Re: [Rdkit-discuss] PathToSubmol on atom indices?
Dear Kangway, Thank you very much! M. On Thu, Jun 4, 2020 at 6:56 PM Chuang, Kangway wrote: > Hi Michal, > > You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related > MolFragmentToSmarts) and specify an atom id list with "atomsToUse": > > e.g. > > rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15]) > > Kangway > -- > *From:* Michal Krompiec > *Sent:* Thursday, June 4, 2020 10:45 AM > *To:* RDKit Discuss > *Subject:* [Rdkit-discuss] PathToSubmol on atom indices? > > Hello, I noticed this was discussed before and I'm wondering if anything's > changed. > Is it possible to extract a substructure from a molecule, based on atom > indices? I understand that Chem.PathToSubmol does something similar, but > takes bond indices. > Best, > Michal > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PathToSubmol on atom indices?
Hi Michal, You can use rdkit.Chem.rdmolfiles.MolFragmentToSmiles (or related MolFragmentToSmarts) and specify an atom id list with "atomsToUse": e.g. rdkit.Chem.rdmolfiles.MolFragmentToSmiles(mol, atomsToUse=[11,13,22,15]) Kangway From: Michal Krompiec Sent: Thursday, June 4, 2020 10:45 AM To: RDKit Discuss Subject: [Rdkit-discuss] PathToSubmol on atom indices? Hello, I noticed this was discussed before and I'm wondering if anything's changed. Is it possible to extract a substructure from a molecule, based on atom indices? I understand that Chem.PathToSubmol does something similar, but takes bond indices. Best, Michal ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] PathToSubmol on atom indices?
Hello, I noticed this was discussed before and I'm wondering if anything's changed. Is it possible to extract a substructure from a molecule, based on atom indices? I understand that Chem.PathToSubmol does something similar, but takes bond indices. Best, Michal ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] check if there is a path between atoms in fragmented molecule
Dear Michal,
You can use
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=path#rdkit.Chem.rdmolops.GetShortestPath
or
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=distance#rdkit.Chem.rdmolops.GetDistanceMatrix
e.g.:
from rdkit import Chem
cx=Chem.MolFromSmiles('C1C1')
bonds=(cx.GetBondBetweenAtoms(1,2).GetIdx(),
cx.GetBondBetweenAtoms(3,4).GetIdx())
fragmented=Chem.FragmentOnBonds(cx,bonds)
mat = Chem.GetDistanceMatrix(cx)
mat[1,2]
1.0
Chem.GetShortestPath(cx, 1, 2)
(1, 2)
mat = Chem.GetDistanceMatrix(fragmented)
mat[1, 2]
1.0
Chem.GetShortestPath(fragmented, 1, 2)
()
Cheers,
p.
On 04/06/2020 16:17, Michal Krompiec wrote:
Hello,
When a molecule is fragmented with Chem.FragmentOnBonds, how can I
check if there still is a path between two given atoms?
For example, this snippet breaks C1-C2 and C3-C4 bonds in cyclohexane,
producing two fragments:
from rdkit import Chem
cx=Chem.MolFromSmiles('C1C1')
bonds=(cx.GetBondBetweenAtoms(1,2).GetIdx(),
cx.GetBondBetweenAtoms(3,4).GetIdx())
fragmented=Chem.FragmentOnBonds(cx,bonds)
Is there a way in RDKit to check if there is a path between, say, C1
and C2, without having to manually traverse the whole molecular graph?
I guess the alternative is to load everything into a graph library
like networkx...
Best wishes,
Michal Krompiec
Merck KGaA
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Scalability of Postgres cartridge
Hi, I've never tried the RDKit PostgreSQL cartridge but I'm curious about it. In particular I wonder how far have people pushed it in terms of database size. The documentation gives examples with several million rows; has anyone tried it with a couple billion rows? How fast are substructure queries with databases of that size? How much storage is needed after accounting for the fingerprints etc. Best regards, Ivan ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Install RDKit (Docker, rapids, rdkit=2020.03.2) ?/
Hi Joey, It looks like there's a dependency conflict in there somewhere that conda is unable to resolve. Unsurprisingly, it looks like at least part of the problem here is the version of boost. The rapids environment that you are using has boost 1.70 installed (and that's probably a dependency of some other package in the environment), but the 2020.03 rdkit builds from conda-forge requires boost 1.72. I was able to make things work by simplifying your dockerfile and letting conda install the most recent compatible version of the RDKit (in this case that ends up being 2019.09.3): FROM rapidsai/rapidsai:0.12-cuda10.1-runtime-ubuntu18.04 ARG ENVNAME=rapids ENV ENVNAME=$ENVNAME #RUN source activate $ENVNAME && \ #conda install boost>='1.72.0,<1.72.1.0a0' cairo>='1.16.0,<1.17.0a0' freetype>='2.9.1,<3.0a0' libgcc-ng>='7.3.0' libstdcxx-ng>='7.3.0' numpy>='1.14.6,<2.0a0' pandas pillow pycairo python>='3.7,<3.8.0a0' python_abi='3.7.* *_cp37m' six RUN source activate $ENVNAME && \ conda list && \ conda install rdkit I hope this helps, -greg On Wed, Jun 3, 2020 at 10:43 PM Storer, Joey (J) wrote: > Hi, > > > > I am trying to run the following Docker file and the container fails to > install rdkit. Other incarnations install either the 2019 version or even > the 2017 version. > > > > *#* > > *FROM rapidsai/rapidsai:0.12-cuda10.1-runtime-ubuntu18.04* > > > > *ARG ENVNAME=rapids* > > *ENV ENVNAME=$ENVNAME* > > > > *RUN source activate $ENVNAME && \* > > *conda install boost>='1.72.0,<1.72.1.0a0' cairo>='1.16.0,<1.17.0a0' > freetype>='2.9.1,<3.0a0' libgcc-ng>='7.3.0' libstdcxx-ng>='7.3.0' > numpy>='1.14.6,<2.0a0' pandas pillow pycairo python>='3.7,<3.8.0a0' > python_abi='3.7.* *_cp37m' six* > > > > *RUN source activate $ENVNAME && \* > > *conda install "rdkit=2020.03.2=py37hdd87690_0"* > > > > *#* > > > > Any advice on getting RDKit into a Rapids/Ubuntu Docker container? > > > > Thanks! > > Joey Storer (Dow, Inc.) > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
