TypeError: No registered converter was able to produce a C++ rvalue of type class

[abuhaby]

• RDKit Version: '2019.03.4'
• Operating system: windows 10, 64bits
• Python version (if relevant): 3.7
• Are you using conda? YES
• If you are using conda, which channel did you install the rdkit from?
• If you are not using conda: how did you install the RDKit?

Description:
When I try to below code in jupyter notebook:

smiles_list = ['C(C(=O)O)N' , 'NC@@HC(O)=O']
mol_list = []
for smiles in smiles_list:
mol = Chem.MolFromSmiles(smiles_list)
mol_list.append(mol)
img = Draw.MolsToGridImage(mol_list)
img

I get the following error message:

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 list

KINDLY HELP ME FIX THE ABOVE ERROR.

[bp-kelley]

You appear to be sending the list into MolFromSmiles: mol = Chem.MolFromSmiles(smiles_list)

…

---- Brian Kelley

On Mar 10, 2020, at 4:07 AM, abuhaby ***@***.***> wrote: mol = Chem.MolFromSmiles(smiles_list)

[ptosco]

@abuhaby Brian is right. You are looping on smiles_list but then pass smiles_list to Chem.MolFromSmiles rather than smiles. Your code should be:

smiles_list = ['C(C(=O)O)N' , 'NC@@HC(O)=O']
mol_list = []
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    mol_list.append(mol)
img = Draw.MolsToGridImage(mol_list)

or, more concisely and efficiently:

mol_list = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
img = Draw.MolsToGridImage(mol_list)

[abuhaby]

@ptosco, Thank you Ptosco. It worked after I applied your fix.
I am trying to learn python and rdkit on the fly. Any suggestion for good learning material for a starter. Especially good resources for cheminformatics related stuff where i can utilize databases, molecular finger and biological activities.

[bp-kelley]

The RDKit blog is a good start:

http://rdkit.blogspot.com

It doesn't talk about databases, but it will give you a head start on some techniques.

[abuhaby]

I will try that. Thanks.

[seyonechithrananda]

@ptosco Thanks for the fix! Ran into the same issue and realized I had accidentally called the list, not the SMILES string itself :)

@abuhaby Brian is right. You are looping on smiles_list but then pass smiles_list to Chem.MolFromSmiles rather than smiles. Your code should be:

smiles_list = ['C(C(=O)O)N' , 'NC@@HC(O)=O']
mol_list = []
for smiles in smiles_list:
    mol = Chem.MolFromSmiles(smiles)
    mol_list.append(mol)
img = Draw.MolsToGridImage(mol_list)

or, more concisely and efficiently:

mol_list = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
img = Draw.MolsToGridImage(mol_list)

[Inioluwajeremiah]

I had the same issue but later discovered that it was because some rows didn't have the canonical smiles notation but rather NaN. This makes it impossible to iterate through the column successfully while trying to generate descriptors using the for loop.

[Inioluwajeremiah]

Do a data clean up to resolve the issue. In my case, the line of code below solved it

 df2 = df[df.canonical_smiles.notna()] 

[charlesxu90]

I had the same issue but later discovered that it was because some rows didn't have the canonical smiles notation but rather NaN. This makes it impossible to iterate through the column successfully while trying to generate descriptors using the for loop.

This explains my problem. There's a Nan in the smiles list, which causes my problem.

[Inioluwajeremiah]

Trust you were able to resolve the issue

…

On Sun, Feb 27, 2022, 9:17 AM Xiaopeng Xu ***@***.***> wrote: I had the same issue but later discovered that it was because some rows didn't have the canonical smiles notation but rather *NaN*. This makes it impossible to iterate through the column successfully while trying to generate descriptors using the for loop. This explains my problem. There's a Nan in the smiles list, which causes my problem. — Reply to this email directly, view it on GitHub <#2994 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALSATJUMRKJFTG6ONR7SKO3U5HM2XANCNFSM4LEZGZYQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[acchu69]

facing the same issue
for this part of the code
df = pd.DataFrame(load_data[0])
smiless=df.astype(str)
smiles_list = [smiless]
mol_list = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
img = Draw.MolsToGridImage(mol_list)
st.write(img)
error message :
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 DataFrame
traceback:
File "C:\Users\Admin\Desktop\alzheimers dd app\app.py", line 101, in
mol_list = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Admin\Desktop\alzheimers dd app\app.py", line 101, in
mol_list = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
^^^^^^^^^^^^^^^^^^^^^^^^^^

[ptosco]

@acchu69 Please do not post on closed issues - post in Discussions if you have a question as it may help others.
In your code above, smiless is a DataFrame, as you call astype(str) on the whole DataFrame:

import pandas as pd

df = pd.DataFrame({"index": [1,2], "smiles": ["C", "CC"]})
type(df.astype(str))
pandas.core.frame.DataFrame

If you want a list of SMILES as strings, you need something like:

smiles_list = df.smiles.astype(str).to_list()
smiles_list
['C', 'CC']