Fix ring_api and parsing of ring output

Author: damianopiovesan

__init__.py

@@ -73,7 +73,7 @@ def ring_plugin(test=False):
 
     pymol.finish_launching()
     cmd.set("defer_builds_mode", 3)
-    cmd.load("/home/alessio/projects/ring-victor/assets/samples/test.cif")
+    cmd.load("1JSU.cif")
     cmd.dss()
     # cmd.show_as("cartoon")
     cmd.util.cbc()

main_window.py

@@ -369,7 +369,6 @@ def extract_element(atom_name):
 
         edgecolors = np.array(list(colors.values()))
         if highlight is not None and len(highlight) > 0:
-            print(highlight)
             edgecolors[highlight] = 'black'
 
         # Visualize the graph
@@ -577,7 +576,7 @@ def run(self):
 
         current_run_config = self.get_current_run_config()
 
-        # If Ring has already been run on that obj and the run config didn't changed then just visualize results
+        # If Ring has already been run on that obj and the run config didn't change then just visualize results
         if obj_name in self.prev_launch_config.keys() and self.prev_launch_config[obj_name] == current_run_config \
                 and not self.widg.override_memory.isChecked():
             self.visualize()
@@ -709,10 +708,10 @@ def visualize(self, selection=None, of_type=None):
         stored.chain_resi = set()
         cmd.iterate(obj, 'stored.chain_resi.add((chain, resi))')
         conn_freq = get_freq(stored.model, self.temp_dir.name)
-
         def draw():
             interactions_per_state = pd.read_csv(file_pth, sep='\t')
 
+
             if len(interactions_per_state) == 0:
                 self.log("No interactions found in the object", warning=True)
                 return
@@ -734,7 +733,8 @@ def draw():
                 for int_type in intTypeMap.keys():
                     interactions_per_type.setdefault(int_type, list())
 
-                for (nodeId1, interaction, nodeId2, _, _, _, atom1, atom2, *_) in df.itertuples(index=False):
+
+                for (nodeId1, interaction, nodeId2, _, _, atom1, atom2, *_) in df.itertuples(index=False):
                     int_type, intRegion = interaction.split(":")
                     node1 = Node(nodeId1)
                     node2 = Node(nodeId2)
@@ -773,10 +773,12 @@ def draw():
                         t += (atom1,)
                     else:
                         t += ("{}/{}/{}".format(node1.chain, str(node1.resi), atom1),)
+
                     if "," in str(atom2):
                         t += (atom2,)
                     else:
                         t += ("{}/{}/{}".format(node2.chain, str(node2.resi), atom2),)
+
                     interactions_per_type[int_type].append(t)
 
                     # Update set of possible selected nodes

ring_api.py

@@ -152,6 +152,7 @@ def run_ring_api(file_pth, run_config, tmp_dir, log_f, progress_f):
     job: Job = Job()
 
     file_name = os.path.basename(file_pth)
+
     _log_f(file_pth, file_name)
 
     parameters = {"task": "ring-plugin-api",
@@ -184,6 +185,7 @@ def run_ring_api(file_pth, run_config, tmp_dir, log_f, progress_f):
         prev_progress = (prev_progress + 0.00001)
 
     if job.status == "success":
+        # TODO check the job has not generated an error
         _log_f("Computation terminated, downloading results")
     else:
         _log_f("Error in the execution of RING, please retry later or launch locally", error=True)

utilities.py

@@ -262,7 +262,7 @@ def get_node_names_ordered(obj, tmp_dir):
 
 def draw_links(interactions, color, object_name, coords, state):
     from pymol import cmd
-
+    # print(coords)
     tup_color = []
     if type(color) is str:
         try:
@@ -274,6 +274,7 @@ def draw_links(interactions, color, object_name, coords, state):
 
     obj = [BEGIN, LINES, COLOR] + tup_color
     for interaction in interactions:
+        # print(interaction)
         valid = True
         if "," in interaction[0]:
             coord1 = ([float(x) for x in interaction[0].split(',')],)
@@ -294,7 +295,9 @@ def draw_links(interactions, color, object_name, coords, state):
         if valid:
             for x, y in zip(coord1, coord2):
                 obj.extend([VERTEX] + x + [VERTEX] + y)
+            # print(interaction, coord1, coord2)
     obj.append(END)
+    # print(obj)
     cmd.load_cgo(obj, object_name, state=state, zoom=False)