[Rdkit-discuss] Build matching 3D structure

2020-07-27 Thread Rafael da Fonseca Lameiro 
Hello
I'm having a hard time trying to build a 3D structure for a new molecule
(new) based on a reference molecule (ref).
In this case, ref is a substructure of new, and I want the coordinates of
their matching atoms to be exactly the same.
I have tried using:
  Chem.rdDepictor.GenerateDepictionMatching3DStructure (only works if both
molecules are the same)

rdkit.Chem.AllChem.ConstrainedEmbed (I get ValueError: molecule doesn't
match the core)

AllChem.AlignMol (I need to input a 3D structure for new, which doesn't
match ref)

I thought about generating a ton of conformers for new using
AllChem.EmbedMultipleConfs and then use the one with the best alignment to
ref, but I figured there should be a better way to do this. I would
appreciate any suggestions.
On a side note, is there a way to convert Chem.rdchem.Conformer objects to
Chem.rdchem.Mol?

Thank you for the help

Rafael
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[Rdkit-discuss] Manganese ion as a radical?

2020-07-27 Thread Lukas Pravda 
Dear rdkit community,

 

I’m not quite sure if this is more of an rdkit or a chemistry related question. 
I’d like to understand why a manganese ion has 3 radical electrons when 
interpreted by rdkit. I have not seen radicals in any other metal ion so far.

 

The code to get the depiction looks like this:

from rdkit import Chem

from rdkit.Chem import Draw

 

width = 500

 

m = Chem.MolFromInchi('InChI=1S/Mn/q+2')

drawer = Draw.rdMolDraw2D.MolDraw2DSVG(width, width)

 

Draw.rdMolDraw2D.PrepareMolForDrawing(m, wedgeBonds=True, kekulize=True, 
addChiralHs=True)

 

drawer.DrawMolecule(m)

drawer.FinishDrawing()

 

with open('2d_mol.svg', 'w') as f:

    svg = drawer.GetDrawingText()

    f.write(svg)

 

print('done')

 

and the depiction you get looks like the one on the page: 
https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/MN Thank you in 
advance for clarification.

 

 

rdkit through python 2020.03.4 on mac 10.15.6

 

Best,

Lukas

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Re: [Rdkit-discuss] Define identical atoms in SMARTS pattern

2020-07-27 Thread Jan Halborg Jensen 
Thanks you to David, Ivan, and Hao for the very useful answers.

Best regards, Jan

> On 24 Jul 2020, at 15.51, Jan Halborg Jensen  wrote:
> 
> Is there a way to find a [C]([#X])[#X] pattern, where X=X, that finds C(C)C, 
> C(O)O, C(F)F, etc., but not C(C)O, etc.?
> 
> Best regards, Jan
> 
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