From b5c2665157106a8b88600759df5fb4d3b15ea4a2 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Thu, 14 Jun 2018 07:18:44 -0500
Subject: [PATCH 01/13] 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                             |  2 +
 .../analysis/hbonds/hbond_analysis.py         | 12 ++---
 package/MDAnalysis/core/topologyobjects.py    | 33 ++++++-------
 package/MDAnalysis/lib/distances.py           | 48 +++++++++++++++++++
 .../core/test_topologyobjects.py              |  8 ++--
 5 files changed, 75 insertions(+), 28 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index d54a313609a..ae564c3d795 100644
--- a/package/CHANGELOG
+++ b/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
diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
index bf6b376479b..f7edc9d031e 100644
--- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
+++ b/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):
diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py
index bd586ec0556..2ca6b111c2d 100644
--- a/package/MDAnalysis/core/topologyobjects.py
+++ b/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
 
diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py
index 01bbeb868d0..4890fbf0283 100644
--- a/package/MDAnalysis/lib/distances.py
+++ b/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])
diff --git a/testsuite/MDAnalysisTests/core/test_topologyobjects.py b/testsuite/MDAnalysisTests/core/test_topologyobjects.py
index 6a1f9adb708..244771bcfd0 100644
--- a/testsuite/MDAnalysisTests/core/test_topologyobjects.py
+++ b/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):

From a40b33ec2a8f5fceb2330c17caf3e71ba551a7bf Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sat, 16 Jun 2018 18:29:26 -0500
Subject: [PATCH 02/13] tests for new functions in lib.distances

---
 .../MDAnalysisTests/lib/test_distances.py     | 89 +++++++++++++++++++
 1 file changed, 89 insertions(+)

diff --git a/testsuite/MDAnalysisTests/lib/test_distances.py b/testsuite/MDAnalysisTests/lib/test_distances.py
index 9a6c5aff6c6..571f4893338 100644
--- a/testsuite/MDAnalysisTests/lib/test_distances.py
+++ b/testsuite/MDAnalysisTests/lib/test_distances.py
@@ -37,3 +37,92 @@ def test_transform_StoR_pass(coord_dtype):
     test_r = mda.lib.distances.transform_StoR(s, box)
 
     assert_equal(original_r, test_r)
+
+
+# different boxlengths to shift a coordinate
+shifts = [
+    ((0, 0, 0), (0, 0, 0), (0, 0, 0), (0, 0, 0)), # no shifting
+    ((1, 0, 0), (0, 1, 1), (0, 0, 1), (1, 1, 0)), # single box lengths
+    ((-1, 0, 1), (0, -1, 0), (1, 0, 1), (-1, -1, -1)), # negative single
+    ((4, 3, -2), (-2, 2, 2), (-5, 2, 2), (0, 2, 2)),  # multiple boxlengths
+]
+
+
+@pytest.mark.parametrize('shift', shifts)
+@pytest.mark.parametrize('periodic', [True, False])
+def test_calc_distance(shift, periodic):
+    box = np.array([10, 10, 10, 90., 90., 90.], dtype=np.float32)
+
+    coords = np.array([[1, 1, 1], [3, 1, 1]], dtype=np.float32)
+
+    shift1, shift2, _, _ = shift
+
+    coords[0] += shift1 * box[:3]
+    coords[1] += shift2 * box[:3]
+
+    box = box if periodic else None
+    result = mda.lib.distances.calc_distance(coords[0], coords[1], box)
+
+    reference = 2.0 if periodic else np.linalg.norm(coords[0] - coords[1])
+
+    assert result == pytest.approx(reference)
+
+
+@pytest.mark.parametrize('case', [
+    # 90 degree angle
+    (np.array([[1, 1, 1], [1, 2, 1], [2, 2, 1]], dtype=np.float32), 90.),
+    # straight line / 180.
+    (np.array([[1, 1, 1], [1, 2, 1], [1, 3, 1]], dtype=np.float32), 180.),
+])
+@pytest.mark.parametrize('shift', shifts)
+@pytest.mark.parametrize('periodic', [True, False])
+def test_calc_angle(case, shift, periodic):
+    def manual_angle(x, y, z):
+        return np.rad2deg(mda.lib.mdamath.angle(y - x, y - z))
+
+    box = np.array([10, 20, 30, 90., 90., 90.], dtype=np.float32)
+    (a, b, c), ref = case
+
+    shift1, shift2, shift3, _ = shift
+
+    a += shift1 * box[:3]
+    b += shift2 * box[:3]
+    c += shift3 * box[:3]
+
+    box = box if periodic else None
+    result = mda.lib.distances.calc_angle(a, b, c, box)
+
+    reference = ref if periodic else manual_angle(a, b, c)
+
+    assert result == pytest.approx(reference, abs=1e-3)
+
+
+@pytest.mark.parametrize('case', [
+    # 0 degree angle (cis)
+    (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 2, 1]], dtype=np.float32), 0.),
+    # 180 degree (trans)
+    (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 0, 1]], dtype=np.float32), 180.),
+])
+@pytest.mark.parametrize('shift', shifts)
+@pytest.mark.parametrize('periodic', [True, False])
+def test_calc_dihedral(case, shift, periodic):
+    def manual_dihedral(a, b, c, d):
+        return np.rad2deg(mda.lib.mdamath.dihedral(b - a, c - b, d - c))
+
+    box = np.array([10., 10., 10., 90., 90., 90.], dtype=np.float32)
+
+    (a, b, c, d), ref = case
+
+    shift1, shift2, shift3, shift4 = shift
+
+    a += shift1 * box[:3]
+    b += shift2 * box[:3]
+    c += shift3 * box[:3]
+    d += shift4 * box[:3]
+
+    box = box if periodic else None
+    result = mda.lib.distances.calc_dihedral(a, b, c, d, box)
+
+    reference = ref if periodic else manual_dihedral(a, b, c, d)
+
+    assert abs(result) == pytest.approx(abs(reference), abs=1e-3)

