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3D-e-Chem / knime-testflow

Test Knime workflows from a Junit test.
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Cannot install #8

Open Trabirider91 opened 4 years ago

Trabirider91 commented 4 years ago

Hello,

I got the following message when I tried to install the nodes in KNIME: Cannot complete the install because some dependencies are not satisfiable nl.esciencecenter.e3dchem.knime.silicosit.feature.feature.group [1.1.3.v201906270957] cannot be installed in this environment because its filter is not applicable.

Any idea how can I solve this issue? I would only need the QeD node. Please help.

Thank you very much. Dani

sverhoeven commented 4 years ago

Thanks for your question, however it would have been better if asked in https://github.com/3D-e-Chem/knime-silicos-it repo.

I suspect your are running on Windows, which is not supported by the KNIME Silicos-it nodes. However the QeD node is a simple wrapper around a Python library.

So if you install QeD Python library then you should be able to make a Python node with the following snippet:

from silicos_it.descriptors import qed

# Input molecules
mol_col = 'RDKit molecule'

# Copy input to output
output_table = input_table.copy()

# Calculate qed on the molecules column
output_table['qed'] = output_table.apply(lambda x: qed.default(x[mol_col]), axis=1)

Hope this helps.

Trabirider91 commented 4 years ago

Hi,

Yes, I am using windows. Sadly I do not have access to a mac or Linux so I will give it a try with python :) I have never used it before, can you possibly give me a bit more on how to make the node and then how do I actually get it into KNIME? It would mean a lot to me.

Thanks Dani

Trabirider91 commented 4 years ago

Thanks for your question, however it would have been better if asked in https://github.com/3D-e-Chem/knime-silicos-it repo.

I suspect your are running on Windows, which is not supported by the KNIME Silicos-it nodes. However the QeD node is a simple wrapper around a Python library.

So if you install QeD Python library then you should be able to make a Python node with the following snippet:

from silicos_it.descriptors import qed

# Input molecules
mol_col = 'RDKit molecule'

# Copy input to output
output_table = input_table.copy()

# Calculate qed on the molecules column
output_table['qed'] = output_table.apply(lambda x: qed.default(x[mol_col]), axis=1)

Hope this helps.

Hi,

So I have tried to play around with python and tried to install the qed as written on the site, BUT I usually get the same error message:

File "C:\Users\Dani\AppData\Local\Programs\Python\Python38-32\lib\site-packages\silicos_it\descriptors\qed.py", line 286 print "Error: no input file given." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Error: no input file given.")?

I have not a clue how to add an input file to it or where should I add it.

If you have a solution please let me know. I would really need this node.

Thank you very much. Dani

sverhoeven commented 4 years ago

The print without (...) is only allowed in Python 2, it is not allowed in Python 3. To run the qed code you will need to install and use Python 2.7