Add support for triclinic boxes to the Amber and CHARMM file parsers.

wrappers/python/simtk/openmm/app/amberprmtopfile.py

@@ -39,6 +39,7 @@ import forcefield as ff
 import element as elem
 import simtk.unit as unit
 import simtk.openmm as mm
+from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
 
 # Enumerated values for implicit solvent model
 
@@ -141,7 +142,8 @@ class AmberPrmtopFile(object):
         # Set the periodic box size.
 
         if prmtop.getIfBox():
-            top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
+            box = prmtop.getBoxBetaAndDimensions()
+            top.setPeriodicBoxVectors(computePeriodicBoxVectors(*(box[1:4] + box[0:1]*3)))
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
                      constraints=None, rigidWater=True, implicitSolvent=None,

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

@@ -52,6 +52,7 @@ except:
 import simtk.unit as units
 import simtk.openmm
 from simtk.openmm.app import element as elem
+from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
 from simtk.openmm.vec3 import Vec3
 import customgbforces as customgb
 
@@ -691,7 +692,6 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     >>> system = readAmberSystem(prmtop_filename)
 
     """
-
     if prmtop_filename is None and prmtop_loader is None:
         raise Exception("Must specify a filename or loader")
     if prmtop_filename is not None and prmtop_loader is not None:

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

@@ -32,7 +32,7 @@ __author__ = "Peter Eastman"
 __version__ = "1.0"
 
 from simtk.openmm import Vec3
-from simtk.unit import nanometers, is_quantity, norm, dot
+from simtk.unit import nanometers, is_quantity, norm, dot, radians
 import math
 
 
@@ -43,12 +43,12 @@ def computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta, gamma):
     instances)
     """
 
-    if u.is_quantity(a_length): a_length = a_length.value_in_unit(u.nanometers)
-    if u.is_quantity(b_length): a_length = a_length.value_in_unit(u.nanometers)
-    if u.is_quantity(c_length): a_length = a_length.value_in_unit(u.nanometers)
-    if u.is_quantity(alpha): alpha = alpha.value_in_unit(u.radians)
-    if u.is_quantity(beta): beta = beta.value_in_unit(u.radians)
-    if u.is_quantity(gamma): gamma = gamma.value_in_unit(u.radians)
+    if is_quantity(a_length): a_length = a_length.value_in_unit(nanometers)
+    if is_quantity(b_length): b_length = b_length.value_in_unit(nanometers)
+    if is_quantity(c_length): c_length = c_length.value_in_unit(nanometers)
+    if is_quantity(alpha): alpha = alpha.value_in_unit(radians)
+    if is_quantity(beta): beta = beta.value_in_unit(radians)
+    if is_quantity(gamma): gamma = gamma.value_in_unit(radians)
 
     # Compute the vectors.
 
@@ -84,8 +84,10 @@ def computeLengthsAndAngles(periodicBoxVectors):
 
     Lengths are returned in nanometers and angles in radians.
     """
-
-    (a, b, c) = vectors.value_in_unit(nanometers)
+    if is_quantity(periodicBoxVectors):
+        (a, b, c) = vectors.value_in_unit(nanometers)
+    else:
+        a, b, c = vectors
     a_length = norm(a)
     b_length = norm(b)
     c_length = norm(c)