem.GetMorganFingerprint(mol, 2) In [9]: elements = fp.GetNonzeroElements(); In

[Rdkit-discuss] compute canonical transform of a conformer fails

Dear community, I want to pick a fragment from a molecule, and canonicalize its conformer in order to align its principal moments of inertia. However, this does not seem to work. Any idea why this could be happening? mol1 = Chem.MolFromSmiles('[H]C([H])=O.[H]N([H])[H]') mol1 = Chem.AddHs(mol1)

Re: [Rdkit-discuss] Availability of new command line Psi4 scripts powered by RDKit

Hi Manish, This is great. I used Psi4 extensively for torsional scans while at Denali. Do you plan to include scripts for torsional scans? Best, JW On Wed, Apr 21, 2021 at 9:11 AM Manish Sud wrote: > Hi All, > > > > I'll like to share with you the availability of the following new command >

Re: [Rdkit-discuss] Availability of new command line Psi4 scripts powered by RDKit

Hi JW, Yes, I do. It’s on the list of things to do. It would be similar to the current script RDKitPerformTorsionScan.py , but use Psi4 on the backend. Thanks, Manish From: JW Feng Sent: Wednesday, April

Re: [Rdkit-discuss] compute canonical transform of a conformer fails

I tested your code on several structures and noticed that it failed on molecules with only one element (NH3, OH2...). Then I checked https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html and saw that the default ignores hydrogens. So try

Re: [Rdkit-discuss] 64 bit Morgan Fingerpronts

Hi Gareth, Thank you. I do exactly as you wrote. That's not the issue. Please note, that all the keys in elements are in range of 2**32 - the main hash function used is definitely 32 bit According to https://www.rdkit.org/docs/source/rdkit.Chem.rdFingerprintGenerator.html both *class