Add a pseudonode to the external links

Author: Peter Kerpedjiev

forna.py

@@ -223,6 +223,13 @@ def create_loop_node(ds, res_list, node_id):
         create_loop_node(loop_elems, residue_list, num_nodes + counter)
         counter += 1
 
+    # create a common node for the external loop
+    eloops = bg.find_external_loops()
+    if len(eloops) > 0:
+        all_residues = it.chain(*[bg.define_residue_num_iterator(e, adjacent=True) for e in eloops])
+        fud.pv('all_residues')
+        create_loop_node(eloops, sorted(all_residues), len(struct["nodes"]))
+
     # link the nodes that are in stems
     for i in range(0, bg.seq_length - 2):
         if i + 1 in pseudoknotted or i + 2 in pseudoknotted or i + 3 in pseudoknotted:

htdocs/js/force.js

@@ -160,16 +160,16 @@ function Graph() {
     .charge(function(d) { if (d.node_type == 'pseudo') 
             return -200; 
         else 
-            return -40;})
+            return -80;})
     .linkDistance(function(d) { return 15 * d.value; })
     .linkStrength(function(d) { if (d.link_type == 'pseudoknot') 
-                  { return 0.001; }
+                  { return 0.0; }
             else
                 { return 8; } })
     .gravity(0.002)
     .nodes(graph.nodes)
     .links(graph.links)
-    .chargeDistance(100)
+    .chargeDistance(110)
     .friction(0.950)
     .size([w, h]);