Re: [Rdkit-discuss] Parsing a PDB file with atoms that are too close, causing bad bond

[Paul E. <pe...@mr...>]

 >  PDB files have no bond information,

This is not true. The chemistry is specified in the Chemical Component Dictionary using the residue 
identifier (so it's a reference to a chemical description, it's not embedded).

https://www.wwpdb.org/data/ccd

https://github.com/pdbeurope/ccdutils

Paul.


On 27/09/2021 11:22, Lewis Martin wrote:
> Very interesting - thank you Francois! PDB re-do does the trick:
> 
> *import requests
> from rdkit import Chem
> 
> def getPDB(code):
>      out = requests.get(f'https://pdb-redo.eu/db/{code}/{code}_final.pdb 
> <https://pdb-redo.eu/db/{code}/{code}_final.pdb>')
>      return out.content
> 
> pdb_string = getPDB('3udn')
> Chem.MolFromPDBBlock(pdb_string)*
> 
> I think this solves it for me, but if anyone knows how to infer correct bonding information without relying 
> on distances, I'd love to hear it too! So far I've noticed that Parmed and PDBFixer infer correct bonds, but 
> they don't determine bond orders, so it's difficult to port the molecule into RDKit.
> 
> Cheers
> Lewis
> 
> 
> 
> On Mon, Sep 27, 2021 at 5:55 PM Francois Berenger <ml...@li... <mailto:ml...@li...>> wrote:
> 
>     Hi Lewis,
> 
>     Just an idea: you might try to load your PDB in UCSF Chimera, then
>     save it as a mol2 or sdf file.
>     Then, try to read this sdf file from rdkit.
> 
>     Another idea: try to get your pdb file through the pdbredo service.
>     https://pdb-redo.eu/ <https://pdb-redo.eu/>
>     They might have fixed a few things; maybe this PDB will read better in
>     rdkit.
> 
>     Regards,
>     F.
> 
>     On 26/09/2021 17:02, Lewis Martin wrote:
>      > Hi RDKit,
>      > While parsing proteins from the PBD with RDKit, I've come across
>      > situations where the distance-based bond determination leads to
>      > 'incorrect' bonds between atoms that are erroneously too close
>      > together. PDB files have no bond information, so it's not really
>      > 'incorrect' (rather the model coordinates are off), but the bonds are
>      > nonphysical - and it means the Mol objects won't sanitize.
>      >
>      > Here's an example:
>      >
>      > import requests
>      > from io import BytesIO
>      > import gzip
>      > from rdkit import Chem
>      >
>      > def getPDB(code):
>      >     out =
>      > requests.get(f'https://files.rcsb.org/download/{code}.pdb1.gz
>     <https://files.rcsb.org/download/%7Bcode%7D.pdb1.gz> [1]')
>      >     binary_stream =  BytesIO(out.content)
>      >     return gzip.open(binary_stream).read()
>      >
>      > pdb_string = getPDB('3udn')
>      > Chem.MolFromPDBBlock(pdb_string)
>      >
>      > Error is:
>      >
>      > RDKit ERROR: [22:38:21] Explicit valence for atom # 573 O, 3, is
>      > greater than permitted
>      >
>      > This is caused by the threonine 72 sidechain being too close to the
>      > TYR71 backbone carbonyl oxygen (this can be visualized at
>      > https://www.rcsb.org/3d-view/3UDN?preset=ligandInteraction&sele=09B
>     <https://www.rcsb.org/3d-view/3UDN?preset=ligandInteraction&sele=09B> ,
>      > TYR71 is near the ligand).
>      >
>      > Does anyone know how to avoid this to create a Chem.Mol? I've tried
>      > using Parmed and PDBFixer, since they use residue templates to
>      > generate the correct bonding topology, but they don't write CONECT
>      > records or SDFs, so the bonds are still lost to RDKit.
>      >
>      > Thanks for your time!
>      > Lewis
>      > PS - why not just use PDBFixer? I'm trying to calculate atom
>      > invariants using RDKit's morgan fingerprinter implementation, so
>      > ultimately I want a sanitized Mol object
>      >
>      > Links:
>      > ------
>      > [1] https://files.rcsb.org/download/%7Bcode%7D.pdb1.gz
>     <https://files.rcsb.org/download/%7Bcode%7D.pdb1.gz>
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> 
> 
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