search

zchwang / IGModel

This is the first model that can simultaneously predict the RMSD of the ligand docking pose and the binding strength against the target.
MIT License
14 stars 1 forks source link

conda environment, problems with runing examples #2

Closed CLG68 closed 4 months ago

CLG68 commented 5 months ago

Hi,

I created an environment that should contain everything needed to run your scripts:

conda create -n igmodel python=3.9 conda activate igmodel conda install -c conda-forge cudatoolkit=11.8 rdkit numpy pandas openbabel spyrmsd lightning-utilities pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 torchmetrics torchtext torchdata --index-url https://download.pytorch.org/whl/cu118 pip install torch-geometric pyyaml pydantic pip install dgl -f https://data.dgl.ai/wheels/cu118/repo.html

I tested cuda support for torch, for DGL,... no problems importing them. so everything seems fine. However, when I run: run_scoring.sh, I get:

(igmodel) christian@christian-linux01:/media/christian/VS/VS/Tool_IGModel$ ./run_scoring.sh

*** Open Babel Warning in ReadMolecule WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4.

============================== *** Open Babel Warning in ReadMolecule WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4.

*** Open Babel Warning in ReadMolecule WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 2 that is less than the observed explicit valence 3. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4.

============================== *** Open Babel Warning in ReadMolecule WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 2 that is less than the observed explicit valence 3. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4. WARNING: Problem interpreting the valence field of an atom The valence field specifies a valence 3 that is less than the observed explicit valence 4.

receptor clipped ... /media/christian/VS/VS/Tool_IGModel/scripts/pocket_features.py:30: UserWarning: Using torch.cross without specifying the dim arg is deprecated. Please either pass the dim explicitly or simply use torch.linalg.cross. The default value of dim will change to agree with that of linalg.cross in a future release. (Triggered internally at ../aten/src/ATen/native/Cross.cpp:63.) n1 = torch.cross(b0, b1) Warnning: psi feats calculate failed ... /home/christian/anaconda3/envs/igmodel/lib/python3.9/site-packages/dgl/heterograph.py:92: DGLWarning: Recommend creating graphs by dgl.graph(data) instead of dgl.DGLGraph(data). dgl_warning( receptor parsed ... 0 1 2 3 4 5 6 7 8 9

zchwang commented 5 months ago

This warning seems to be from OpenBabel and should not affect the scoring.

CLG68 commented 5 months ago

Hi,

I also have torch/DGL warnings and "psi feats calculate failed ..." . I'm not sure what are "psi feats" are. There was no indication on the version of different packages for the environment on read.me page so I tried to install the latest stable DGL and limited the version of pytorch and Cuda to be compatible with it. I installed the latest version of openbabel available on conda-forge. as the one under pip is impossible to compile

I've got these results:

  | pred_rmsd | pred_pkd 1bcu-1 | 0.40509105 | 4.184812 1bcu-2 | 0.64704967 | 4.1000247 1bcu-3 | 2.626471 | 2.096566 1bcu-4 | 3.638276 | 1.0680594 1bcu-8 | 3.763526 | 1.7014754 1bcu-5 | 3.8416123 | 1.5569208 1bcu-6 | 4.9769936 | -0.40310478 1bcu-7 | 5.079344 | -0.46507454 1bcu-10 | 7.3024893 | -2.5734262 1bcu-9 | 7.5148563 | -2.7400494

zchwang commented 5 months ago

Hi, the PSI angles are usually not computed for residues located at the protein chain terminus, so this warning does not affect the outcome.

CLG68 commented 4 months ago

Hi,

Do you get the same scores from this set? If everything seems to be ok, I'll find a way to suppress the warnings.

Thanks again for your help, Christian

CLG68 commented 4 months ago

Hi, Maybe you could add the 2 attached files. With conda env -f environment.yml, they will create a functional environment named igmodel. Just rename environment.txt to environment.yml as Github did not let me attach a yml file. environment.txt requirements.txt Best, Christian