rdkit version and warning

[sonjaleo]

Because of the RDKit version 2020.03.3 used in KinFragLib, a warning is showing up <frozen importlib._bootstrap>:219: RuntimeWarning: to-Python converter for boost::shared_ptr<RDKit::FilterCatalogEntry const> already registered; second conversion method ignored. When updating RDKit to the current version, this warning disappears. Actually, when updating RDKit, there occurs another problem with the pandas DataFrames in notebooks/custom_kinfraglib/1_1_custom_filters_unwanted_substructures.ipynb

I also found this warning in

• https://projects.volkamerlab.org/teachopencadd/talktorials/T003_compound_unwanted_substructures.html
• https://colab.research.google.com/github/DarkMatterAI/mrl/blob/master/nbs/tutorials/tutorials.generative_models.vae.ipynb

[dominiquesydow]

Actually, when updating RDKit, there occurs another problem with the pandas DataFrames in notebooks/custom_kinfraglib/1_1_custom_filters_unwanted_substructures.ipynb

What kind of problem occurs in this case?

[sonjaleo]

Actually, when updating RDKit, there occurs another problem with the pandas DataFrames in notebooks/custom_kinfraglib/1_1_custom_filters_unwanted_substructures.ipynb

What kind of problem occurs in this case?

It cannot display any pandas DataFrames anymore. I can check later what kind of error message is shown when trying to access a DataFrame.

[sonjaleo]

After doing it again and checking the web again, I found that you already had that problem in TeachOpenCadd https://githubmemory.com/repo/volkamerlab/teachopencadd/issues/131

`--------------------------------------------------------------------------- ValueError Traceback (most recent call last) ~/.local/lib/python3.8/site-packages/IPython/core/formatters.py in call(self, obj) 700 type_pprinters=self.type_printers, 701 deferred_pprinters=self.deferred_printers) --> 702 printer.pretty(obj) 703 printer.flush() 704 return stream.getvalue()

~/.local/lib/python3.8/site-packages/IPython/lib/pretty.py in pretty(self, obj) 392 if cls is not object \ 393 and callable(cls.dict.get('repr')): --> 394 return _repr_pprint(obj, self, cycle) 395 396 return _default_pprint(obj, self, cycle)

~/.local/lib/python3.8/site-packages/IPython/lib/pretty.py in _reprpprint(obj, p, cycle) 698 """A pprint that just redirects to the normal repr function.""" 699 # Find newlines and replace them with p.break() --> 700 output = repr(obj) 701 lines = output.splitlines() 702 with p.group():

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/core/frame.py in repr(self) 993 else: 994 width = None --> 995 self.to_string( 996 buf=buf, 997 max_rows=max_rows,

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/core/frame.py in to_string(self, buf, columns, col_space, header, index, na_rep, formatters, float_format, sparsify, index_names, justify, max_rows, min_rows, max_cols, show_dimensions, decimal, line_width, max_colwidth, encoding) 1129 decimal=decimal, 1130 ) -> 1131 return fmt.DataFrameRenderer(formatter).to_string( 1132 buf=buf, 1133 encoding=encoding,

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in to_string(self, buf, encoding, line_width) 1051 1052 string_formatter = StringFormatter(self.fmt, line_width=line_width) -> 1053 string = string_formatter.to_string() 1054 return save_to_buffer(string, buf=buf, encoding=encoding) 1055

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/string.py in to_string(self) 23 24 def to_string(self) -> str: ---> 25 text = self._get_string_representation() 26 if self.fmt.should_show_dimensions: 27 text = "".join([text, self.fmt.dimensions_info])

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/string.py in _get_string_representation(self) 38 return self._empty_info_line 39 ---> 40 strcols = self._get_strcols() 41 42 if self.line_width is None:

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/string.py in _get_strcols(self) 29 30 def _get_strcols(self) -> list[list[str]]: ---> 31 strcols = self.fmt.get_strcols() 32 if self.fmt.is_truncated: 33 strcols = self._insert_dot_separators(strcols)

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in get_strcols(self) 538 Render a DataFrame to a list of columns (as lists of strings). 539 """ --> 540 strcols = self._get_strcols_without_index() 541 542 if self.index:

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in _get_strcols_without_index(self) 802 int(self.col_space.get(c, 0)), *(self.adj.len(x) for x in cheader) 803 ) --> 804 fmt_values = self.format_col(i) 805 fmt_values = _make_fixed_width( 806 fmt_values, self.justify, minimum=header_colwidth, adj=self.adj

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in format_col(self, i) 816 frame = self.tr_frame 817 formatter = self._get_formatter(i) --> 818 return format_array( 819 frame.iloc[:, i]._values, 820 formatter,

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in format_array(values, formatter, float_format, na_rep, digits, space, justify, decimal, leading_space, quoting) 1238 ) 1239 -> 1240 return fmt_obj.get_result() 1241 1242

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in get_result(self) 1269 1270 def get_result(self) -> list[str]: -> 1271 fmt_values = self._format_strings() 1272 return _make_fixed_width(fmt_values, self.justify) 1273

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in _format_strings(self) 1332 for i, v in enumerate(vals): 1333 if not is_float_type[i] and leading_space: -> 1334 fmt_values.append(f" {_format(v)}") 1335 elif is_float_type[i]: 1336 fmt_values.append(float_format(v))

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/format.py in _format(x) 1312 else: 1313 # object dtype -> 1314 return str(formatter(x)) 1315 1316 vals = extract_array(self.values, extract_numpy=True)

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/printing.py in pprint_thing(thing, _nest_lvl, escape_chars, default_escapes, quote_strings, max_seq_items) 231 result = f"'{as_escaped_string(thing)}'" 232 else: --> 233 result = as_escaped_string(thing) 234 235 return result

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/pandas/io/formats/printing.py in as_escaped_string(thing, escape_chars) 207 escape_chars = escape_chars or () 208 --> 209 result = str(thing) 210 for c in escape_chars: 211 result = result.replace(c, translate[c])

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/rdkit/Chem/PandasTools.py in PrintAsBase64PNGString(x, renderer) 381 return svg.toxml() 382 else: --> 383 data = Draw._moltoimg(x, molSize, highlightAtoms, "", returnPNG=True, kekulize=True) 384 return '' % _get_image( 385 data)

~/anaconda3/envs/kinfraglib/lib/python3.8/site-packages/rdkit/Chem/Draw/init.py in _moltoimg(mol, sz, highlights, legend, returnPNG, drawOptions, **kwargs) 479 highlightBonds=bondHighlights) 480 else: --> 481 d2d.DrawMolecule(mc, legend=legend or "", highlightAtoms=highlights or []) 482 d2d.FinishDrawing() 483 if returnPNG:

ValueError: bad query type1`

Did you found a solution for this by now?

[dominiquesydow]

Can you please provide a minimal example of your problem?

In the issue that you referenced, I think the problem was that some molecules could not be displayed in the grid image, while the rest of the molecules were just fine. We did not fix this; we simply decided to display only those molecules that were not problematic.

[sonjaleo]

Can you please provide a minimal example of your problem?

In the issue that you referenced, I think the problem was that some molecules could not be displayed in the grid image, while the rest of the molecules were just fine. We did not fix this; we simply decided to display only those molecules that were not problematic.

Just load the environment, update rdkit (I used the newest version 2021.09.2) and then run notebooks/custom_kinfraglib/1_1_custom_filters_unwanted_substructures.ipynb After trying to display the Brenk structures, it crashes.

You are right, it does not seem to be a problem with only this one structure. I tried it after removing this structure, but the error is still there.