From 0da4f4fdc42dc6499b4d6a0b8fc9c3886983f788 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sat, 16 Jun 2018 18:32:09 -0500
Subject: [PATCH 03/13] simplified docstrings

---
 package/MDAnalysis/lib/distances.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py
index 4890fbf0283..e82455935f9 100644
--- a/package/MDAnalysis/lib/distances.py
+++ b/package/MDAnalysis/lib/distances.py
@@ -905,7 +905,6 @@ def calc_angle(a, b, c, box=None):
       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
     """
@@ -921,7 +920,6 @@ def calc_dihedral(a, b, c, d, box=None):
       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
     """

From 0931383da977b4b851169811c939433d7ee4ae09 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sun, 17 Jun 2018 13:59:51 -0500
Subject: [PATCH 04/13] added more tests for single distance calculations

---
 testsuite/MDAnalysisTests/lib/test_distances.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_distances.py b/testsuite/MDAnalysisTests/lib/test_distances.py
index 571f4893338..611b31c60d1 100644
--- a/testsuite/MDAnalysisTests/lib/test_distances.py
+++ b/testsuite/MDAnalysisTests/lib/test_distances.py
@@ -51,7 +51,7 @@ def test_transform_StoR_pass(coord_dtype):
 @pytest.mark.parametrize('shift', shifts)
 @pytest.mark.parametrize('periodic', [True, False])
 def test_calc_distance(shift, periodic):
-    box = np.array([10, 10, 10, 90., 90., 90.], dtype=np.float32)
+    box = np.array([10, 20, 30, 90., 90., 90.], dtype=np.float32)
 
     coords = np.array([[1, 1, 1], [3, 1, 1]], dtype=np.float32)
 
@@ -73,6 +73,8 @@ def test_calc_distance(shift, periodic):
     (np.array([[1, 1, 1], [1, 2, 1], [2, 2, 1]], dtype=np.float32), 90.),
     # straight line / 180.
     (np.array([[1, 1, 1], [1, 2, 1], [1, 3, 1]], dtype=np.float32), 180.),
+    # 45
+    (np.array([[1, 1, 1], [1, 2, 1], [2, 1, 1]], dtype=np.float32), 45.),
 ])
 @pytest.mark.parametrize('shift', shifts)
 @pytest.mark.parametrize('periodic', [True, False])
@@ -102,6 +104,14 @@ def manual_angle(x, y, z):
     (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 2, 1]], dtype=np.float32), 0.),
     # 180 degree (trans)
     (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 0, 1]], dtype=np.float32), 180.),
+    # 90 degree
+    (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 1, 2]], dtype=np.float32), 90.),
+    # other 90 degree
+    (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 1, 0]], dtype=np.float32), 90.),
+    # 45 degree
+    (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 2, 2]], dtype=np.float32), 45.),
+    # 135
+    (np.array([[1, 2, 1], [1, 1, 1], [2, 1, 1], [2, 0, 2]], dtype=np.float32), 135.),
 ])
 @pytest.mark.parametrize('shift', shifts)
 @pytest.mark.parametrize('periodic', [True, False])

