Hi Mateo,
On Thu, Jun 6, 2019 at 6:29 PM Mateo Vacacela <mvacac...@cdrd.ca> wrote:
>
>
> I’m getting the following error when trying to sanitize a protein from a
> published pdb file (1E66):
>
>
>
> ValueError: Sanitization error: Explicit valence for atom # 1254 C, 5, is
> greater than permitted
>
>
The error message is telling you what the problem is: there's a carbon atom
in the system that has a valence (=number of bonds - charges) of 5. That's
illegal for carbon. This type of error typically indicates a problem with
the input file.
I will note that I downloaded the PDB file for 1E66 from the PDB website
and it worked fine for me, so something may have happened to the file you
are using?
In [6]: import requests
In [9]: d = requests.get('https://files.rcsb.org/download/1E66.pdb')
In [10]: d.content[:5]
Out[10]: b'HEADE'
In [12]: with open('1e66.pdb','wb+') as outf:
...: outf.write(d.content)
...:
In [13]: m = Chem.MolFromPDBFile('1e66.pdb',sanitize=False,removeHs=False)
In [14]: nm = Chem.SanitizeMol(m)
In [15]:
>
>
> Here is the script I’m running to recreate the error. I’ve replicated it
> based off of a script from the deepchem library:
>
>
This script is very strange.
> ######## Script Starts ########
>
> import tempfile
>
> import os
>
> from rdkit import Chem
>
> from rdkit.Chem import rdmolops
>
>
>
> protein_pdb = 'receptor.pdb'
>
>
>
> with open(protein_pdb) as protein_file:
>
> protein_pdb_lines = protein_file.readlines()
>
>
>
> tempdir = tempfile.mkdtemp()
>
>
>
> protein_pdb_file = os.path.join(tempdir, "protein.pdb")
>
> with open(protein_pdb_file, "w") as protein_f:
>
> protein_f.writelines(protein_pdb_lines)
>
>
This first bit seems to just be copying the file, I'm not sure why you
would want to do that.
> molecule_file = protein_pdb_file
>
> my_mol = Chem.MolFromPDBFile(str(molecule_file), sanitize=False,
> removeHs=False)
>
> mol = Chem.SanitizeMol(my_mol) # Error occurs here
>
>
This doesn't sense. It's shorter (and produces the same result) to just do:
mol = Chem.MolFromPDBFile(str(molecule_file), removeHs=False)
That will sanitize the structure but leave the Hs.
-greg
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
