b3c7adeefcf38e2b579980c1342f05fcdbafb4c5
examples/diffdock
... | ... | @@ -0,0 +1,57 @@ |
1 | +DiffDock Example |
|
2 | +Mar. 9, 2023 |
|
3 | + |
|
4 | +Version 73ef67f |
|
5 | + |
|
6 | +``` |
|
7 | + |
|
8 | +#!/usr/bin/env bash |
|
9 | + |
|
10 | +## DiffDock example |
|
11 | +## Args: none |
|
12 | +## |
|
13 | +## James Vincent - biogrids.org |
|
14 | +## vincent@hkl.hms.harvard.edu |
|
15 | +## Mar 9, 2023 |
|
16 | + |
|
17 | +:<<ACKNOWLEDGE |
|
18 | + |
|
19 | +If your use of BioGrids compiled software was an important element in |
|
20 | +your publication, please include the following statement in your work: |
|
21 | +"Software used in the project was installed and configured by BioGrids |
|
22 | +(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.) |
|
23 | + |
|
24 | +ACKNOWLEDGE |
|
25 | + |
|
26 | +# Load cuda |
|
27 | +module load cuda/11.5.2 |
|
28 | +gpu_out=gpu_load.out # for monitoring gpu use |
|
29 | + |
|
30 | +# Verify we have a working GPU |
|
31 | +echo -e "hostname: $HOSTNAME \n\n" |
|
32 | +echo -e "nvidia-smi output \n\n" |
|
33 | +nvidia-smi |
|
34 | + |
|
35 | +# Start nvidia-smi monitor of gpu |
|
36 | +nvidia-smi --query-gpu=timestamp,name,utilization.gpu,utilization.memory,memory.total,memory.free,memory.used --format=csv -l 5 >& ${gpu_out} & |
|
37 | + |
|
38 | + |
|
39 | +# Activate SBGrid env |
|
40 | +export SBGRID_ALLOW=true |
|
41 | +source /programs/sbgrid.shrc |
|
42 | + |
|
43 | +# Copy sample data |
|
44 | +cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/data ./ |
|
45 | +cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/workdir ./ |
|
46 | +mkdir results |
|
47 | + |
|
48 | +out_dir="./results/user_predictions_small" |
|
49 | +input_csv="./data/protein_ligand_example_csv.csv" |
|
50 | + |
|
51 | +# Run job |
|
52 | +export SSL_CERT_FILE=/programs//x86_64-linux/diffdock/73ef67f/ssl/cacert.pem |
|
53 | +python.diffdock -m inference --protein_ligand_csv ${input_csv} --out_dir ${out_dir} \ |
|
54 | + --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise |
|
55 | + |
|
56 | + |
|
57 | +``` |