Re: [Rdkit-discuss] How to get substructure matches with different atoms?
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!
> 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)
> in
> 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" 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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>
>
>
>
>
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Re: [Rdkit-discuss] How to get substructure matches with different atoms?
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)
in
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" wrote:
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"))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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Re: [Rdkit-discuss] How to get substructure matches with different atoms?
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"))
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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[Rdkit-discuss] How to get substructure matches with different atoms?
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? ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Adding molecules to pandas dataframe
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 demonstrating: https://gist.github.com/greglandrum/914ae66fd2f97addbbd472ae726567b1 -greg On Thu, Jul 25, 2019 at 4:45 PM Gianluca Sforna wrote: > 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 and examples I found around always assume you have a > SMILES string to start with. > > Any pointers? > > -- > Gianluca Sforna > > > ___ > 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] Adding molecules to pandas dataframe
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"] = mols Best, Christos Christos Kannas Scientific Software Developer (Cheminformatics) On Thu, 25 Jul 2019 at 15:45, Gianluca Sforna wrote: > 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 and examples I found around always assume you have a > SMILES string to start with. > > Any pointers? > > -- > Gianluca Sforna > > > ___ > 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] Adding molecules to pandas dataframe
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 and examples I found around always assume you have a SMILES string to start with. Any pointers? -- Gianluca Sforna ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
