mcsorkun / chemplot Goto Github PK

Hi!

When trying to install with pip, I get errors with the matplotlib and scikit-learn libraries, even though both are installed and up to date.
At the bottom, I paste the fragment of the entire output from the console, where the errors occur. The whole output is attached as a txt file. I have no idea what to do with this problem. I'm using PowerShell with system administrator privileges. RDkit is installed and activated.

chemplot_install_error.txt

 `Extracting freetype-2.6.1.tar.gz
  Building freetype in build\freetype-2.6.1
  msbuild build\freetype-2.6.1\builds\windows\vc2010\freetype.sln /t:Clean;Build /p:Configuration=Release;Platform=x64
  error: command 'msbuild' failed: None
  [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for matplotlib`

  error: could not create 'build\bdist.win-amd64\wheel\.\sklearn\datasets\tests\data\openml\292\api-v1-json-data-list-data_name-          
  australian-limit-2-data_version-1-status-deactivated.json.gz': No such file or directory
  INFO:
  ########### EXT COMPILER OPTIMIZATION ###########
  INFO: Platform      :
    Architecture: x64
    Compiler    : msvc

  CPU baseline  :
    Requested   : 'min'
    Enabled     : SSE SSE2 SSE3
    Flags       : none
    Extra checks: none

  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
    Generated   : none
  INFO: CCompilerOpt.cache_flush[857] : write cache to path -> D:\Users\aleniak\AppData\Local\Temp\pip-install-1uih_fd0\scikit-learn_a2e09175a0394b6b907b9332707bf76e\build\temp.win-amd64-cpython-310\Release\ccompiler_opt_cache_ext.py
  INFO:
  ########### CLIB COMPILER OPTIMIZATION ###########
  INFO: Platform      :
    Architecture: x64
    Compiler    : msvc

  CPU baseline  :
    Requested   : 'min'
    Enabled     : SSE SSE2 SSE3
    Flags       : none
    Extra checks: none

  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2 AVX512F AVX512CD AVX512_SKX AVX512_CLX AVX512_CNL AVX512_ICL
    Generated   : none
  INFO: CCompilerOpt.cache_flush[857] : write cache to path -> D:\Users\aleniak\AppData\Local\Temp\pip-install-1uih_fd0\scikit-learn_a2e09175a0394b6b907b9332707bf76e\build\temp.win-amd64-cpython-310\ccompiler_opt_cache_clib.py
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for scikit-learn
Failed to build matplotlib scikit-learn
ERROR: Could not build wheels for matplotlib, scikit-learn, which is required to install pyproject.toml-based projects`

Add pipeline for automatic testing when pushing commits.

When using similarity type 'structural' together with t-SNE, an AttributeError: 'list' object has no attribute 'shape' is thrown. Code to reproduce the error:

from chemplot import Plotter, load_data

data_BBBP = load_data("BBBP")
cp_BBBP = Plotter.from_smiles(data_BBBP["smiles"], target=data_BBBP["target"], target_type="C", sim_type="structural")
cp_BBBP.tsne()

I will be submitting a pull request for a proposed fix shortly.

Hi @mcsorkun , Hi @dajtmullaj ,

When we initiate the Plotter with a given data it always tends to generate an ECFP fingerprint size of 2048. Is it possible to modify the fingerprint size before generating the fingerprints for a given dataset?

Hi,
I am the user of the chemplot, I want to use the figure that come out from the chemplot.

But I have two problems:

1. I want to remove the color of background, and use a transparent or white background. Can you provide this selection for the users?
2. The scatter points is small for me, and I wan they are larger than the default one. Can you provide the selection of marker size for the users?
   In this case, the code is nicer to the users. I will thank you vey much if my problems can be solved.

Hi!

Has anyone had trouble importing "Panel" from bokeh.models (err msg copied below)?