From 7a11becb293eaa12127c702ea85e797c209634c2 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sun, 17 Jun 2018 14:02:39 -0500
Subject: [PATCH 05/13] finalised changelog

defaulted Bond.value pbc to True to match other objects
---
 package/CHANGELOG                          | 6 ++++--
 package/MDAnalysis/core/topologyobjects.py | 4 +++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index ae564c3d795..b104e006aad 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -35,6 +35,10 @@ 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)
 
 Fixes
   * rewind in the SingleFrameReader now reads the frame from the file (Issue #1929)
@@ -51,8 +55,6 @@ 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
diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py
index 2ca6b111c2d..f26936c4074 100644
--- a/package/MDAnalysis/core/topologyobjects.py
+++ b/package/MDAnalysis/core/topologyobjects.py
@@ -191,11 +191,13 @@ def partner(self, atom):
         else:
             raise ValueError("Unrecognised Atom")
 
-    def length(self, pbc=False):
+    def length(self, pbc=True):
         """Length of the bond.
 
         .. versionchanged:: 0.11.0
            Added pbc keyword
+        .. versionchanged:: 0.18.1
+           Changed default of pbc to True
         """
         box = self.universe.dimensions if pbc else None
 

From 0f005f2a0d0d56a966ede42b8d44febcb252911d Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sun, 17 Jun 2018 14:04:06 -0500
Subject: [PATCH 06/13] changed default to pbc to True in TopologyObjects

---
 package/MDAnalysis/core/topologyobjects.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py
index f26936c4074..6abfb02eb33 100644
--- a/package/MDAnalysis/core/topologyobjects.py
+++ b/package/MDAnalysis/core/topologyobjects.py
@@ -218,7 +218,7 @@ class Angle(TopologyObject):
     """
     btype = 'angle'
 
-    def angle(self, pbc=False):
+    def angle(self, pbc=True):
         """Returns the angle in degrees of this Angle.
 
         Angle between atoms 0 and 2 with apex at 1::
@@ -266,7 +266,7 @@ class Dihedral(TopologyObject):
     # http://cbio.bmt.tue.nl/pumma/uploads/Theory/dihedral.png
     btype = 'dihedral'
 
-    def dihedral(self, pbc=False):
+    def dihedral(self, pbc=True):
         """Calculate the dihedral angle in degrees.
 
         Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle

From 5353f95a4ed918058e9084714db3d9936a4752cc Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Tue, 19 Jun 2018 11:47:42 -0500
Subject: [PATCH 07/13] fixed make_whole now Bond.length() defaults to pbc=True

---
 package/MDAnalysis/core/topologyobjects.py | 4 ++--
 package/MDAnalysis/lib/mdamath.py          | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py
index 6abfb02eb33..0844efa987e 100644
--- a/package/MDAnalysis/core/topologyobjects.py
+++ b/package/MDAnalysis/core/topologyobjects.py
@@ -237,7 +237,7 @@ def angle(self, pbc=True):
         .. versionchanged:: 0.17.0
            Fixed angles close to 180 giving NaN
         .. versionchanged:: 0.18.1
-           Added pbc keyword
+           Added pbc keyword, default True
         """
         box = self.universe.dimensions if pbc else None
 
@@ -286,7 +286,7 @@ def dihedral(self, pbc=True):
 
