removed obsolete functions from lib.distances

package/CHANGELOG

@@ -67,8 +67,6 @@ Enhancements
   * Calculations in *Group.center() are performed in double precision (#PR1936)
   * Functions in lib.distances accept coordinate arrays of arbitrary dtype
     (PR #1936)
-  * Added calc_distance, calc_angle and calc_dihedral to lib.distances
-    (Issue #1262 #1938)
   * Added pbc kwarg to Bond/Angle/Dihedral/Improper object value method,
     default True. (Issue #1938)
   * ChainReader can correctly handle continuous trajectories split into multiple files,
@@ -81,7 +79,8 @@ Enhancements
   * Added analysis.dihedrals with Ramachandran class to analysis module (PR #1997)
   * Added augment functionality to create relevant images of particles 
   * Most functions in `MDanalysis.lib.distances` previously only accepting
-    arrays of coordinates now also accept single coordinates as input (PR #2048)
+    arrays of coordinates now also accept single coordinates as input (PR #2048,
+    Issues #1262 #1938)
   * Performance improvements to make_whole (PR #1965)
   * Performance improvements to fragment finding (PR #2028)
   * Added user defined boxes in density code (PR #2005)

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -807,7 +807,7 @@ def _get_bonded_hydrogens_list(self, atom, **kwargs):
             hydrogens = [
                 a for a in self.u.atoms[atom.index + 1:atom.index + 4]
                 if (a.name.startswith(('H', '1H', '2H', '3H')) and
-                    distances.calc_distance(atom.position, a.position, box) < self.r_cov[atom.name[0]])
+                    distances.calc_bonds(atom.position, a.position, box=box) < self.r_cov[atom.name[0]])
                 ]
         except IndexError:
             hydrogens = []  # weird corner case that atom is the last one in universe
@@ -993,10 +993,12 @@ def _get_timestep():
                     for h in donor_h_set:
                         res = ns_acceptors.search(h, self.distance)
                         for a in res:
-                            angle = distances.calc_angle(d.position, h.position,
-                                                         a.position, box=box)
+                            angle = distances.calc_angles(d.position,
+                                                          h.position,
+                                                          a.position, box=box)
+                            angle = np.rad2deg(angle)
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = distances.calc_distance(donor_atom.position, a.position, box)
+                            dist = distances.calc_bonds(donor_atom.position, a.position, box=box)
                             if angle >= self.angle and dist <= self.distance:
                                 self.logger_debug(
                                     "S1-D: {0!s} <-> S2-A: {1!s} {2:f} A, {3:f} DEG".format(h.index, a.index, dist, angle))
@@ -1019,10 +1021,12 @@ def _get_timestep():
                                     (h.index, a.index) in already_found or
                                     (a.index, h.index) in already_found):
                                 continue
-                            angle = distances.calc_angle(d.position, h.position,
-                                                         a.position, box=box)
+                            angle = distances.calc_angles(d.position,
+                                                          h.position,
+                                                          a.position, box=box)
+                            angle = np.rad2deg(angle)
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = distances.calc_distance(donor_atom.position, a.position, box)
+                            dist = distances.calc_bonds(donor_atom.position, a.position, box=box)
                             if angle >= self.angle and dist <= self.distance:
                                 self.logger_debug(
                                     "S1-A: {0!s} <-> S2-D: {1!s} {2:f} A, {3:f} DEG".format(a.index, h.index, dist, angle))

package/MDAnalysis/analysis/hbonds/wbridge_analysis.py

@@ -636,11 +636,12 @@ def run(self, **kwargs):
                         res = ns_acceptors.search(h, self.distance)
                         for a in res:
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = distances.calc_distance(donor_atom.position,
-                                                           a.position)
+                            dist = distances.calc_bonds(donor_atom.position,
+                                                        a.position)
                             if dist <= self.distance:
-                                angle = distances.calc_angle(d.position, h.position,
+                                angle = distances.calc_angles(d.position, h.position,
                                                              a.position)
+                                angle = np.rad2deg(angle)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "S1-D: {0!s} <-> W-A: {1!s} {2:f} A, {3:f} DEG"\
@@ -662,11 +663,12 @@ def run(self, **kwargs):
                         res = ns_acceptors.search(h, self.distance)
                         for a in res:
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = distances.calc_distance(donor_atom.position,
-                                                           a.position)
+                            dist = distances.calc_bonds(donor_atom.position,
+                                                        a.position)
                             if dist <= self.distance:
-                                angle = distances.calc_angle(d.position, h.position,
+                                angle = distances.calc_angles(d.position, h.position,
                                                              a.position)
+                                angle = np.rad2deg(angle)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "S1-A: {0!s} <-> W-D: {1!s} {2:f} A, {3:f} DEG"\
@@ -712,11 +714,12 @@ def run(self, **kwargs):
                         res = ns_acceptors.search(h, self.distance)
                         for a in res:
                             donor_atom = h if self.distance_type != 'heavy'  else d
-                            dist = distances.calc_distance(donor_atom.position,
-                                                           a.position)
+                            dist = distances.calc_bonds(donor_atom.position,
+                                                        a.position)
                             if dist <= self.distance:
-                                angle = distances.calc_angle(d.position, h.position,
+                                angle = distances.calc_angles(d.position, h.position,
                                                              a.position)
+                                angle = np.rad2deg(angle)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "WB-D: {0!s} <-> S2-A: {1!s} {2:f} A, {3:f} DEG"\
@@ -736,11 +739,12 @@ def run(self, **kwargs):
                         res = ns_acceptors.search(h, self.distance)
                         for a in res:
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = distances.calc_distance(donor_atom.position,
-                                                           a.position)
+                            dist = distances.calc_bonds(donor_atom.position,
+                                                        a.position)
                             if dist <= self.distance:
-                                angle = distances.calc_angle(d.position, h.position,
+                                angle = distances.calc_angles(d.position, h.position,
                                                              a.position)
+                                angle = np.rad2deg(angle)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "WB-A: {0!s} <-> S2-D: {1!s} {2:f} A, {3:f} DEG"\

package/MDAnalysis/core/topologyobjects.py

@@ -201,7 +201,7 @@ def length(self, pbc=True):
         """
         box = self.universe.dimensions if pbc else None
 
-        return distances.calc_distance(self[0].position, self[1].position, box)
+        return distances.calc_bonds(self[0].position, self[1].position, box)
 
     value = length
 
@@ -241,8 +241,8 @@ def angle(self, pbc=True):
         """
         box = self.universe.dimensions if pbc else None
 
-        return distances.calc_angle(
-            self[0].position, self[1].position, self[2].position, box)
+        return np.rad2deg(distances.calc_angles(
+            self[0].position, self[1].position, self[2].position, box))
 
     value = angle
 
@@ -291,8 +291,8 @@ def dihedral(self, pbc=True):
         box = self.universe.dimensions if pbc else None
         A, B, C, D = self.atoms
 
-        return distances.calc_dihedral(
-            A.position, B.position, C.position, D.position, box)
+        return np.rad2deg(distances.calc_dihedrals(
+            A.position, B.position, C.position, D.position, box))
 
     value = dihedral