Add a reducePeriodicBoxVectors function, since many helpers (like the one in

mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.

wrappers/python/simtk/openmm/app/internal/unitcell.py

@@ -79,6 +79,24 @@ def computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta, gamma):
     b = b - a*round(b[0]/a[0])
     return (a, b, c)*nanometers
 
+def reducePeriodicBoxVectors(periodicBoxVectors):
+    """ Reduces the representation of the PBC. periodicBoxVectors is expected to
+    be an unpackable iterable of length-3 iterables
+    """
+    if is_quantity(periodicBoxVectors):
+        a, b, c = periodicBoxVectors.value_in_unit(nanometers)
+    else:
+        a, b, c = periodicBoxVectors
+    a = Vec3(*a)
+    b = Vec3(*b)
+    c = Vec3(*c)
+
+    c = c - b*round(c[1]/b[1])
+    c = c - a*round(c[0]/a[0])
+    b = b - a*round(b[0]/a[0])
+
+    return (a, b, c) * nanometers
+
 def computeLengthsAndAngles(periodicBoxVectors):
     """Convert periodic box vectors to lengths and angles.
 

wrappers/python/tests/TestUnitCell.py

 import unittest
 import math
+from simtk.openmm import Vec3
 from simtk.unit import *
 from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
 from simtk.openmm.app.internal.unitcell import computeLengthsAndAngles
+from simtk.openmm.app.internal.unitcell import reducePeriodicBoxVectors
 
 def strip_units(x):
     if is_quantity(x): return x.value_in_unit_system(md_unit_system)
@@ -12,6 +14,25 @@ class TestAmberPrmtopFile(unittest.TestCase):
 
     """Test the AmberPrmtopFile.createSystem() method."""
 
+    def testReducePBCVectors(self):
+        """ Checks that reducePeriodicBoxVectors properly reduces vectors """
+        a = Vec3(4.24388485, 0.0, 0.0)
+        b = Vec3(-1.4146281691908937, 4.001173048368583, 0.0)
+        c = Vec3(-1.4146281691908937, -2.0005862820516203, 3.4651176446201674)
+        vecs = reducePeriodicBoxVectors((a, b, c)*nanometers)
+        vecs2 = computePeriodicBoxVectors(4.24388485, 4.24388485, 4.24388485,
+                109.4712190*degrees, 109.4712190*degrees, 109.4712190*degrees)
+
+        # Check that the vectors are the same
+        a1, a2, a3 = vecs
+        b1, b2, b3 = vecs2
+        for x, y in zip(a1, b1):
+            self.assertAlmostEqual(strip_units(x), strip_units(y))
+        for x, y in zip(a2, b2):
+            self.assertAlmostEqual(strip_units(x), strip_units(y))
+        for x, y in zip(a3, b3):
+            self.assertAlmostEqual(strip_units(x), strip_units(y))
+
     def testComputePBCVectors(self):
         """ Tests computing periodic box vectors """
         deg90 = 90 * degrees