         .. versionadded:: 0.9.0
         .. versionchanged:: 0.18.1
-           Added pbc keyword
+           Added pbc keyword, default True
         """
         box = self.universe.dimensions if pbc else None
         A, B, C, D = self.atoms
diff --git a/package/MDAnalysis/lib/mdamath.py b/package/MDAnalysis/lib/mdamath.py
index eccc43fdf55..dd58ea12bab 100644
--- a/package/MDAnalysis/lib/mdamath.py
+++ b/package/MDAnalysis/lib/mdamath.py
@@ -416,7 +416,7 @@ def make_whole(atomgroup, reference_atom=None):
                     continue
                 if other in ref_points:
                     continue
-                if b.length() > box_length:
+                if b.length(pbc=False) > box_length:
                     # Vector from ref atom to other
                     vec = other.position - ref.position
                     # Apply pbc to this vector

From 61157394f803a73370bf01b4292a6182cb0ec500 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Tue, 19 Jun 2018 11:54:13 -0500
Subject: [PATCH 08/13] completely removed HBondAnalysis' distance methods

---
 .../analysis/hbonds/hbond_analysis.py         | 22 ++++++----------
 .../analysis/hbonds/wbridge_analysis.py       | 25 +++++++++++++------
 2 files changed, 24 insertions(+), 23 deletions(-)

diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
index f7edc9d031e..42b3d9f37f4 100644
--- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
+++ b/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
-                    self.calc_eucl_distance(atom, a, box) < self.r_cov[atom.name[0]])
+                    distances.calc_distance(atom.position, a.position, box) < self.r_cov[atom.name[0]])
                 ]
         except IndexError:
             hydrogens = []  # weird corner case that atom is the last one in universe
@@ -993,9 +993,10 @@ def _get_timestep():
                     for h in donor_h_set:
                         res = ns_acceptors.search(h, self.distance)
                         for a in res:
-                            angle = self.calc_angle(d, h, a, box=box)
+                            angle = distances.calc_angle(d.position, h.position,
+                                                         a.position, box=box)
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = self.calc_eucl_distance(donor_atom, a, box)
+                            dist = distances.calc_distance(donor_atom.position, a.position, 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))
@@ -1018,9 +1019,10 @@ def _get_timestep():
                                     (h.index, a.index) in already_found or
                                     (a.index, h.index) in already_found):
                                 continue
-                            angle = self.calc_angle(d, h, a, box=box)
+                            angle = distances.calc_angle(d.position, h.position,
+                                                         a.position, box=box)
                             donor_atom = h if self.distance_type != 'heavy' else d
-                            dist = self.calc_eucl_distance(donor_atom, a, box)
+                            dist = distances.calc_distance(donor_atom.position, a.position, 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))
@@ -1035,16 +1037,6 @@ def _get_timestep():
         logger.info("HBond analysis: complete; timeseries  %s.timeseries",
                     self.__class__.__name__)
 
-    @staticmethod
-    def calc_angle(d, h, a, box=None):
-        """Calculate the angle (in degrees) between two atoms with H at apex."""
-        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 distances.calc_distance(a1.position, a2.position, box)
-
     @property
     def timeseries(self):
         """Time series of hydrogen bonds.
diff --git a/package/MDAnalysis/analysis/hbonds/wbridge_analysis.py b/package/MDAnalysis/analysis/hbonds/wbridge_analysis.py
index 308f7d077a4..e55272c7a2a 100644
--- a/package/MDAnalysis/analysis/hbonds/wbridge_analysis.py
+++ b/package/MDAnalysis/analysis/hbonds/wbridge_analysis.py
@@ -292,6 +292,7 @@ class WaterBridgeAnalysis_OtherFF(WaterBridgeAnalysis):
 from .hbond_analysis import HydrogenBondAnalysis
 from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
 from MDAnalysis.lib.log import ProgressMeter, _set_verbose
+from MDAnalysis.lib import distances
 from MDAnalysis import SelectionWarning
 
