Improved performance of writeModel() (#4679)

wrappers/python/openmm/app/dcdfile.py

@@ -122,6 +122,7 @@ class DCDFile(object):
         if is_quantity(positions):
             positions = positions.value_in_unit(nanometers)
         import numpy as np
+        positions = np.asarray(positions)
         if np.isnan(positions).any():
             raise ValueError('Particle position is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan')
         if np.isinf(positions).any():

wrappers/python/openmm/app/pdbfile.py

@@ -344,6 +344,7 @@ class PDBFile(object):
         if is_quantity(positions):
             positions = positions.value_in_unit(angstroms)
         import numpy as np
+        positions = np.asarray(positions)
         if np.isnan(positions).any():
             raise ValueError('Particle position is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan')
         if np.isinf(positions).any():

wrappers/python/openmm/app/pdbxfile.py

@@ -419,6 +419,7 @@ class PDBxFile(object):
         if is_quantity(positions):
             positions = positions.value_in_unit(angstroms)
         import numpy as np
+        positions = np.asarray(positions)
         if np.isnan(positions).any():
             raise ValueError('Particle position is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan')
         if np.isinf(positions).any():

wrappers/python/openmm/app/xtcfile.py

@@ -91,6 +91,7 @@ class XTCFile(object):
         if is_quantity(positions):
             positions = positions.value_in_unit(nanometers)
         import numpy as np
+        positions = np.asarray(positions)
         if np.isnan(positions).any():
             raise ValueError(
                 "Particle position is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan"