Added single distance calculations to lib.distances

calc_distance, calc_angle and calc_dihedral

Fixes Issue #1262 #1938

redid 180 degree angle test for new function

package/CHANGELOG

@@ -51,6 +51,8 @@ Fixes
   * PDBWriter now properly sets start value
 
 Changes
+  * Added calc_distance, calc_angle and calc_dihedral to lib.distances
+    (Issue #1262 #1938)
   * TopologyAttrs are now statically typed (Issue #1876)
   * updated meta data for new PyPi (#1837)
   * AtomGroup.atoms, ResidueGroup.residues, and SegmentGroup.segments now return

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -328,7 +328,8 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 from MDAnalysis import MissingDataWarning, NoDataError, SelectionError, SelectionWarning
 from MDAnalysis.lib.log import ProgressMeter, _set_verbose
 from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
-from MDAnalysis.lib.distances import calc_bonds, calc_angles
+from MDAnalysis.lib import distances
+from MDAnalysis.lib.distances import calc_bonds
 
 
 logger = logging.getLogger('MDAnalysis.analysis.hbonds')
@@ -1037,17 +1038,12 @@ def _get_timestep():
     @staticmethod
     def calc_angle(d, h, a, box=None):
         """Calculate the angle (in degrees) between two atoms with H at apex."""
-        v1= d.position
-        v2= h.position
-        v3= a.position
-        angle= calc_angles(v1[None, :], v2[None, :], v3[None, :], box=box)
-
-        return np.rad2deg(angle[0])
+        return distances.calc_angle(d.position, h.position, a.position, box)
 
     @staticmethod
     def calc_eucl_distance(a1, a2, box=None):
         """Calculate the Euclidean distance between two atoms. """
-        return calc_bonds(a1.position[None, :], a2.position[None, :], box=box)[0]
+        return distances.calc_distance(a1.position, a2.position, box)
 
     @property
     def timeseries(self):

package/MDAnalysis/core/topologyobjects.py

@@ -197,13 +197,9 @@ def length(self, pbc=False):
         .. versionchanged:: 0.11.0
            Added pbc keyword
         """
-        if pbc:
-            box = self.universe.dimensions
-            return distances.self_distance_array(
-                np.array([self[0].position, self[1].position]),
-                box=box)[0]
-        else:
-            return mdamath.norm(self[0].position - self[1].position)
+        box = self.universe.dimensions if pbc else None
+
+        return distances.calc_distance(self[0].position, self[1].position, box)
 
     value = length
 
@@ -220,7 +216,7 @@ class Angle(TopologyObject):
     """
     btype = 'angle'
 
-    def angle(self):
+    def angle(self, pbc=False):
         """Returns the angle in degrees of this Angle.
 
         Angle between atoms 0 and 2 with apex at 1::
@@ -238,10 +234,13 @@ def angle(self):
         .. versionadded:: 0.9.0
         .. versionchanged:: 0.17.0
            Fixed angles close to 180 giving NaN
+        .. versionchanged:: 0.18.1
+           Added pbc keyword
         """
-        a = self[0].position - self[1].position
-        b = self[2].position - self[1].position
-        return np.rad2deg(mdamath.angle(a, b))
+        box = self.universe.dimensions if pbc else None
+
+        return distances.calc_angle(
+            self[0].position, self[1].position, self[2].position, box)
 
     value = angle
 
@@ -265,7 +264,7 @@ class Dihedral(TopologyObject):
     # http://cbio.bmt.tue.nl/pumma/uploads/Theory/dihedral.png
     btype = 'dihedral'
 
-    def dihedral(self):
+    def dihedral(self, pbc=False):
         """Calculate the dihedral angle in degrees.
 
         Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle
@@ -284,12 +283,14 @@ def dihedral(self):
         4 decimals (and is only tested to 3 decimals).
 
         .. versionadded:: 0.9.0
+        .. versionchanged:: 0.18.1
+           Added pbc keyword
         """
+        box = self.universe.dimensions if pbc else None
         A, B, C, D = self.atoms
-        ab = A.position - B.position
-        bc = B.position - C.position
-        cd = C.position - D.position
-        return np.rad2deg(mdamath.dihedral(ab, bc, cd))
+
+        return distances.calc_dihedral(
+            A.position, B.position, C.position, D.position, box)
 
     value = dihedral
 

package/MDAnalysis/lib/distances.py

@@ -879,3 +879,51 @@ def apply_PBC(incoords, box, backend="serial"):
                backend=backend)
 
     return coords
+
+
+def calc_distance(a, b, box=None):
+    """Distance between a and b
+
+    Parameters
+    ----------
+    a, b : numpy.ndarray
+      single coordinate vectors
+    box : numpy.ndarray, optional
+      simulation box, if given periodic boundary conditions will be applied
+
+    .. versionadded:: 0.18.1
+    """
+    return calc_bonds(a[None, :], b[None, :], box=box)[0]
+
+
+def calc_angle(a, b, c, box=None):
+    """Angle (in degrees) between a, b and c, where b is apex of angle
+
+    Parameters
+    ----------
+    a, b, c : numpy.ndarray
+      single coordinate vectors
+    box : numpy.ndarray, optional
+      simulation box, if given periodic boundary conditions will be applied
+      to the vectors a->b and b->c.
+
+    .. versionadded:: 0.18.1
+    """
+    return np.rad2deg(calc_angles(a[None, :], b[None, :], c[None, :], box=box)[0])
+
+
+def calc_dihedral(a, b, c, d, box=None):
+    """Dihedral angle (in degrees) between planes (a, b, c) and (b, c, d)
+
+    Parameters
+    ----------
+    a, b, c, d : numpy.ndarray
+      single coordinate vectors
+    box : numpy.ndarray, optional
+      simulation box, if given periodic boundary conditions will be applied
+      to the vectors a->b and b->c.
+
+    .. versionadded:: 0.18.1
+    """
+    return np.rad2deg(
+        calc_dihedrals(a[None, :], b[None, :], c[None, :], d[None, :], box)[0])

testsuite/MDAnalysisTests/core/test_topologyobjects.py

@@ -163,14 +163,14 @@ def test_angle_180(self):
         # we edit the coordinates, so make our own universe
         u = mda.Universe(PSF, DCD)
         angle = u.atoms[210].angles[0]
-        coords = np.array([[ 83.37363434,  65.01402283,  35.03564835],
-                           [ 82.28535461,  59.99816513,  34.94399261],
-                           [ 81.19387817,  54.97631073,  34.85218048]],
+        coords = np.array([[1, 1, 1],
+                           [2, 1, 1],
+                           [3, 1, 1]],
                           dtype=np.float32)
 
         angle.atoms.positions = coords
 
-        assert_almost_equal(angle.value(), -180.0, self.precision)
+        assert_almost_equal(angle.value(), 180.0, self.precision)
 
     # Dihedral class check
     def test_dihedral(self, PSFDCD):