Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

[Illimar Hugo Rekand]

Thanks, Paolo, for a good and clear example.


I adapted your code into my workflow to calculate some Lipinski-properties of 
RNA pdb-structures, and ran into some issues. I'm not sure if I should make a 
new thread or throw this onto this one I already created?


I used the following code under


from rdkit import Chem
from rdkit.Chem import rdmolops, Lipinski
from urllib.request import urlopen
import gzip
import pprint
pp = pprint.PrettyPrinter(indent=4)


Lipinski_dic = {'FractionCSP3':Lipinski.FractionCSP3,
                'HeavyAtomCount':Lipinski.HeavyAtomCount,
                'NHOHCount': Lipinski.NHOHCount,
                "NOCount":Lipinski.NOCount,
                "NumAliphaticCarbocycles": Lipinski.NumAliphaticCarbocycles,
                "NumAliphaticHeterocycles" : Lipinski.NumAliphaticHeterocycles,
                'NumAliphaticRings' :  Lipinski.NumAliphaticRings,
                'NumAromaticCarbocycles' : Lipinski.NumAromaticCarbocycles,
                'NumAromaticHeterocycles' : Lipinski.NumAromaticHeterocycles,
                'NumAromaticRings' : Lipinski.NumAromaticRings,
                'NumHAcceptors' : Lipinski.NumHAcceptors,
                'NumHDonors' : Lipinski.NumHDonors,
                'NumHeteroatoms' : Lipinski.NumHeteroatoms,
                'NumRotatableBonds' : Lipinski.NumRotatableBonds,
                'NumSaturatedCarbocycles' : Lipinski.NumSaturatedCarbocycles,
                'NumSaturatedHeterocycles' : Lipinski.NumSaturatedHeterocycles,
                'NumSaturatedRings' : Lipinski.NumSaturatedRings,
                'RingCount' : Lipinski.RingCount
                }

url =  "https://files.rcsb.org/download/1arj.pdb.gz";
pdb_data = gzip.decompress(urlopen(url).read())
mol = Chem.RWMol(Chem.MolFromPDBBlock(pdb_data))
bonds_to_cleave = {(b.GetBeginAtomIdx(), b.GetEndAtomIdx()) for b in 
mol.GetBonds() if b.GetBeginAtom().GetPDBResidueInfo().GetIsHeteroAtom() ^ 
b.GetEndAtom().GetPDBResidueInfo().GetIsHeteroAtom()}
[mol.RemoveBond(*b) for b in bonds_to_cleave]
hetatm_frags = [f for f in rdmolops.GetMolFrags(mol, asMols=True, 
sanitizeFrags=True) if f.GetNumAtoms() and 
f.GetAtomWithIdx(0).GetPDBResidueInfo().GetIsHeteroAtom()]
for hetatm in hetatm_frags:
    res_name = hetatm.GetAtomWithIdx(0).GetPDBResidueInfo().GetResidueName()
    calculated_props = {}
    for prop in Lipinski_dic:
        function = Lipinski_dic[prop]
        x = function(hetatm)
        calculated_props[prop] = x
    pp.pprint(calculated_props)


and as you can see the properties of the ligand doesn't match up with what is 
expected (The number of SP3-atoms doesn't match up). When parsing through the 
structure 3got, it fails to recognize the aromatic rings of the ligand A2F. I'm 
assuming this is caused by RDKit not assigning bond orders correctly when 
reading in RNA and DNA pdb files (something which I have reported in earlier on 
this mailing list)?


Running hetatm.UpdatePropertyCache(strict=True) does not remedy this problem. 
Is there a clever way I can fix this quickly without waiting for this to be 
fixed in a future version?


Illimar Rekand
Ph.D. candidate,
Brenk-lab, Haug-lab
Department of Biomedicine
Department of Chemistry
University of Bergen


________________________________
From: Illimar Hugo Rekand
Sent: Monday, December 16, 2019 5:55:56 PM
To: Paolo Tosco
Subject: Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand


Hey, Paolo,


thanks for a good and clear example!


all the best,


Illimar Rekand
Ph.D. candidate,
Brenk-lab, Haug-lab
Department of Biomedicine
Department of Chemistry
University of Bergen


________________________________
From: Paolo Tosco <paolo.tosco.m...@gmail.com>
Sent: Monday, December 16, 2019 5:52:18 PM
To: Illimar Hugo Rekand; rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

Hi Illimar,

this gist:

https://gist.github.com/ptosco/2ee199b219b27e01052a7a1433b3bd22

shows a way to achieve this.

Cheers,
p.

On 16/12/2019 16:07, Illimar Hugo Rekand wrote:
> Hello, everyone
>
>
> Is there a simple way to create a mol object from just the HETATM/ligand 
> lines from a pdb-file?
>
> Would it be viable to create a function where you could create a mol object 
> from specific lines within a pdb-file?
>
>
> Illimar Rekand
> Ph.D. candidate,
> Brenk-lab, Haug-lab
> Department of Biomedicine
> Department of Chemistry
> University of Bergen
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


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