Comments (5)
FaSalih
commented on July 26, 2024
1
You're a life saver! I was about to lose weeks off my life trying to upgrade all of this to a newer TensorFlow version.
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ghsanti
commented on July 26, 2024
1
tl;dr: Try installing python 3.12 instead (using conda or mamba).
You don't need poetry necessarily the key is to have the deps from pyproject.toml this means you can also install it with pip. I use poetry to keep track of that process.
Edit: notebooks do run with some mods, but need a much larger noise value to get any new molecule; I'm unsure why yet, and whether it's a bug in my code or not.
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ghsanti
commented on July 26, 2024
Great, it's a complex env so if something fails let me know. Also, I removed TerminalGRU for the moment @FaSalih. In practical terms it means that you may get less accuracy, but probably a lot of algorithmic improvements from the newer packages' versions.
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FaSalih
commented on July 26, 2024
@ghsanti I am having a little trouble with the required python version. I'm get the following error when I try to run either of the poetry commands
(cvae) [fsalih@crcfe02 cvae]$ poetry install --without dev --sync # unless you want dev deps.
Current Python version (3.11.9) is not allowed by the project (~3.12.4).
Please change python executable via the "env use" command.
(cvae) [fsalih@crcfe02 cvae]$ poetry install --only-main
Current Python version (3.11.9) is not allowed by the project (~3.12.4).
Please change python executable via the "env use" command.
In the environment creation command you specify a python version below 3.12, but the pyproject.toml file specifies python = "~3.12.4" under [tool.poetry.dependencies].
What's the right python version? And do I need these poetry commands?
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ghsanti
commented on July 26, 2024
@FaSalih I did the first test on the notebook (I just uploaded the trained model, so you should not need to train it to test.)
Feel free to open any question in the repo, I won't spam here anymore :-)
This is what I get (there are still things im unsure, but result makes sense imho.)
And the distances from 'O=C1Cc2[nH]ccc2N1':
smiles distance count frequency \
0 O=C1Cc2[nH]ccc2N1 0.000004 359 0.637655
1 O=C1Cc2[nH]ccc2C1 1.400370 4 0.007105
2 O=C1Nc2[nH]ccc2N1 1.667291 1 0.001776
3 O=C1Cc2[nH]ccc2O1 2.085738 53 0.094139
4 O=C1Cc2[nH]ncc2N1 2.117460 2 0.003552
5 O=C1Cc2[nH]ccc21 3.644159 128 0.227353
6 O=c1Cc2[nH]ccc21 3.971362 2 0.003552
7 O=C1Oc2[nH]ccc21 4.014803 1 0.001776
8 O=C1Cc2[nH]cnc21 4.133598 2 0.003552
9 O=C1Cc2[nH]ncc21 4.218965 1 0.001776
10 O=C1C=2[nH]ccc2C1 4.328512 1 0.001776
11 O=C1Ccc[nH]cccn1 4.531935 1 0.001776
12 O=c1oc2[nH]ccc2O1 5.580686 1 0.001776
13 O=C1CcC[nH]cccc1 5.901025 1 0.001776
14 O=C1CC2[nH]cc2CC1 6.280135 1 0.001776
15 O=C1Ocn[nH]cc1O 7.617425 1 0.001776
16 O=CNCC1[n-]cccc1 8.793110 1 0.001776
17 O=C1Cc2nonccc21 9.234937 1 0.001776
18 O=C1CC=Cn2nccc21 10.604646 1 0.001776
19 O=C1cc[nH]c(O)c1 11.585962 1 0.001776
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Related Issues (20)
- ...For time-series...
- Exact Python package versions
- I am trying to use your model to get the encoded representation of the smiles. HOT 1
- name 'vae' is not defined
- Is the Gaussian process for optimization of molecules included in the repository? HOT 1
- trying using the conda method HOT 3
- intro_to_chemvae.ipynb loading model AttributeError: 'str' object has no attribute 'decode' HOT 3
- Dense layer in variational_layers is not saved and cannot be used to generate latent variables
- AttributeError: 'TerminalGRU' object has no attribute 'preprocess_input' HOT 1
- GPU Support
- FileNotFoundError: [Errno 2] No such file or directory: 'zinc.json' HOT 1
- Hello
- updated version of this VAE?
- Paper
- Where can I find the model prediction result?
- Which RDkit version is used in this project?
- Version incompatible
- Metaclass conflict HOT 1
- Trouble Setting up Chemvae
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