[Rdkit-discuss] Generating all trans structure

Hello, I want to generate a structure file (PDB) of a chemical (chain of C) that have all TRANS conformation for any single bond like "". Is there any possible way to do it with RDKIT? Input: SMILES string of chemical Output: PDB file with as many TRANS conformation as possible. Thank

Re: [Rdkit-discuss] Get list of dihedrals using atom names/numbers from PDB

Hi Angelica, if torsion_lists is the tuple of of (non_ring, ring) torsion lists in mol: torsion_lists = TorsionFingerprints.CalculateTorsionLists(mol) you can get the same list where the atom index is replaced by a (PDB_atom_serial, PDB_atom_name) tuple as follows: torsion_lists_sn =

[Rdkit-discuss] Get list of dihedrals using atom names/numbers from PDB

I’m trying to use the module rdkit.Chem.TorsionFingerprints.CalculateTorsionLists to print out a list of torsions. I pass in a PDB file using Chem.MolFromPDBFile, and would ideally like the torsion list to specify the atoms using the atom names and/or numbers from the PDB file. Right now I get

Re: [Rdkit-discuss] ForwardSDMolSupplier, stdin, and python 3.7

Hi Paolo, Thank you, that does it. --Andy On Wed, Mar 27, 2019 at 12:53 PM Paolo Tosco wrote: > Hi Andy, > > for that to work with Python 3 you will need to replace sys.stdin with > sys.stdin.buffer. > > HTH, cheers > Paolo > > On 03/27/19 18:32, Andy wrote: > > Hi, > > I have used the git

Re: [Rdkit-discuss] ForwardSDMolSupplier, stdin, and python 3.7

Hi Andy, for that to work with Python 3 you will need to replace sys.stdin with sys.stdin.buffer. HTH, cheers Paolo On 03/27/19 18:32, Andy wrote: Hi, I have used the git version of rdkit for years (local build with python 2.7). The last update pushed me to use python3, and, in addition

Re: [Rdkit-discuss] Smarts conversion help

As Pat pointed out, what's happening here is that you have an explicit H in your SMARTS. The RDKit has a function, MergeQueryHs(), to merge this into the query of the atom it's connected to. Here's the application to your example: In [2]:

Re: [Rdkit-discuss] Open-source business models and the RDKit

One of the goals of ATOM is to fund work that will be open sourced. I think any of the partners can choose to hire consultants for the work. https://atomscience.org/ Atom atomscience.org Transforming drug discovery. The Accelerating Therapeutics for Opportunities in

Re: [Rdkit-discuss] Smarts conversion help

On Tue, Mar 26, 2019 at 8:22 PM Patrick Walters wrote: > HI Xiaobo, > > There's an explicit hydrogen in the SMARTS that shouldn't be there. I > also wouldn't include the single bonds around the ring closures. > To be fair, that explicit hydrogen was in the original SMILES string, so it is

Re: [Rdkit-discuss] Open-source business models and the RDKit (Greg Landrum)

This is an interesting discussion and suspect this does not only apply to open-source software developers, there are similar challenges for small independent software companies. On CICAG (http://www.rsccicag.org ) we have been discussing the possibility of organising

Re: [Rdkit-discuss] Open-source business models and the RDKit

On Mar 27, 2019, at 08:24, Francois Berenger wrote: > As an open-source project, I feel rdkit is quite successful. > So, the user community is not so small. > Some people who cannot contribute time could contribute money to the project > (especially if it is tax-deductible, I guess). I think the

Re: [Rdkit-discuss] Open-source business models and the RDKit

On Wed, Mar 27, 2019 at 10:46 AM Czodrowski, Paul < paul.czodrow...@tu-dortmund.de> wrote: > I’m not sure if you are asking about T5 Informatics: for me, it would be > absolutely fine that it goes through T5 Informatics. > Yeah, I was specifically talking about T5 Informatics. > In terms of

Re: [Rdkit-discuss] Open-source business models and the RDKit

I’m not sure if you are asking about T5 Informatics: for me, it would be absolutely fine that it goes through T5 Informatics. In terms of legal aspects, there might be a conflict of interest (between Greg/RDKit and Greg/T5 Informatics), but I’m not sure about this.. If it was of any help: what

Re: [Rdkit-discuss] Open-source business models and the RDKit

> > > If rdkit was accepted at the software freedom conservancy, I understand > the management fee would be 10%: > > https://sfconservancy.org/projects/apply/ > > https://sfconservancy.org/projects/services/ A question since I genuinely don't know: is it important to anyone that this go through

Re: [Rdkit-discuss] Open-source business models and the RDKit

On 27/03/2019 16:24, Francois Berenger wrote: On 27/03/2019 01:46, Greg Landrum wrote: And now that I've included two other messages, here's (part of) my take on this. The viability of open-source business models is something I'm deeply interested in (I pay rent these days thanks to income

Re: [Rdkit-discuss] Open-source business models and the RDKit

On 27/03/2019 01:46, Greg Landrum wrote: And now that I've included two other messages, here's (part of) my take on this. The viability of open-source business models is something I'm deeply interested in (I pay rent these days thanks to income from two open-source companies) and, like Andrew,