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 <masg...@163.com> wrote:
> 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)
> AllChem.GetBestRMS(mols[0],mols[1],map=list(zip(a,b)))
>
> The AllChem.GetBestRMS arise a ValueError:
>
> ---------------------------------------------------------------------------
> ValueError Traceback (most recent call last)
> <ipython-input-74-fd80273b39cc> in <module>
> 1 a = mols[0].GetSubstructMatch(generic)
> 2 b = mols[1].GetSubstructMatch(generic)
> ----> 3 AllChem.GetBestRMS(mols[0],mols[1],map=list(zip(a,b)))
>
> ValueError: sequence does not support length query
>
> Is its usage different from the atomMap parameter in Chem.
> rdMolAlign.AlignMol？
>
> Best Regards,
> M.
>
> At 2019-07-26 01:07:13, "Paolo Tosco" <paolo.tosco.m...@gmail.com> wrote:
>
> Dear Masgils,
>
> you may try something along these lines, i.e. make atoms and/or bonds
> generic on one of the molecules with rdmolops.AdjustQueryProperties() in
> order to get subtructures to match, and then use rdMolAlign.GetBestRMS():
>
> piperidine =
> Chem.AddHs(Chem.MolFromSmiles("C1CC(C)CCN1"))AllChem.EmbedMolecule(piperidine)AllChem.MMFFOptimizeMolecule(piperidine)piperidine_noh
> = Chem.RemoveHs(piperidine)
>
> piperazine =
> Chem.AddHs(Chem.MolFromSmiles("C1CN(C)CCN1"))AllChem.EmbedMolecule(piperazine)AllChem.MMFFOptimizeMolecule(piperazine)piperazine_noh
> = Chem.RemoveHs(piperazine)
>
> piperidine_noh
>
> piperazine_noh
>
> piperidine_noh.GetSubstructMatches(piperazine_noh)
>
> ()
>
> params = AllChem.AdjustQueryParameters()
>
> params.makeAtomsGeneric = True
>
> params.makeBondsGeneric = True
>
> piperazine_noh_generic = AllChem.AdjustQueryProperties(
> piperazine_noh, params)
>
> piperazine_noh_generic
>
> piperidine_noh.GetSubstructMatches(piperazine_noh_generic)
>
> ((0, 1, 2, 3, 4, 5, 6),)
>
> AllChem.GetBestRMS(piperazine_noh_generic, piperidine_noh)
>
> 0.39432427325884206
>
>
> Hope this helps, cheers
> p.
>
> On 07/25/19 16:53, Masgils wrote:
>
> 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?
>
>
>
>
>
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