 logger = logging.getLogger('MDAnalysis.analysis.wbridges')
@@ -634,9 +635,11 @@ 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 = self.calc_eucl_distance(donor_atom, a)
+                            dist = distances.calc_distance(donor_atom.position,
+                                                           a.position)
                             if dist <= self.distance:
-                                angle = self.calc_angle(d, h, a)
+                                angle = distances.calc_angle(d.position, h.position,
+                                                             a.position)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "S1-D: {0!s} <-> W-A: {1!s} {2:f} A, {3:f} DEG"\
@@ -658,9 +661,11 @@ 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 = self.calc_eucl_distance(donor_atom, a)
+                            dist = distances.calc_distance(donor_atom.position,
+                                                           a.position)
                             if dist <= self.distance:
-                                angle = self.calc_angle(d, h, a)
+                                angle = distances.calc_angle(d.position, h.position,
+                                                             a.position)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "S1-A: {0!s} <-> W-D: {1!s} {2:f} A, {3:f} DEG"\
@@ -706,9 +711,11 @@ 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 = self.calc_eucl_distance(donor_atom, a)
+                            dist = distances.calc_distance(donor_atom.position,
+                                                           a.position)
                             if dist <= self.distance:
-                                angle = self.calc_angle(d, h, a)
+                                angle = distances.calc_angle(d.position, h.position,
+                                                             a.position)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "WB-D: {0!s} <-> S2-A: {1!s} {2:f} A, {3:f} DEG"\
@@ -728,9 +735,11 @@ 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 = self.calc_eucl_distance(donor_atom, a)
+                            dist = distances.calc_distance(donor_atom.position,
+                                                           a.position)
                             if dist <= self.distance:
-                                angle = self.calc_angle(d, h, a)
+                                angle = distances.calc_angle(d.position, h.position,
+                                                             a.position)
                                 if angle >= self.angle:
                                     self.logger_debug(
                                         "WB-A: {0!s} <-> S2-D: {1!s} {2:f} A, {3:f} DEG"\

From be1ce8cfaa96dfa457efd556d5a4c7b6a5c11b45 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Wed, 20 Jun 2018 09:32:28 -0500
Subject: [PATCH 09/13] removed unused import

---
 package/MDAnalysis/analysis/hbonds/hbond_analysis.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
index 42b3d9f37f4..ac38eceb8a9 100644
--- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
+++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py
@@ -329,7 +329,6 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 from MDAnalysis.lib.log import ProgressMeter, _set_verbose
 from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
 from MDAnalysis.lib import distances
-from MDAnalysis.lib.distances import calc_bonds
 
 
 logger = logging.getLogger('MDAnalysis.analysis.hbonds')

From c4fc8ec6d423668d493f79e61ea0421ec6c577e0 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sat, 23 Jun 2018 19:11:04 -0500
Subject: [PATCH 10/13] maybe fixed the docs?

---
 package/MDAnalysis/lib/distances.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py
index e82455935f9..d25f5cd8aac 100644
--- a/package/MDAnalysis/lib/distances.py
+++ b/package/MDAnalysis/lib/distances.py
@@ -887,9 +887,9 @@ def calc_distance(a, b, box=None):
     Parameters
     ----------
     a, b : numpy.ndarray
-      single coordinate vectors
+        single coordinate vectors
     box : numpy.ndarray, optional
-      simulation box, if given periodic boundary conditions will be applied
+        simulation box, if given periodic boundary conditions will be applied
 
     .. versionadded:: 0.18.1
     """
@@ -902,9 +902,10 @@ def calc_angle(a, b, c, box=None):
     Parameters
     ----------
     a, b, c : numpy.ndarray
-      single coordinate vectors
-    box : numpy.ndarray, optional
-      simulation box, if given periodic boundary conditions will be applied
+        single coordinate vectors
+    box : numpy.ndarray
+        simulation box if given periodic boundary conditions will be applied to
+        the vectors between atoms
 
     .. versionadded:: 0.18.1
     """
@@ -917,9 +918,9 @@ def calc_dihedral(a, b, c, d, box=None):
     Parameters
     ----------
     a, b, c, d : numpy.ndarray
-      single coordinate vectors
+        single coordinate vectors
     box : numpy.ndarray, optional
-      simulation box, if given periodic boundary conditions will be applied
+        simulation box, if given periodic boundary conditions will be applied
 
     .. versionadded:: 0.18.1
     """

From 068934372d42048bc4e92d903fa434cfc89ee86b Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sun, 24 Jun 2018 10:51:59 -0500
Subject: [PATCH 11/13] really really fixed the docs

---
 package/MDAnalysis/lib/distances.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py
index d25f5cd8aac..0411a6d4ab0 100644
--- a/package/MDAnalysis/lib/distances.py
+++ b/package/MDAnalysis/lib/distances.py
@@ -891,6 +891,7 @@ def calc_distance(a, b, box=None):
     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]
@@ -907,6 +908,7 @@ def calc_angle(a, b, c, box=None):
         simulation box if given periodic boundary conditions will be applied to
         the vectors between atoms
 
