Re: [Rdkit-discuss] RD Kit PostgreSQL in a container
you might want to look at these that we're been using for several years: https://hub.docker.com/r/informaticsmatters/rdkit-cartridge-debian/tags This the GitHub repo for this and several other flavours of RDKit container images: https://github.com/InformaticsMatters/docker-rdkit Tim 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 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 one? Ideally I’d start from one of the existing dockerfiles. RDKit Postgresql in the current distribution is version 11.2, the dockerfiles on the hub include an 11 and an 11.6 version. Any idea as to which one to use? I’m new to dockerfiles, I’d appreciate any suggestions Regards, Webster Homer This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. ___ 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
Re: [Rdkit-discuss] Clearing isotope info
On Dec 12, 2019, at 17:39, Rafal Roszak wrote:
> I also had situation when I need to generate smiles with either
> isotopes or stereochemistry but not both. Maybe it is worth to add two
> options to ChemMolToSmiles function:
>
> dontIncludeStereochemistry=True/False
> dontIncludeIsotopes=True/False
>
> Right now it is not straightforward to generate smiles w/o isotopes
> (but with stereochemistry) - one need to remove isotope, export to
> smiles and restore isotopes.
Bear in mind a few complications. I believe the following correctly implements
what you describe:
from rdkit import Chem
def MolWithoutIsotopesToSmiles(mol):
atom_data = [(atom, atom.GetIsotope()) for atom in mol.GetAtoms()]
for atom, isotope in atom_data:
if isotope:
atom.SetIsotope(0)
smiles = Chem.MolToSmiles(mol)
for atom, isotope in atom_data:
if isotope:
atom.SetIsotope(isotope)
return smiles
>>> mol = Chem.MolFromSmiles("[19F][13C@H]([16OH])[35Cl]")
>>> MolWithoutIsotopesToSmiles(mol)
'O[C@@H](F)Cl'
Testing reveals two problems with my implementation:
1) isotopic hydrogens
Consider the same structure with tritium instead of fluorine:
>>> mol = Chem.MolFromSmiles("[3H][13C@H]([16OH])[35Cl]")
>>> MolWithoutIsotopesToSmiles(mol)
'[H][C@H](O)Cl'
That output should be 'OCCl'.
2) stereochemistry assignment needs to be recalculated after the isotopes have
been removed:
>>> mol = Chem.MolFromSmiles("C[C@H]([13CH3])CI")
>>> MolWithoutIsotopesToSmiles(mol)
'C[C@@H](C)CI'
>>> Chem.CanonSmiles("C[C@H]([CH3])CI")
'CC(C)CI'
2b) This includes directional bonds
>>> mol = Chem.MolFromSmiles("C/C(=C/CO)/[11CH3]")
>>> MolWithoutIsotopesToSmiles(mol)
'C/C(C)=C/CO'
>>> Chem.CanonSmiles("C/C(=C/CO)/[CH3]")
'CC(C)=CCO'
Andrew
da...@dalkescientific.com
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[Rdkit-discuss] RMSD between embedded conformers and input 3D structure
Hi guys,
I am trying to get RMSD between embedded conformers and reference 3D
structure (no Hs) in the input file. Please see example below:
from rdkit import Chem
from rdkit.Chem import AllChem
suppl = Chem.SDMolSupplier("mol.sdf")
for mol in suppl:
# Adding Hs
mh = Chem.AddHs(mol, addCoords=True)
# embedding
AllChem.EmbedMultipleConfs(mh, numConfs=100, numThreads=0)
cids = [conf.GetId() for conf in mh.GetConformers()]
# optimization
for cid in cids:
mp = AllChem.MMFFGetMoleculeProperties(mh, mmffVariant='MMFF94s')
ff = AllChem.MMFFGetMoleculeForceField(mh, mp, confId=cid)
ff.Initialize()
ff.Minimize(maxIts=1000)
# rms to reference structure in input file
m = Chem.RemoveHs(mh)
bestRmsList = []
for i in range(len(cids)):
bestRmsList.append(AllChem.GetBestRMS(m, mol, prbId=cids[i]))
print(min(bestRmsList))
As you can see, Hs are added for embedding and optimization, and then
removed for RMSD calculation (only compare heavy atoms). I pick "m" as
"probe" and "mol" as "reference" (not quite sure about this part).
Is this the right or proper way to do it? Any suggestions? I am still
learning RDKit. Many thanks!
Best,
Leon
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Re: [Rdkit-discuss] Clearing isotope info
Well, the there is already the isomericSmiles option in Chem.MolToSmiles() that handles stereo. But it's true that there isn't one for isotopes. An alternative might be to use the standardizer (rdMolStandardize package) as my process is already using part of this and does seem to have some stuff there for isotopes, but I couldn't figure out how to use this. On 12/12/2019 16:39, Rafal Roszak wrote: On Wed, 11 Dec 2019 10:53:47 + Tim Dudgeon wrote: I'm wanting to write isomeric smiles that does not include isotope information. I also had sytuation when I need to generate smiles with either isotopes or stereochemistry but not both. Maybe it is worth to add two options to ChemMolToSmiles function: dontIncludeStereochemistry=True/False dontIncludeIsotopes=True/False Right now it is not straightforward to generate smiles w/o isotopes (but with stereochemistry) - one need to remove isotope, export to smiles and restore isotopes. Best, Rafał ___ 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
Re: [Rdkit-discuss] Clearing isotope info
On Wed, 11 Dec 2019 10:53:47 + Tim Dudgeon wrote: > I'm wanting to write isomeric smiles that does not include isotope > information. I also had sytuation when I need to generate smiles with either isotopes or stereochemistry but not both. Maybe it is worth to add two options to ChemMolToSmiles function: dontIncludeStereochemistry=True/False dontIncludeIsotopes=True/False Right now it is not straightforward to generate smiles w/o isotopes (but with stereochemistry) - one need to remove isotope, export to smiles and restore isotopes. Best, Rafał ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
