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import unittest
from validateConstraints import *
from openmm.app import *
from openmm import *
from openmm.unit import *
import openmm.app.element as elem
try:
from scipy.io import netcdf_file
SCIPY_IMPORT_FAILED = False
except ImportError:
SCIPY_IMPORT_FAILED = True
def compareByElement(array1, array2, cmp):
for x, y in zip(array1, array2):
cmp(x, y)
class TestAmberInpcrdFile(unittest.TestCase):
"""Test the Amber inpcrd file parser"""
def test_CrdVelBox(self):
""" Test parsing ASCII restarts with crds, vels, and box """
cmp = self.assertAlmostEqual
inpcrd = AmberInpcrdFile('systems/crds_vels_box.rst7')
self.assertEqual(len(inpcrd.positions), 2101)
compareByElement(inpcrd.positions[-1].value_in_unit(angstroms),
[3.5958082, 8.4176792, -8.2954064], cmp)
compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picoseconds),
[0.3091332*20.455, 0.7355925*20.455, -0.1206961*20.455], cmp)
compareByElement(inpcrd.boxVectors[0].value_in_unit(angstroms),
[30.2642725, 0.0, 0.0], cmp)
@unittest.skipIf(SCIPY_IMPORT_FAILED, "Scipy is not installed")
def test_NetCDF(self):
""" Test NetCDF restart file parsing """
cmp = self.assertAlmostEqual
inpcrd = AmberInpcrdFile('systems/amber.ncrst')
self.assertEqual(len(inpcrd.positions), 2101)
compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
[6.82122492718229, 6.6276250662042, -8.51668999892245],
cmp)
compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picosecond),
[0.349702202733541*20.455, 0.391525333168534*20.455,
0.417941679767662*20.455], cmp)
self.assertAlmostEqual(inpcrd.boxVectors[0][0].value_in_unit(angstroms),
30.2642725, places=6)
def test_CrdBox(self):
""" Test parsing ASCII restarts with only crds and box """
inpcrd = AmberInpcrdFile('systems/crds_box.rst7')
self.assertEqual(len(inpcrd.positions), 18660)
self.assertTrue(inpcrd.velocities is None)
self.assertTrue(inpcrd.boxVectors is not None)
def test_CrdVel(self):
inpcrd = AmberInpcrdFile('systems/crds_vels.rst7')
self.assertTrue(inpcrd.boxVectors is None)
self.assertTrue(inpcrd.velocities is not None)
def test_CrdOnly(self):
inpcrd = AmberInpcrdFile('systems/crdsonly.rst7')
self.assertTrue(inpcrd.boxVectors is None)
self.assertTrue(inpcrd.velocities is None)
def test_CrdBoxTruncoct(self):
# Check that the box vectors come out correct.
inpcrd = AmberInpcrdFile('systems/tz2.truncoct.rst7')
ac = Vec3(42.4388485, 0.0, 0.0) * angstroms
bc = Vec3(-14.146281691908937, 40.011730483685835, 0.0) * angstroms
cc = Vec3(-14.146281691908937, -20.0058628205162, 34.651176446201672) * angstroms
a, b, c = inpcrd.getBoxVectors()
diffa = ac - a
diffb = bc - b
diffc = cc - c
self.assertAlmostEqual(norm(diffa)/angstroms, 0)
self.assertAlmostEqual(norm(diffb)/angstroms, 0)
self.assertAlmostEqual(norm(diffc)/angstroms, 0)
# Make sure angles and lengths come out about right
la = norm(a).in_units_of(angstroms)
lb = norm(b).in_units_of(angstroms)
lc = norm(c).in_units_of(angstroms)
self.assertAlmostEqual(la/angstroms, 42.4388485, 6)
self.assertAlmostEqual(lb/angstroms, 42.4388485, 6)
self.assertAlmostEqual(lc/angstroms, 42.4388485, 6)
self.assertAlmostEqual(dot(a,b)/la/lb, cos(109.4712190*degrees), 6)
self.assertAlmostEqual(dot(a,c)/la/lc, cos(109.4712190*degrees), 6)
self.assertAlmostEqual(dot(b,c)/lc/lb, cos(109.4712190*degrees), 6)
if __name__ == '__main__':
unittest.main()
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