Merge branch 'master' of github.com:pandegroup/openmm

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

@@ -166,7 +166,7 @@ class CharmmPsfFile(object):
     GB_FORCE_GROUP = 6
 
     @_catchindexerror
-    def __init__(self, psf_name):
+    def __init__(self, psf_name, periodicBoxVectors=None, unitCellDimensions=None):
         """Opens and parses a PSF file, then instantiates a CharmmPsfFile
         instance from the data.
 
@@ -174,6 +174,11 @@ class CharmmPsfFile(object):
         ----------
         psf_name : str
             Name of the PSF file (it must exist)
+        periodicBoxVectors : tuple of Vec3
+            the vectors defining the periodic box
+        unitCellDimensions : Vec3
+            the dimensions of the crystallographic unit cell.  For
+            non-rectangular unit cells, specify periodicBoxVectors instead.
 
         Raises
         ------
@@ -449,7 +454,14 @@ class CharmmPsfFile(object):
         self.group_list = group_list
         self.title = title
         self.flags = psf_flags
-        self.box_vectors = None
+        if unitCellDimensions is not None:
+            if periodicBoxVectors is not None:
+                raise ValueError("specify either periodicBoxVectors or unitCellDimensions, but not both")
+            if u.is_quantity(unitCellDimensions):
+                unitCellDimensions = unitCellDimensions.value_in_unit(u.nanometers)
+            self.box_vectors = (Vec3(unitCellDimensions[0], 0, 0), Vec3(0, unitCellDimensions[1], 0), Vec3(0, 0, unitCellDimensions[2]))*u.nanometers
+        else:
+            self.box_vectors = periodicBoxVectors
 
     @staticmethod
     def _convert(string, type, message):

wrappers/python/tests/TestCharmmFiles.py

@@ -93,12 +93,10 @@ class TestCharmmFiles(unittest.TestCase):
     def test_NBFIX(self):
         """Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf')
+        psf = CharmmPsfFile('systems/ala3_solv.psf', unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
         crd = CharmmCrdFile('systems/ala3_solv.crd')
         params = CharmmParameterSet('systems/par_all36_prot.prm',
                                     'systems/toppar_water_ions.str')
-        # Box dimensions (found from bounding box)
-        psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
 
         # Turn off charges so we only test the Lennard-Jones energies
         for a in psf.atom_list:
@@ -169,12 +167,11 @@ class TestCharmmFiles(unittest.TestCase):
     def testSystemOptions(self):
         """ Test various options in CharmmPsfFile.createSystem """
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf')
+        psf = CharmmPsfFile('systems/ala3_solv.psf',
+                            periodicBoxVectors=(Vec3(32.7119500, 0, 0)*angstroms, Vec3(0, 32.9959600, 0)*angstroms, Vec3(0, 0, 33.0071500)*angstroms))
         crd = CharmmCrdFile('systems/ala3_solv.crd')
         params = CharmmParameterSet('systems/par_all36_prot.prm',
                                     'systems/toppar_water_ions.str')
-        # Box dimensions (found from bounding box)
-        psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
 
         # Check some illegal options
         self.assertRaises(ValueError, lambda: