PDB Import issue : MolFromPDBFile() vs MolFromPDBBlock()

[urekam712]

Kindly refer the file attached
The data from the file is used for both MolFromPDBFile() and MolFromPDBBlock()

#PDB FILE
from rdkit import Chem
from rdkit.Chem import AllChem, Draw, rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw import rdMolDraw2D, rdDepictor
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
k = Chem.MolFromPDBFile("DNA.pdb")

print(k)
d2d = Draw.MolDraw2DSVG(1000, 1000, -1, -1, True)
d2d.DrawMolecule(k)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
SVG(txt)

OUTPUT:

from rdkit import Chem
from rdkit.Chem import AllChem, Draw, rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw import rdMolDraw2D, rdDepictor
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
from rdkit import rdBase
from rdkit.Chem import Draw
print(rdBase.rdkitVersion)


pdb = "---pl add pdb string copied from the file attached below ---" 
m = Chem.MolFromPDBBlock(pdb)

print(m)
d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
SVG(txt)

output:

DNA.pdb.txt

[joseerlang]

Hi there,
I'm pretty new to the project, I'm still starting to understand it, but I think you need to use the function
Chem.MolToPDBBlock function before calling MolFromPDBBlock . You have an example in the following test

rdkit/Code/GraphMol/Wrap/rough_test.py

Line 3315 in a087cfd

m = Chem.MolFromPDBBlock(Chem.MolToPDBBlock(m))

[urekam712]

Hi there, I'm pretty new to the project, I'm still starting to understand it, but I think you need to use the function Chem.MolToPDBBlock function before calling MolFromPDBBlock . You have an example in the following test

rdkit/Code/GraphMol/Wrap/rough_test.py

Line 3315 in a087cfd

m = Chem.MolFromPDBBlock(Chem.MolToPDBBlock(m))

refer this file pdbparser.cpp : https://github.com/rdkit/rdkit/blob/a087cfd894497e98936245605dd87ca7f0f3de2a/Code/GraphMol/FileParsers/PDBParser.cpp

where MolFromPDBFile calls ---> MolFromPDBDataStream( file data getting parsed) ---> MolFromPDBBlock

this is obvious that MolFromPDBFile depends on MolFromPDBBlock

then why this difference between importing MolFromPDBFile vs MolFromPDBBlock

@joseerlang

@

[joseerlang]

Hi @urekam712 ,

I think the problem you have in your code has to do with the way you define the pdb variable, because you are putting a string without the carriage returns and that is influencing the calling of the MolFromPDBBlock method.

I leave you an example that works in my installation so that you can try it in yours.

fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'1CRN.pdb')
with open(fileN, 'r') as f:
pdb = f.read()

m = Chem.MolFromPDBBlock(pdb)

print(m)
d2d = Draw.MolDraw2DSVG(250, 200, -1, -1, True)
d2d.DrawMolecule(m)
d2d.FinishDrawing()
txt = d2d.GetDrawingText()
SVG(txt)

[joseerlang]

@urekam712 could this ticket be closed?