add notebook showing molecule manipulation w/RDKit

[janash]

@paulcraig - see this notebook for suggestion on molecule manipulation and optimization using RDKit. This starts from the ideal structure pulled from the PDB

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paulcraig commented on 2024-06-26T09:55:05Z
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Line #6.    constrained_mol

I got an error on my laptop and on chemcompute.org when I tried to execute this cell: The kernel stopped and needed to be restarted (or something like that). Then I just did it again on my notebook and got this message:

ValueError                                Traceback (most recent call last)
Cell In[8], line 5
      1 # Repeat process on methyl ligand
      3 mod_ligand_methylH = Chem.AddHs(mod_ligand_methyl)
----> 5 constrained_mol = AllChem.ConstrainedEmbed(mod_ligand_methylH, mod_ligand_methyl, useTethers=True)
      6 constrained_mol

File ~/anaconda3/lib/python3.10/site-packages/rdkit/Chem/AllChem.py:313, in ConstrainedEmbed(mol, core, useTethers, coreConfId, randomseed, getForceField, **kwargs)
    311 ci = EmbedMolecule(mol, coordMap=coordMap, randomSeed=randomseed, **kwargs)
    312 if ci < 0:
--> 313   raise ValueError('Could not embed molecule.')
    315 algMap = [(j, i) for i, j in enumerate(match)]
    317 if not useTethers:
    318   # clean up the conformation

ValueError: Could not embed molecule.

[janash]

It's working for me locally - I'll try it on chemcompute and see what happens. It could be something with the RDKit version