Re: [Rdkit-discuss] Conformer generation using ETKDG

Hi Jordan, On Thu, Oct 5, 2017 at 6:48 AM, Jordan McCone wrote: > > I have a .smi file which has a number of smiles strings in it. I would > like to generate a single 3D conformer using ETKDG for every smiles string > in the list, > If you google around, you will find a

[Rdkit-discuss] Conformer generation using ETKDG

Hi all, I have a .smi file which has a number of smiles strings in it. I would like to generate a single 3D conformer using ETKDG for every smiles string in the list, and then get the output as a single .mol2 file. I am very new to rdkit and even python, and as much as i'd to do this myself, I

Re: [Rdkit-discuss] Atom mapping

Hi Jan, I'm not aware of an implementation of atom mapping for reactions based on the RDKit. -greg On Wed, Oct 4, 2017 at 9:03 AM, Jan Halborg Jensen wrote: > I just came across this paper http://pubs.acs.org/doi/ > abs/10.1021/acs.jctc.7b00764 which presents an variant

Re: [Rdkit-discuss] nitrogen valence issues

Hi Brian, When you pasted that into the email the formatting of the mol block did end up screwed up, which makes this hard to reproduce. Could you please attach the mol block to the message as a file? -greg On Thu, Oct 5, 2017 at 2:21 AM, Bennion, Brian wrote: > Hello, > >

[Rdkit-discuss] nitrogen valence issues

Hello, After looking at the email list and seeing that this error has cropped up several times for aromatic/aliphatic heterocyclic nitrogens I still haven't been able to resolve the valence =4 error for one of the azo groups in a molecule that has 7. The first couple of azo groups seem to be

Re: [Rdkit-discuss] Fresh install of RDKit not functioning

Hi Greg, Many thanks for the help, works now, I can now use this amazing software! Cheers, Jordan On Wed, Oct 4, 2017 at 10:35 PM, Greg Landrum wrote: > Hi Jordan, > > Sorry this is frustrating. This is, unfortunately, connected to the > problem I posted about here: >

[Rdkit-discuss] Atom mapping

I just came across this paper http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00764 which presents an variant of the Fewest Bonds First with Constructive Count Vector method by Crabtree and Mehta (https://dl.acm.org/citation.cfm?id=1498697) Has anyone implemented anything similar in with RDKit?

Re: [Rdkit-discuss] Warning for conda users

Dear all, Just to make sure this thread contains the relevant info: The same problem also affects conda installs on Windows, at least with python v2.7. The solution is to downgrade your conda version to v4.3.25 I've confirmed that the current RDKit distributions work with v4.3.25 of conda and

Re: [Rdkit-discuss] Fresh install of RDKit not functioning

Hi Jordan, Sorry this is frustrating. This is, unfortunately, connected to the problem I posted about here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg07315.html At the time I thought that only the Mac (and possibly linux) was affected, but thanks to your warning I've

[Rdkit-discuss] Fresh install of RDKit not functioning

Hi, Another case of 'my rdkit doesn't work'. I have been trying to get it working for a very long time now (on and off for the last few days). I would really like to use the ETKDG function of this software to generate the 3D conformers of ligands for a virtual screening library. I have tried to

Re: [Rdkit-discuss] "Markush SMARTS" ?

Hi Alexis, I'm trying to make sure I understand the use case: you want to search for aromatic rings that have one F and one Cl or aromatic rings that have exactly two substitutions? If you just wanted to determine whether or not there is a match, you could use this recursive SMARTS for the first