Rdkit run with streamlit leads to argument error

Using Streamlit
1

The following example works fine if it is run directly from the python file.

import streamlit as st

from rdkit import Chem
from rdkit.Chem import Draw

compound_smiles = 'C'
list_compounds = [Chem.MolFromSmiles(compound_smiles)]
fig = Draw.MolsToGridImage(list_compounds, legends = ['methane'],
                               molsPerRow = 1, maxMols = 1)

If it is run with streamlit, it produces the following error:

ArgumentError: Python argument types in MolDraw2D.DrawMolecules(MolDraw2DCairo, list) did not match C++ signature: DrawMolecules(RDKit::MolDraw2D {lvalue} self, boost::python::api::object mols, boost::python::api::object highlightAtoms=None, boost::python::api::object highlightBonds=None, boost::python::api::object highlightAtomColors=None, boost::python::api::object highlightBondColors=None, boost::python::api::object highlightAtomRadii=None, boost::python::api::object confIds=None, boost::python::api::object legends=None)

Traceback:

File "/home/lili/SDSC/Projects/MSEI/raw-data-preprocessing/conda-env-full/lib/python3.7/site-packages/streamlit/ScriptRunner.py", line 322, in _run_script
    exec(code, module.__dict__)
File "/home/lili/SDSC/Projects/MSEI/raw-data-preprocessing/trystuff/rdkit-streamlit-minimalexample.py", line 9, in <module>
    molsPerRow = 1, maxMols = 1)
File "/home/lili/SDSC/Projects/MSEI/raw-data-preprocessing/conda-env-full/lib/python3.7/site-packages/rdkit/Chem/Draw/__init__.py", line 497, in MolsToGridImage
    highlightBondLists=highlightBondLists, **kwargs)
File "/home/lili/SDSC/Projects/MSEI/raw-data-preprocessing/conda-env-full/lib/python3.7/site-packages/rdkit/Chem/Draw/__init__.py", line 443, in _MolsToGridImage
    highlightBonds=highlightBondLists, **kwargs)

Any idea how this could be solved?

Thanks in advance!

2

Hi @Lili, welcome to the Streamlit community!

Where does this work when you are running it, and what is it supposed to do? On my Ubuntu 18.04 machine, it doesn’t work either:

Python 3.8.3 (default, May 19 2020, 18:47:26) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.15.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from rdkit import Chem                                                                           

In [2]: from rdkit.Chem import Draw                                                                      

In [3]: compound_smiles = 'C'                                                                            

In [4]: list_compounds = [Chem.MolFromSmiles(compound_smiles)]                                           

In [5]: fig = Draw.MolsToGridImage(list_compounds, legends = ['methane'], 
   ...:                                molsPerRow = 1, maxMols = 1)                                      
---------------------------------------------------------------------------
ArgumentError                             Traceback (most recent call last)
<ipython-input-5-d6f40020f9da> in <module>
----> 1 fig = Draw.MolsToGridImage(list_compounds, legends = ['methane'],
      2                                molsPerRow = 1, maxMols = 1)

~/miniconda3/envs/maddy/lib/python3.8/site-packages/rdkit/Chem/Draw/__init__.py in MolsToGridImage(mols, molsPerRow, subImgSize, legends, highlightAtomLists, highlightBondLists, useSVG, **kwargs)
    575                           highlightBondLists=highlightBondLists, **kwargs)
    576   else:
--> 577     return _MolsToGridImage(mols, molsPerRow=molsPerRow, subImgSize=subImgSize, legends=legends,
    578                             highlightAtomLists=highlightAtomLists,
    579                             highlightBondLists=highlightBondLists, **kwargs)

~/miniconda3/envs/maddy/lib/python3.8/site-packages/rdkit/Chem/Draw/__init__.py in _MolsToGridImage(mols, molsPerRow, subImgSize, legends, highlightAtomLists, highlightBondLists, drawOptions, **kwargs)
    522           setattr(dops, k, v)
    523           del kwargs[k]
--> 524     d2d.DrawMolecules(list(mols), legends=legends, highlightAtoms=highlightAtomLists,
    525                       highlightBonds=highlightBondLists, **kwargs)
    526     d2d.FinishDrawing()

ArgumentError: Python argument types in
    MolDraw2D.DrawMolecules(MolDraw2DCairo, list)
did not match C++ signature:
    DrawMolecules(RDKit::MolDraw2D {lvalue} self, boost::python::api::object mols, boost::python::api::object highlightAtoms=None, boost::python::api::object highlightBonds=None, boost::python::api::object highlightAtomColors=None, boost::python::api::object highlightBondColors=None, boost::python::api::object highlightAtomRadii=None, boost::python::api::object confIds=None, boost::python::api::object legends=None)

So I’m not sure this is a Streamlit issue, unless there is an interaction somewhere on install.

3

Hi @randyzwitch, thanks for your answer!

It works on my Ubuntu 18.04 with Python 3.7.7. The code should draw an image with the molecular structure of methane based on its so-called smiles (‘C’).

Any idea where I can start looking to solve this?

4

Not sure where to get started, but what I do know is that Cairo is one of those fiddly C libraries that needs just the right setup, and it sounds like this one of those problems that conda was created to fix.

Given that it complains about the function signature, I suspect that the issue is that the Python library requires a specific version of Cairo, and if there is a different version installed, then Python binds to that wrong version and everything blows up. :frowning:

5

Simply adding this line

from rdkit.Chem.Draw import IPythonConsole

to the imports solved it. Glad it was so easy!

Thanks a lot for your time!

1 Like
6

Awesome, glad you figured it out! Does this now allow for use within Streamlit?

7

Yes, now it runs smoothly within streamlit.

1 Like