Re: [Rdkit-discuss] Writing a Tripos MOL2 file with charges

Thank you everyone for all of your help. I decided the best solution was Mr. Wójcikowsk's pull request. Thank you! If it wasn't for this, I would have used a different program. Make that pull request happen! :-D Thanks once again. -Jonathan On Mon, Oct 31, 2016 at 11:16 AM, Paolo Tosco

Re: [Rdkit-discuss] Writing a Tripos MOL2 file with charges

Dear James, this is a small variation on Greg's reply (he was faster than me!): https://gist.github.com/ptosco/02af3456720d54c37ffc488056df02d4 While Greg's reply showed how to set a molecule property as a list of per-atom partial charges, here I have set each partial charge as an atom

Re: [Rdkit-discuss] Writing a Tripos MOL2 file with charges

Hi, If you really desperately need it, there is a mockup of MolToMol2Block() and MolToMol2File() by Jan and myself [see https://github.com/rdkit/rdkit/pull/415], but it's still rough around the eadges at best. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl

Re: [Rdkit-discuss] Writing a Tripos MOL2 file with charges

Is there any supported format that outputs partial charges? The speed of RDKit is phenomenal (0.02 seconds) vs obabel's 2 seconds, but if I cannot output partial charges I'll be forced to use obabel. Thank you for your time. -James On Mon, Oct 31, 2016 at 1:00 AM, Greg Landrum

Re: [Rdkit-discuss] Writing a Tripos MOL2 file with charges

Hi James, Due to problems with the general ambiguity of the format the RDKIt does not have a mol2 writer. -greg On Mon, Oct 31, 2016 at 12:22 AM +0100, "James Johnson" wrote: Hello all, I've been trying to output my 3D mol object that has Gasteiger

[Rdkit-discuss] Writing a Tripos MOL2 file with charges

Hello all, I've been trying to output my 3D mol object that has Gasteiger charges to mol2 file format. How would I go about that? I've only found it for mol and pdb. Here is the code I'be been using if that helps: ~~~ from rdkit