Thnx!

from chemplot import Plotter
Traceback (most recent call last):
File "", line 1, in
File "/data/applic/ChemPlot/chemplot/init.py", line 1, in
from .chemplot import Plotter
File "/data/applic/ChemPlot/chemplot/chemplot.py", line 26, in
from bokeh.models import ColorBar, HoverTool, Panel, Tabs
ImportError: cannot import name 'Panel' from 'bokeh.models' (/data/miniconda3/envs/chemplot_env/lib/python3.9/site-packages/bokeh/models/init.py)

Hello Chemplot team!.

I write because only can run UMAP and PCA in the APP. Any recomendation for run t-SNE in the APP.

Thank you very much for help me,

Hi mcsorkun,

Thanks a lot for the great tool.
Just wondering, what would be the best way to hide all the hydrogens when using the interactive_plot?
I tried to preprocess the smiles by rdkit.Chem.rdmolops.RemoveHs, but in the bokeh HTML the 2D images rendered by interactive_plot are still with hydrogens, for example:

Would be great to have an option in interactive_plot to do this.

Hi,

I am slowly learning chemplot. Is it possible to compare the tsne generated from chemplot with tanimoto distance based tsne and use your interactive visualization? Please guide.

thanks,
Jessie

Hello,

is it possible to control the type/number of descriptors calculated for the dataset by Mordor when using the , those that are afterwards used in the dimensionality reduction process?. How is the selection of descriptors managed by ChemPlot?

thanks in advance for the support,

regards

Alfredo

Hi, ChemPlot developer,
I noticed that web application of ChemPlot doesn't seem to be able to save as a vector image, can you add this feature? Thanks.
Peter

Hi Experts

I was running here: https://mcsorkun-chemplot-web-web-app-chemplot-jrrecy.streamlitapp.com/

But see the error below when I tried to create visualization:

File "/home/appuser/.conda/lib/python3.7/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 556, in _run_script
exec(code, module.dict)
File "/app/chemplot-web/web_app_chemplot.py", line 401, in
log_error_info(data_SMILES, data_target, str(error))
File "/app/chemplot-web/web_app_chemplot.py", line 113, in log_error_info
worksheet.update([['SMILES', 'targets']] + values)
File "/home/appuser/.conda/lib/python3.7/site-packages/gspread/utils.py", line 600, in wrapper
return f(*args, **kwargs)
File "/home/appuser/.conda/lib/python3.7/site-packages/gspread/worksheet.py", line 740, in update
{"values": values, "majorDimension": kwargs["major_dimension"]}
File "/home/appuser/.conda/lib/python3.7/site-packages/gspread/spreadsheet.py", line 215, in values_update
r = self.client.request("put", url, params=params, json=body)
File "/home/appuser/.conda/lib/python3.7/site-packages/gspread/client.py", line 65, in request
headers=headers,
File "/home/appuser/.conda/lib/python3.7/site-packages/requests/sessions.py", line 647, in put
return self.request("PUT", url, data=data, **kwargs)
File "/home/appuser/.conda/lib/python3.7/site-packages/google/auth/transport/requests.py", line 486, in request
**kwargs
File "/home/appuser/.conda/lib/python3.7/site-packages/requests/sessions.py", line 573, in request
prep = self.prepare_request(req)
File "/home/appuser/.conda/lib/python3.7/site-packages/requests/sessions.py", line 496, in prepare_request
hooks=merge_hooks(request.hooks, self.hooks),
File "/home/appuser/.conda/lib/python3.7/site-packages/requests/models.py", line 371, in prepare
self.prepare_body(data, files, json)
File "/home/appuser/.conda/lib/python3.7/site-packages/requests/models.py", line 513, in prepare_body
raise InvalidJSONError(ve, request=self)

Could you help please?

Qing

I get this error.
cp_BACE.interactive_plot(show_plot=True)
Any idea what is the problem?

