installation and examples

[mbatgh]

hi ,

i downloaded the Docker image as in: docker pull omendezlucio/deepdock docker run -it omendezlucio/deepdock:latest then copy/paste the source from https://github.com/OptiMaL-PSE-Lab/DeepDock/blob/main/examples/Score_example.ipynb into a python script:

from rdkit import Chem import deepdock from deepdock.models import * from deepdock.DockingFunction import score_compound from deepdock.DockingFunction import calculate_atom_contribution import numpy as np import torch np.random.seed(123) torch.cuda.manual_seed_all(123) device = 'cuda' if torch.cuda.is_available() else 'cpu' ligand_model = LigandNet(28, residual_layers=10, dropout_rate=0.10) target_model = TargetNet(4, residual_layers=10, dropout_rate=0.10) model = DeepDock(ligand_model, target_model, hidden_dim=64, n_gaussians=10, dropout_rate=0.10, dist_threhold=7.).to(device) checkpoint = torch.load(deepdock.path[0]+'/../Trained_models/DeepDock_pdbbindv2019_13K_minTestLoss.chk', map_location=torch.device(device)) model.load_state_dict(checkpoint['model_state_dict']) target_ply = deepdock.path[0]+'/../data/1z6e_protein.ply' real_mol = Chem.MolFromMol2File(deepdock.path[0]+'/../data/1z6e_ligand.mol2',sanitize=False, cleanupSubstructures=False) score = score_compound(real_mol, target_ply, model, dist_threshold=3., seed=123, device=device) score

I called the script test.py and said: python3 test.py

this runs for a few seconds, without any errors or warnings, and then exits without giving me any output, shouldn't the final command (score) print out the score to stdout? talking about commands ... are there any plans to make a documentation for deepdock?

when inside docker i cannot execute the jupyter notebook, as there is no browser in this image. therefore i tried to install form source as outlined on the webpage. I say:

git clone https://github.com/OptiMaL-PSE-Lab/DeepDock.git cd DeepDock/ conda create --name mydd conda activate mydd git submodule update --init --recursive conda install -c conda-forge rdkit=2019.09.1 pip install -r requirements.txt

the last command starts running, and then i get: [...] Looking in links: https://pytorch-geometric.com/whl/torch-1.4.0.html, https://pytorch-geometric.com/whl/torch-1.4.0.html, https://pytorch-geometric.com/whl/torch-1.4.0.html, https://pytorch-geometric.com/whl/torch-1.4.0.html Collecting torch==1.4.0 Using cached torch-1.4.0-cp38-cp38-manylinux1_x86_64.whl (753.4 MB) Collecting torch-scatter==2.0.4+cu101 Using cached https://data.pyg.org/whl/torch-1.4.0/torch_scatter-2.0.4%2Bcu101-cp38-cp38-linux_x86_64.whl (10.6 MB) Discarding https://data.pyg.org/whl/torch-1.4.0/torch_scatter-2.0.4%2Bcu101-cp38-cp38-linux_x86_64.whl (from https://pytorch-geometric.com/whl/torch-1.4.0.html): Requested torch-scatter==2.0.4+cu101 from https://data.pyg.org/whl/torch-1.4.0/torch_scatter-2.0.4%2Bcu101-cp38-cp38-linux_x86_64.whl (from -r requirements.txt (line 3)) has inconsistent version: filename has '2.0.4+cu101', but metadata has '2.0.4' ERROR: Could not find a version that satisfies the requirement torch-scatter==2.0.4+cu101 (from versions: latest+cpu, latest+cu92, latest+cu100, latest+cu101, 0.3.0, 1.0.2, 1.0.3, 1.0.4, 1.1.0, 1.1.1, 1.1.2, 1.2.0, 1.3.0, 1.3.1, 1.3.2, 1.4.0, 2.0.2, 2.0.3, 2.0.3+cpu, 2.0.3+cu100, 2.0.3+cu101, 2.0.3+cu92, 2.0.4, 2.0.4+cpu, 2.0.4+cu100, 2.0.4+cu101, 2.0.4+cu92, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.9) ERROR: No matching distribution found for torch-scatter==2.0.4+cu101

any suggestions on how to deal with that? (my system is Ubuntu 20.04.4)

thanks! michael

[zhiyixu]

same error, have you solve it yet?

[kjemist]

bumping this, had the same issue