Re: [Rdkit-discuss] RD Kit PostgreSQL in a container

Hi, I am working on for this for the next Chembience release (0.3.0 which I hope will be out in January). It adds RDKit to the official Postgres container repository at https://hub.docker.com/_/postgres If you checkout https://github.com/chembience/chembience-postgresql-rdkit.git *and use branch

Re: [Rdkit-discuss] Perceived bond orders of RNA PDB-files

On 04/12/2019 08:28, Illimar Hugo Rekand wrote: Hello, everyone I was wondering if there is any reason for why aromaticity and perceived bond orders are not set properly when using the MolFromPDB-function for RNA PDB files, while it works perfectly for protein PDB files? You shouldn't be

Re: [Rdkit-discuss] decomposing products to reactants from an rxn

Yep started to use the GitHub wiki also recently, but not sure how well this is indexed. There’s also quite a lot of useful content on several things on various blogs (yours, iwatobipen, Pat’s etc … ) but when you have to dive into a whole new area you haven’t used before in rdkit (reaction

Re: [Rdkit-discuss] Clustering changes conformer ID?

Hi Greg, Thanks for the help! Sorry for the confusion. I was trying to get symmetric RMS matrix using GetBestRMS, because the GetConformerRMSMatrix use standard RMS method without considering symmetry. A further question, is it possible to include the "GetBestRMS " option for

Re: [Rdkit-discuss] RD Kit PostgreSQL in a container

Hi, you might want to take a look at this Docker image maintained by Matt Swain: https://github.com/mcs07/docker-postgres-rdkit Cheers, p. On 04/12/2019 18:36, Webster Homer wrote: I’m looking at running  RD Kit Postgresql cartridge in a docker container. Has anyone done this? There are

[Rdkit-discuss] RD Kit PostgreSQL in a container

I'm looking at running RD Kit Postgresql cartridge in a docker container. Has anyone done this? There are PostgreSQL containers available on line at https://hub.docker.com/_/postgres if there is an existing dockerfile with the RDKit extension, that would be great. If not has anyone built

Re: [Rdkit-discuss] decomposing products to reactants from an rxn

Indeed that seems to work rather well. I forgot to use Initialize during my naive initial tests, that's probably why nothing worked back at the time. Would be cool to have these examples somewhere findable via google  Thanks a lot for the helpwe'll check a bit further on larger sets of

Re: [Rdkit-discuss] decomposing products to reactants from an rxn

On Wed, Dec 4, 2019 at 3:45 PM Peter Schmidtke < peter.schmid...@discngine.com> wrote: > > Would be cool to have these examples somewhere findable via google  > That's an interesting meta-point. I agree, but I wonder what an effective way to do this is. Using jupyter to answer questions and

Re: [Rdkit-discuss] Perceived bond orders of RNA PDB-files

Hi Illimar, that's because the StandardPDBDoubleBond() function in ProximityBonds.cpp only takes into account standard amino acids, but not nucleotides. I'll submit a PR later tonight to include standard DNA and RNA bases. Cheers, p. On 04/12/2019 08:28, Illimar Hugo Rekand wrote: Hello,

Re: [Rdkit-discuss] decomposing products to reactants from an rxn

On Tue, Dec 3, 2019 at 8:37 PM Peter Schmidtke < peter.schmid...@discngine.com> wrote: > > We’re currently working on an algorithm to make that work in a purely > pythonic way (for now). Let’s see if we can come up with something sensible > and good to have your simple example. It is exactly the

[Rdkit-discuss] Perceived bond orders of RNA PDB-files

Hello, everyone I was wondering if there is any reason for why aromaticity and perceived bond orders are not set properly when using the MolFromPDB-function for RNA PDB files, while it works perfectly for protein PDB files? Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of

Re: [Rdkit-discuss] handling of stereo information from mol files when not sanitizing

On Tue, Dec 3, 2019 at 9:58 PM Rasmus "Termo" Lundsgaard < termope...@gmail.com> wrote: > Hi Greg. > > Thks for your gist. I guess the line: > > nbrs = [(x.GetOtherAtomIdx(1),x.GetIdx()) for x in atom.GetBonds()] > > should be: > nbrs = [(x.GetOtherAtomIdx(atom.GetIdx()),x.GetIdx()) for x in >