Merge pull request #148 from jyaacoub/final-paper

Author: jyaacoub

.gitignore

@@ -229,3 +229,6 @@ results/*/model_media/*/train_log/*.json
 results/model_checkpoints.tar.gz
 *.out
 DDP_outs
+SBATCH/outs/*
+SBATCH/samples/*
+downloaded_ligands/

SBATCH/DDP_train_folds.sh

@@ -9,7 +9,7 @@
 #SBATCH -c 4
 #SBATCH --mem=4G
 
-#SBATCH --output=./outs/%x.out
+#SBATCH --output=/home/jyaacoub/projects/def-sushant/jyaacoub/MutDTA/SBATCH/outs/%x.out
 ##SBATCH --array=0-4 # WARNING: Doesnt work with submitit
 
 module load StdEnv/2020 && module load gcc/9.3.0 && module load arrow/12.0.1

SBATCH/download.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+cd ~/projects/def-sushant/jyaacoub/MutDTA/
+source .venv/bin/activate
+
+python -u << EOF
+
+from src.data_prep import Downloader 
+
+Downloader.download_SDFs(
+    ligand_ids=
+    [
+        'CHEMBL1200978',
+        'CHEMBL1201182',
+        'CHEMBL1201438',
+        'CHEMBL1201561',
+        'CHEMBL1201576',
+        'CHEMBL1201827',
+        'CHEMBL159',
+        'CHEMBL1908360',
+        'CHEMBL2105741',
+        'CHEMBL2360464',
+        'CHEMBL3137309',
+        'CHEMBL359744',
+        'CHEMBL3989514',
+        'CHEMBL413',
+        'CHEMBL428647',
+        'CHEMBL90555',
+        'CHEMBL92'
+    ],
+    save_dir= './downloaded_ligands',
+    max_workers=5
+)
+
+EOF

SBATCH/plot_mutagenesis.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+cd /lustre06/project/6069023/jyaacoub/MutDTA/
+source .venv/bin/activate
+
+numpy_matrix_fp="/lustre06/project/6069023/jyaacoub/MutDTA/SBATCH/outs/mutagenesis_tests/1a30_ligand/davis_DG/0_5.npy"
+pdb_file="/lustre06/project/6069023/jyaacoub/MutDTA/SBATCH/samples/input/mutagenesis/P67870.pdb"
+output_image="out.png"
+res_start=0
+res_end=1000
+
+
+python -u << EOF
+from matplotlib import pyplot as plt
+import numpy as np
+from src.analysis.mutagenesis_plot import plot_sequence
+from src.utils.residue import Chain
+
+muta = np.load('${numpy_matrix_fp}')
+pdb_file = '${pdb_file}'
+
+# Plots the full sequence:
+# plot_sequence(muta, pro_seq=Chain(pdb_file).sequence)
+
+
+# Plot a specific residue range (e.g.: a pocket)
+res_range = (${res_start}, ${res_end})
+plot_sequence(muta[:,res_range[0]:res_range[1]], pro_seq=Chain(pdb_file).sequence[res_range[0]:res_range[1]])
+
+plt.savefig('${output_image}')
+EOF

SBATCH/run_mutagenesis.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
-#SBATCH -t 30:00
-#SBATCH --job-name=run_mutagenesis_davis_DG_custom
+#SBATCH -t 5:00
+#SBATCH --job-name=run_mutagenesis_davis_DG_test
 #SBATCH --mem=10G
 
 #SBATCH --gpus-per-node=a100:1
@@ -38,7 +38,6 @@ python -u run_mutagenesis.py \
                     --ligand_id "1a30_ligand" \
                     --pdb_file "${proj_dir}/SBATCH/samples/input/mutagenesis/P67870.pdb" \
                     --out_path "${OUT_DIR}/" \
-                    --res_start 0 \
-                    --res_end 5 \
+                    --mutations E5A E6A V7A \
                     --model_opt davis_DG \
-                    --fold ${SLURM_ARRAY_TASK_ID}
+                    --fold ${SLURM_ARRAY_TASK_ID}