added clash count in calc_DockQ output

bjornwallner · Mar 20, 2024 · cffe74f · cffe74f
1 parent 7fcd297
commit cffe74f
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
@@ -432,7 +432,7 @@ def calc_DockQ2(
     info["fnonnat"] = fnonnat
     info["nonnat_count"] = nonnat_count
     info["model_total"] = model_total
-
+    
     info["len1"] = native1_size
     info["len2"] = native2_size
     info["class1"] = class1
@@ -484,7 +484,7 @@ def calc_DockQ(
     atom_for_sup = ("CA", "C", "N", "O", "P") if not use_CA_only else ("CA", "P")
     fnat_threshold = 4.0 if capri_peptide else 5.0
     interface_threshold = 8.0 if capri_peptide else 10.0
-
+    clash_threshold=2.0
     # total number of native contacts is calculated on untouched native structure
     ref_res_distances = get_residue_distances(ref_chains[0], ref_chains[1], "ref")
     nat_total = np.nonzero(np.asarray(ref_res_distances) < fnat_threshold**2)[
@@ -590,7 +590,7 @@ def calc_DockQ(
     info["fnonnat"] = fnonnat
     info["nonnat_count"] = nonnat_count
     info["model_total"] = model_total
-
+    info["clashes"]=np.nonzero(np.asarray(sample_res_distances) < clash_threshold**2)[0].shape[0]
     info["len1"] = ref_group1_size
     info["len2"] = ref_group2_size
     info["class1"] = class1