Hi Luke,
Finally I was able to try this one. Thank you!
All the best,
Joanna
________________________________
From: Luke Zulauf <l...@zymergen.com>
Sent: Wednesday, July 15, 2020 1:02 AM
To: ITS RDC <itsrdc...@outlook.com>
Cc: rdkit-discuss@lists.sourceforge.net <rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Trouble with Chem.MolFromSmiles
Hi Joanna,
There's no need to call MolFromSmiles if you're using a MolSupplier (which
generates Mol objects already) - you just need to iterate over the Mol objects
it generates:
from rdkit import Chem
from rdkit.Chem import rdmolfiles
# Create the mol supplier, reading from the input file
supplier = Chem.SmilesMolSupplier('directory/filename.smi', delimiter='\t',
titleLine=False)
# Iterate over the molecules. We can either convert the supplier to a list of
molecules:
molecules = list(supplier)
# Or simply iterate over the supplier directly:
for molecule in supplier:
# Add explicit Hs
# Convert to sdf
pass
I hope that helps!
Luke Zulauf
Staff Software Engineer, Cheminformatics
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On Tue, Jul 14, 2020 at 8:59 AM ITS RDC
<itsrdc...@outlook.com<mailto:itsrdc...@outlook.com>> wrote:
Hi all,
I have a SMILES list containing 251 SMILES strings (collected from a csv file)
which I needed to convert to mol files because Open Babel is not doing its job
in adding explicit Hs in batches before being converted to .sdf so I can
process the molecules in rdkit and PyRx. So I am trying to use RDKit as an
alternative to generate what I need.
I used the following:
from rdkit import Chem
from rdkit.Chem import rdmolfiles
suppl_smiles = []
temp =
Chem.SmilesMolSupplier('directory/filename.smi',delimiter='\t',titleline=False)
y = len(temp)
for x in range (y):
suppl_smiles.append(temp)
temp2 = suppl_smiles[x]
temp3 = Chem.MolFromSmiles(temp2)
The one in highlight always returns the following:
TypeError: No registered converter was able to produce a C++ rvalue of type
class std::basic_string<wchar_t,struct std::char_traits<wchar_t>,class
std::allocator<wchar_t> > from this Python object of type SmilesMolSupplier
I have been looking in GitHub, Source Forge, and other fora regarding batch
conversion of smiles to mol files (I only encountered sdf containing multiple
molecules to smiles which I already figured out) but I have not seen using
MolFromSmiles using calling the tuple index as an object. I'd appreciate your
help. Thank you.
Joanna
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