+
     .. versionadded:: 0.18.1
     """
     return np.rad2deg(calc_angles(a[None, :], b[None, :], c[None, :], box=box)[0])
@@ -922,6 +924,7 @@ def calc_dihedral(a, b, c, d, box=None):
     box : numpy.ndarray, optional
         simulation box, if given periodic boundary conditions will be applied
 
+
     .. versionadded:: 0.18.1
     """
     return np.rad2deg(

From f3cbffdc8bee42a321c6142a5680554268c6541c Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Sun, 24 Jun 2018 11:03:23 -0500
Subject: [PATCH 12/13] more doc fixes in lib.distances

---
 package/MDAnalysis/lib/distances.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/lib/distances.py b/package/MDAnalysis/lib/distances.py
index 0411a6d4ab0..773eed09336 100644
--- a/package/MDAnalysis/lib/distances.py
+++ b/package/MDAnalysis/lib/distances.py
@@ -413,7 +413,7 @@ def transform_RtoS(inputcoords, box, backend="serial"):
         The dimensions must be provided in the same format as returned
         by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`: ``[lx,
         ly, lz, alpha, beta, gamma]``.
-    backend : str
+    backend : str, optional
         Select the type of acceleration; "serial" is always available. Other
         possibilities are "OpenMP" (OpenMP).
 
@@ -422,6 +422,7 @@ def transform_RtoS(inputcoords, box, backend="serial"):
     outcoords : array
         A n x 3 array of fractional coordiantes.
 
+
     .. versionchanged:: 0.13.0
        Added *backend* keyword.
     .. versionchanged:: 0.19.0
@@ -475,14 +476,14 @@ def transform_StoR(inputcoords, box, backend="serial"):
         The dimensions must be provided in the same format as returned
         by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`: ``[lx,
         ly, lz, alpha, beta, gamma]``.
-    backend : str
+    backend : str, optional
         Select the type of acceleration; "serial" is always available. Other
         possibilities are "OpenMP" (OpenMP).
 
     Returns
     -------
     outcoords : array
-        A n x 3 array of fracional coordiantes.
+        A n x 3 array of fractional coordiantes.
 
 
     .. versionchanged:: 0.13.0

From 68446bd398ab83a1c3348cc94e2e039f63465ab8 Mon Sep 17 00:00:00 2001
From: richardjgowers <richardjgowers@gmail.com>
Date: Fri, 29 Jun 2018 10:12:51 -0500
Subject: [PATCH 13/13] use np.testing.assert_almost_equal not pytest.approx

---
 testsuite/MDAnalysisTests/lib/test_distances.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/testsuite/MDAnalysisTests/lib/test_distances.py b/testsuite/MDAnalysisTests/lib/test_distances.py
index 611b31c60d1..61857fffe73 100644
--- a/testsuite/MDAnalysisTests/lib/test_distances.py
+++ b/testsuite/MDAnalysisTests/lib/test_distances.py
@@ -23,7 +23,7 @@
 from __future__ import absolute_import
 import pytest
 import numpy as np
-from numpy.testing import assert_equal
+from numpy.testing import assert_equal, assert_almost_equal
 
 import MDAnalysis as mda
 
@@ -65,7 +65,7 @@ def test_calc_distance(shift, periodic):
 
     reference = 2.0 if periodic else np.linalg.norm(coords[0] - coords[1])
 
-    assert result == pytest.approx(reference)
+    assert_almost_equal(result, reference, decimal=3)
 
 
 @pytest.mark.parametrize('case', [
@@ -96,7 +96,7 @@ def manual_angle(x, y, z):
 
     reference = ref if periodic else manual_angle(a, b, c)
 
-    assert result == pytest.approx(reference, abs=1e-3)
+    assert_almost_equal(result, reference, decimal=3)
 
 
 @pytest.mark.parametrize('case', [
@@ -135,4 +135,4 @@ def manual_dihedral(a, b, c, d):
 
     reference = ref if periodic else manual_dihedral(a, b, c, d)
 
-    assert abs(result) == pytest.approx(abs(reference), abs=1e-3)
+    assert_almost_equal(abs(result), abs(reference), decimal=3)