Dear Masgils,
Try:
AllChem.GetBestRMS(mols[0],mols[1],map=[list(zip(a,b))])
I hope this works.
Regards,
Omar
On Fri, Jul 26, 2019 at 4:52 AM Masgils wrote:
> Dear Paolo,
> Thank you very much. It was very helpful.
> I get atom idx of the corresponding structure in each molecule successful!
Dear Paolo,
Thank you very much. It was very helpful.
I get atom idx of the corresponding structure in each molecule successful!
But there is another problem.
When I used:
a = mols[0].GetSubstructMatch(generic)
b = mols[1].GetSubstructMatch(generic)
Dear Masgils,
you may try something along these lines, i.e. make atoms and/or bonds
generic on one of the molecules withrdmolops.AdjustQueryProperties() in
order to get subtructures to match, and then use rdMolAlign.GetBestRMS():
piperidine = Chem.AddHs(Chem.MolFromSmiles("C1CC(C)CCN1"))
Hi, all
Is it possible use GetSubstructMatches() to match a substructure with one or
two atom different from ref_mol? (eg. a Piperidine ring and a Piperazing ring)
And how to get the RMSD between corresponding atoms of two substructures?
___
Hi Gianluca,
This one turns out to be pretty easy: you just add the molecules as a
column and then call:
PandasTools.RenderImagesInAllDataFrames(images=True)
Or, if you just want to change the rendering for a single DataFrame, you
can call:
PandasTools.ChangeMoleculeRendering(df)
Here's a gist
Hi Gianluca,
Yes you can do that.
You create a list of molecule objects from the mol2 files and then you
assign this list to a new column in your dataframe.
I.e. (Pythopsuedocode...)
mols = list()
for mol2 in mol2_files:
mol = Chem.MolFromMol2(mol2)
mols.append(mol)
df["Molecule"] =
Hi all,
is it possible to manually add molecules to a pandas dataframe? I am
reading a bunch of mol2 files, adding some properties (including some
atom highlighting), then I'd like to add the resulting molecule to the
dataframe in order to show its depiction along with the data.
However, API docs
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