examples/diffdock
... ...
@@ -1,57 +0,0 @@
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
-```
examples/diffdock.md
... ...
@@ -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
+```