Better printout

Author: olegsobolev

mmtbx/building/cablam_idealization.py

@@ -192,7 +192,7 @@ def fix_cablam_outlier(self, chain, outlier):
       print(s[0], s[1], s[2], end=' ', file=self.log)
       if len(s[3]) > 0:
         for e in s[3]:
-          print("| %s, %.2f, %.2f|" % (e[0], e[1], e[2]), end=' ', file=self.log)
+          print("| %s -- > %s, %.2f, %.2f|" % (e[0], e[3].id_str(), e[1], e[2]), end=' ', file=self.log)
       print(file=self.log)
     rot_angle = self._pick_rotation_angle(scores, self.params.require_h_bond)
     # rotate
@@ -338,7 +338,7 @@ def good_hbond(angle, distance):
             weight=1).angle_model
         if good_hbond(angle, atom.distance(O_atom)):
           # print "Potential bond:", atom.id_str(), atom.distance(O_atom), angle
-          results.append(('NH', atom.distance(O_atom), angle))
+          results.append((O_atom.id_str(), atom.distance(O_atom), angle, atom))
       if atom.name.strip() == 'O':
         # now we want to find attached N atom (another one)
         another_C_atom = atom.parent().get_atom("C")
@@ -349,7 +349,7 @@ def good_hbond(angle, distance):
               weight=1).angle_model
           if good_hbond(angle, atom.distance(N_atom)):
             # print "Potential backwards bond:", atom.id_str(), atom.distance(N_atom), angle
-            results.append(('CO', atom.distance(N_atom), angle))
+            results.append((N_atom.id_str(), atom.distance(N_atom), angle, atom))
     self.atoms_around_cutted = filtered_atoms_around_cutted
     return results
 

mmtbx/programs/cablam_idealization.py

@@ -59,8 +59,10 @@ def run(self):
     results = self.cablam_id.get_results()
 
     flat_cablam_results = [item for sublist in results.cablam_results.values() for item in sublist]
+    print("Rotated residues (angle, chain id, resnum, resname, alpha, beta):", file=self.logger)
     for cr, angle in flat_cablam_results:
-      print(f'{angle:3d} {cr.chain_id} {cr.resid} {cr.resname} {cr.feedback.alpha} {cr.feedback.alpha}')
+      a = angle if angle !=360 else 0
+      print(f'{a:3d} {cr.chain_id} {cr.resid} {cr.resname} {cr.feedback.alpha} {cr.feedback.alpha}', file=self.logger)
       # print(angle, cr)
 
     print(f"Total number of outliers in starting model: {results.n_initial_cablam_outliers}", file=self.logger)