'''python
{
"name": "AttributeError",
"message": "unexpected attribute 'plot_width' to figure, similar attributes are outer_width, width or min_width",
"stack": "---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[7], line 1
----> 1 cp_BACE.interactive_plot(show_plot=True)

File ~/bin/miniconda39/envs/cheminfo/lib/python3.12/site-packages/chemplot/chemplot.py:542, in Plotter.interactive_plot(self, size, kind, remove_outliers, is_colored, clusters, filename, show_plot, title)
540 tabs = None
541 if kind == "scatter":
--> 542 p, tabs = self.__interactive_scatter(x, y, df_data, size, is_colored, clusters, title)
543 else:
544 p = self.__interactive_hex(x, y, df_data, size, title)

File ~/bin/miniconda39/envs/cheminfo/lib/python3.12/site-packages/chemplot/chemplot.py:626, in Plotter.__interactive_scatter(self, x, y, df_data, size, is_colored, clusters, title)
623 TOOLTIPS = parameters.TOOLTIPS_TARGET
625 # Create plot
--> 626 p = figure(title=title, plot_width=size, plot_height=size, tools=tools, tooltips=TOOLTIPS)
628 if len(self.__target) == 0 or not(is_colored):
629 p.circle(x=x, y=y, size=2.5, alpha=0.8, source=df_data)

File ~/bin/miniconda39/envs/cheminfo/lib/python3.12/site-packages/bokeh/plotting/_figure.py:195, in figure.init(self, *arg, **kw)
193 for name in kw.keys():
194 if name not in names:
--> 195 self._raise_attribute_error_with_matches(name, names | opts.properties())
197 super().init(*arg, **kw)
199 self.x_range = get_range(opts.x_range)

File ~/bin/miniconda39/envs/cheminfo/lib/python3.12/site-packages/bokeh/core/has_props.py:375, in HasProps._raise_attribute_error_with_matches(self, name, properties)
372 if not matches:
373 matches, text = sorted(properties), "possible"
--> 375 raise AttributeError(f"unexpected attribute {name!r} to {self.class.name}, {text} attributes are {nice_join(matches)}")

AttributeError: unexpected attribute 'plot_width' to figure, similar attributes are outer_width, width or min_width"
}
'''

Installing build dependencies ... done
Getting requirements to build wheel ... done
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
Preparing metadata (pyproject.toml) ... error
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

... that makes the link to your research paper machine readable. See https://citation-file-format.github.io/

Hello,

Very sorry to bother you. I need a 3D representation created using chemplot. How I can do that? I created a umap using tailored similarity. Now I am being asked to create a 3D plot using the same.

cp_BACE = Plotter.from_smiles(data_BACE["smiles"], target=data_BACE["target"], target_type="R", sim_type="tailored")

If chemplot dosen't create 3D plot at the moment, can you guide me how I can get the output with 3 dimensions printed? Would I just print cp_BACE and it's elements? Thanks so much.

Hello,

thanks for this great set of tools. I was going through the tutorials from https://chemplot.readthedocs.io/en/latest/api.html
putting everything in a python script but I couldn't figure out how to load local data sets using something similar to load_data function?
and also do you have any plans to add some other properties like radar charts to this set.

Thanks,
Amir

Good day team chemplot!
I write because a have some problems to run chemplot on google colab. I installed the necessary software to run chemplot but the following code did not run.

Do you have any idea what happen?.

Thanks very much for information and help me,

Hello!

Thanks for uploading the packaged. I'm currently running on an M1 Mac with python 3.10 and I get this error when loading the tutorial dataset file.
Any idea why that might be?
Thanks

>> bokeh info
Python version      :  3.10.9 (main, Jan 11 2023, 09:18:20) [Clang 14.0.6 ]
IPython version     :  8.12.0
Tornado version     :  6.2
Bokeh version       :  3.1.0

Hi Chemplot,

Currently, it's great we can hover on one point in the interactive map and see the associated structure. Can you please add a functionality (bokeh or similar) to be able to select more than one point to show the structure.

Thanks so much,
Jessie