Comments

Author: damianopiovesan

src/geometre/draw.py

@@ -31,14 +31,14 @@ def pymol_drawing(filepath, geometric_centers, rot_centers, twist_axis, pitch_ax
     for i in range(num_centers):
         cmd.pseudoatom('geo_centers', pos=tuple(geometric_centers[i]))
         # Uncommented lines preserved from original function:
-        # cmd.pseudoatom('ref_1', pos=tuple(geometric_centers[i] + 6 * unit_vector))
-        # cmd.pseudoatom('ref_2', pos=tuple(geometric_centers[i] - 6 * unit_vector))
-        # cmd.select('unit_1', selection='model ref_1 and name PS{}'.format(str(i + 1)))
-        # cmd.select('unit_2', selection='model ref_2 and name PS{}'.format(str(i + 1)))
-        # cmd.distance('unit_vector', selection1='unit_1', selection2='unit_2')
+        cmd.pseudoatom('ref_1', pos=tuple(geometric_centers[i] + 6 * unit_vector))
+        cmd.pseudoatom('ref_2', pos=tuple(geometric_centers[i]))
+        cmd.select('unit_1', selection='model ref_1 and name PS{}'.format(str(i + 1)))
+        cmd.select('unit_2', selection='model ref_2 and name PS{}'.format(str(i + 1)))
+        cmd.distance('unit_vector', selection1='unit_1', selection2='unit_2')
 
         if i < num_centers - 1:
-            unit_vector = units_rots[i] @ (rots[i][0].apply(unit_vector))
+            unit_vector = units_rots[i] @ (rots[i][0].apply(unit_vector))  # matrix multiplication
             unit_vector = rots[i][1].apply(unit_vector, inverse=True)
 
 
@@ -77,6 +77,9 @@ def pymol_drawing(filepath, geometric_centers, rot_centers, twist_axis, pitch_ax
         cmd.distance('curvature_axis', selection1='point1', selection2='curvature_point')
 
 
+
+
+
     # Place pseudoatoms for the last geometric center
     l = np.sqrt(np.sum((geometric_centers[-1] - geometric_centers[-2]) ** 2, axis=0)) * 1.5
     cmd.pseudoatom('twist_ref', pos=tuple(geometric_centers[-1] + l * twist_axis[-1][1]))

src/geometre/geometry.py

@@ -126,21 +126,21 @@ def widest_circle_fit(units, centers, window):
         # considering all the projected coordinates of the C-alpha
         circle = CircleModel()
         circle.estimate(pca_centers)
-        res = minimize(widest_circle, circle.params[0:2], args=(data_transformed))
+        res = minimize(widest_circle, circle.params[0:2], args=data_transformed)
 
-        center = res.x
+        center = res.x  # The best argument of the minimization result
         centers_list.append(pca.inverse_transform(center))
         index_list.append([*range(min_index, max_index)])
 
-        # Fun is the value of the objective function at x
-        # Here we are changing the sign for keeping the smallest crown
+        # Fun is the value of the objective function at x (i.e. the inverse of the best crown width)
+        # Here we are changing the sign for keeping the best crown
         score_list.append(-res.fun)
 
-    # Select the widest crown
+
+    # For each unit of each window, select centers corresponding to the best score (widest crown)
     def_centers = np.empty((num_units, 3))
     best_score = np.full(num_units, -np.inf)
 
-    # For each unit of each window, select centers corresponding to the best score (widest crown)
     # Iterate windows
     for center, indexes, score in zip(centers_list, index_list, score_list):
         # Iterate units

src/geometre/process.py

@@ -95,18 +95,18 @@ def compute(filepath, chain, units_ids, ins_ids=None, window=6):
     rot_centers = widest_circle_fit(units_coords, geometric_centers, window=window)
     logger.debug("Geometric centers and rotation centers calculated.")
 
-    # Calculate rotation angle (yaw angle) for each pair of units
+    # Calculate rotation angle (yaw angle / curvature) for each pair of units
     rot_angles = [get_angle(rot_centers[i] - geometric_centers[i], rot_centers[i] - geometric_centers[i + 1])
         for i in range(num_centers - 1)]
 
     # Calculate the axes
     pitch_axis, twist_axis, rots = build_ref_axes(geometric_centers, rot_centers)
     logger.debug("Reference axes built for geometry calculations.")
 
-    # Calculate rotations and scores
+    # Calculate rotations and scores with TM-align
     units_rots, tmscores = [], []
     for i in range(num_centers - 1):
-        # TM-align
+
         # We provide rots to superimpose the reference systems of the two consecutive units
         alignment = get_unit_rotation(units_coords[i:i + 2], units_seqs[i:i + 2], rots[i])
         units_rots.append(alignment.u)  # Rotation matrix