AttributeError: 'MolDraw2DSVG' object has no attribute 'SetDrawOptions'
LiuCMU opened this issue · comments
import pandas as pd
import mols2grid
smiles = ["CCO", "c1ccccc1", "N", "CO", "O=S(=O)(-O)(-O)", "CCC", "CCC=O"]
df = pd.DataFrame({"smi": smiles,
"id": range(1, len(smiles) + 1)})
mg = mols2grid.MolGrid(df, smiles_col="smi", size=(110, 90))
mg.display(subset=["id", "img"], n_cols=7)
I was trying to visualize a list of SMILES, as shown in your colab. But I got the following error message.
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-26-cbf1ce952db4> in <module>
7 "id": range(1, len(smiles) + 1)})
8 # setup the grid
----> 9 mg = mols2grid.MolGrid(df, smiles_col="smi", size=(110, 90))
10 mg.display(subset=["id", "img"], n_cols=7)
~/anaconda3/lib/python3.7/site-packages/mols2grid/molgrid.py in __init__(self, df, smiles_col, mol_col, coordGen, useSVG, mapping, **kwargs)
74 dataframe.dropna(axis=0, subset=[mol_col], inplace=True)
75 # generate drawings
---> 76 dataframe["img"] = dataframe[mol_col].apply(self.mol_to_img, **kwargs)
77 self.dataframe = dataframe
78 self.mol_col = mol_col
~/anaconda3/lib/python3.7/site-packages/pandas/core/series.py in apply(self, func, convert_dtype, args, **kwds)
4133 else:
4134 values = self.astype(object)._values
-> 4135 mapped = lib.map_infer(values, f, convert=convert_dtype)
4136
4137 if len(mapped) and isinstance(mapped[0], Series):
pandas/_libs/lib.pyx in pandas._libs.lib.map_infer()
~/anaconda3/lib/python3.7/site-packages/pandas/core/series.py in f(x)
4118
4119 def f(x):
-> 4120 return func(x, *args, **kwds)
4121
4122 else:
~/anaconda3/lib/python3.7/site-packages/mols2grid/molgrid.py in mol_to_img(self, mol, **kwargs)
170 """Convert an RDKit mol to an HTML img tag containing a drawing of the
171 molecule"""
--> 172 img = self.draw_mol(mol, **kwargs)
173 if self.useSVG:
174 return img
~/anaconda3/lib/python3.7/site-packages/mols2grid/molgrid.py in draw_mol(self, mol, size, use_coords, MolDrawOptions, **kwargs)
158 for key, value in kwargs.items():
159 setattr(MolDrawOptions, key, value)
--> 160 d2d.SetDrawOptions(MolDrawOptions)
161 if not use_coords:
162 mol = deepcopy(mol)
AttributeError: 'MolDraw2DSVG' object has no attribute 'SetDrawOptions'
could you please take a look maybe? Thanks!
Hi @LiuCMU,
Which version of RDKit are you using ? You can check that with:
import rdkit
print(rdkit.__version__)Hi, thanks for the quick response:))
my RDKit version is 2019.03.2
Try updating RDKit to version 2019.09.1 or above: conda install -c conda-forge 'rdkit>=2019.09.1' and tell me if that works
Hi, I've updated to RDKit 2019.09.3. This gives me the Value Error:
# example dataframe
import pandas as pd
smiles = ["CCO", "c1ccccc1", "N", "CO", "O=S(=O)(-O)(-O)", "CCC", "CCC=O"]
df = pd.DataFrame({"smi": smiles,
"id": range(1, len(smiles) + 1)})
# setup the grid
mg = mols2grid.MolGrid(df, smiles_col="smi", size=(110, 90))
mg.display(subset=["id", "img"], n_cols=7)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-327fbcd76707> in <module>
6 "id": range(1, len(smiles) + 1)})
7 # setup the grid
----> 8 mg = mols2grid.MolGrid(df, smiles_col="smi", size=(110, 90))
9 mg.display(subset=["id", "img"], n_cols=7)
~/anaconda3/lib/python3.7/site-packages/mols2grid/molgrid.py in __init__(self, df, smiles_col, mol_col, coordGen, useSVG, mapping, **kwargs)
74 dataframe.dropna(axis=0, subset=[mol_col], inplace=True)
75 # generate drawings
---> 76 dataframe["img"] = dataframe[mol_col].apply(self.mol_to_img, **kwargs)
77 self.dataframe = dataframe
78 self.mol_col = mol_col
~/anaconda3/lib/python3.7/site-packages/pandas/core/series.py in apply(self, func, convert_dtype, args, **kwds)
4133 else:
4134 values = self.astype(object)._values
-> 4135 mapped = lib.map_infer(values, f, convert=convert_dtype)
4136
4137 if len(mapped) and isinstance(mapped[0], Series):
pandas/_libs/lib.pyx in pandas._libs.lib.map_infer()
~/anaconda3/lib/python3.7/site-packages/pandas/core/series.py in f(x)
4118
4119 def f(x):
-> 4120 return func(x, *args, **kwds)
4121
4122 else:
~/anaconda3/lib/python3.7/site-packages/mols2grid/molgrid.py in mol_to_img(self, mol, **kwargs)
170 """Convert an RDKit mol to an HTML img tag containing a drawing of the
171 molecule"""
--> 172 img = self.draw_mol(mol, **kwargs)
173 if self.useSVG:
174 return img
~/anaconda3/lib/python3.7/site-packages/mols2grid/molgrid.py in draw_mol(self, mol, size, use_coords, MolDrawOptions, **kwargs)
163 mol.RemoveAllConformers()
164 hl_atoms = getattr(mol, "__sssAtoms", [])
--> 165 d2d.DrawMolecule(mol, highlightAtoms=hl_atoms)
166 d2d.FinishDrawing()
167 return d2d.GetDrawingText()
ValueError: Bad Conformer Id
Hmmm it appears I've messed up with the minimal RDKit version! I could reproduce the bug with 2019.09.3, but 2020.03.1 works fine so try with this version instead
The error comes from the drawing code that expects atomic coordinates to already exist in v2019 of RDKit and crashes otherwise, while v2020 generates them if needed.
So alternatively, you could try the following code and keep v2019:
from rdkit import Chem
from rdkit.Chem import AllChem
# generate molecules
smiles = ["CCO", "c1ccccc1", "N", "CO", "O=S(=O)(-O)(-O)", "CCC", "CCC=O"]
mols = [Chem.MolFromSmiles(s) for s in smiles]
for i, mol in enumerate(mols):
# set properties
mol.SetIntProp("id", i)
# generate 2D coordinates
AllChem.Compute2DCoords(mol)
# setup the grid
mg = mols2grid.MolGrid.from_mols(mols, size=(110, 90))
mg.display(subset=["id", "img"], n_cols=7)Hi, thank you very much! After updating RDKit to 2020.09.1.0, the script works well for me (sorry for the sluggish feedback, I don't know why but my desktop takes a very long time to uninstall old RDKit vai conda:))
I've updated the installation instructions on the readme file with the correct rdkit version.
If you install mols2grid from conda the correct rdkit version will now automatically be installed, which closes this issue.