feat(mutagenesis): support for custom point mutations

run_mutagenesis.py

@@ -109,7 +109,43 @@
 original_seq = pdb_original.sequence
 
 original_pkd = MODEL(pro.to(DEVICE), lig.to(DEVICE))
-print("Original pkd:", original_pkd)
+print("Original pkd:", original_pkd, end="\n\n")
+
+if MUTATIONS:
+    mut_pdb_file = run_modeller_multiple(PDB_FILE, MUTATIONS)
+    print(mut_pdb_file)
+    pro, _ = get_protein_features(mut_pdb_file, MODEL_PARAMS['feature_opt'], MODEL_PARAMS['edge_opt'])
+    mut_pkd = MODEL(pro.to(DEVICE), lig.to(DEVICE))
+    print("\nMutated pkd:", mut_pkd)
+else:
+    logging.warning("No mutations were passed in - running full saturation mutagenesis")
+    # zero indexed res range to mutate:
+    res_range = (max(RES_START, 0), min(RES_END, len(original_seq)))
+
+    from src.utils.mutate_model import run_modeller
+    amino_acids = ResInfo.amino_acids[:-1] # not including "X" - unknown
+    muta = np.zeros(shape=(len(amino_acids), len(original_seq)))
+
+    with tqdm(range(*res_range), ncols=100, total=(res_range[1]-res_range[0]), 
+              desc='Saturation mutagenesis') as t:
+        for j in t:
+            for i, AA in enumerate(amino_acids):
+                if i%2 == 0:
+                    t.set_postfix(res=j, AA=i+1)
+
+                if original_seq[j] == AA: # skip same AA modifications 
+                    muta[i,j] = original_pkd
+                    continue
+                out_pdb_fp = run_modeller(PDB_FILE, j+1, ResInfo.code_to_pep[AA], "A")
+
+                pro, _ = get_protein_features(out_pdb_fp, MODEL_PARAMS['feature_opt'], MODEL_PARAMS['edge_opt'])
+                assert pro.pro_seq != original_seq and pro.pro_seq[j] == AA, \
+                    f"ERROR in modeller, {pro.pro_seq} == {original_seq} \nor {pro.pro_seq[j]} != {AA}"
+
+                muta[i,j] = MODEL(pro.to(DEVICE), lig.to(DEVICE))
+
+                # delete after use
+                os.remove(out_pdb_fp)
 
 if MUTATIONS:
     mut_pdb_file = run_modeller_multiple(PDB_FILE, MUTATIONS)