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https://github.com/openmm/openmm
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792028058b
* Fix import of netcdf_file for scipy 1.14 * Fix indentation --------- Co-authored-by: Timothy Palpant <tim@atommapper.com>
92 lines
3.9 KiB
Python
92 lines
3.9 KiB
Python
import unittest
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from validateConstraints import *
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from openmm.app import *
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from openmm import *
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from openmm.unit import *
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import openmm.app.element as elem
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try:
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from scipy.io import netcdf_file
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SCIPY_IMPORT_FAILED = False
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except ImportError:
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SCIPY_IMPORT_FAILED = True
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def compareByElement(array1, array2, cmp):
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for x, y in zip(array1, array2):
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cmp(x, y)
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class TestAmberInpcrdFile(unittest.TestCase):
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"""Test the Amber inpcrd file parser"""
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def test_CrdVelBox(self):
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""" Test parsing ASCII restarts with crds, vels, and box """
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cmp = self.assertAlmostEqual
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inpcrd = AmberInpcrdFile('systems/crds_vels_box.rst7')
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self.assertEqual(len(inpcrd.positions), 2101)
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compareByElement(inpcrd.positions[-1].value_in_unit(angstroms),
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[3.5958082, 8.4176792, -8.2954064], cmp)
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compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picoseconds),
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[0.3091332*20.455, 0.7355925*20.455, -0.1206961*20.455], cmp)
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compareByElement(inpcrd.boxVectors[0].value_in_unit(angstroms),
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[30.2642725, 0.0, 0.0], cmp)
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@unittest.skipIf(SCIPY_IMPORT_FAILED, "Scipy is not installed")
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def test_NetCDF(self):
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""" Test NetCDF restart file parsing """
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cmp = self.assertAlmostEqual
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inpcrd = AmberInpcrdFile('systems/amber.ncrst')
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self.assertEqual(len(inpcrd.positions), 2101)
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compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
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[6.82122492718229, 6.6276250662042, -8.51668999892245],
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cmp)
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compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picosecond),
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[0.349702202733541*20.455, 0.391525333168534*20.455,
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0.417941679767662*20.455], cmp)
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self.assertAlmostEqual(inpcrd.boxVectors[0][0].value_in_unit(angstroms),
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30.2642725, places=6)
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def test_CrdBox(self):
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""" Test parsing ASCII restarts with only crds and box """
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inpcrd = AmberInpcrdFile('systems/crds_box.rst7')
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self.assertEqual(len(inpcrd.positions), 18660)
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self.assertTrue(inpcrd.velocities is None)
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self.assertTrue(inpcrd.boxVectors is not None)
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def test_CrdVel(self):
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inpcrd = AmberInpcrdFile('systems/crds_vels.rst7')
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self.assertTrue(inpcrd.boxVectors is None)
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self.assertTrue(inpcrd.velocities is not None)
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def test_CrdOnly(self):
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inpcrd = AmberInpcrdFile('systems/crdsonly.rst7')
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self.assertTrue(inpcrd.boxVectors is None)
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self.assertTrue(inpcrd.velocities is None)
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def test_CrdBoxTruncoct(self):
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# Check that the box vectors come out correct.
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inpcrd = AmberInpcrdFile('systems/tz2.truncoct.rst7')
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ac = Vec3(42.4388485, 0.0, 0.0) * angstroms
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bc = Vec3(-14.146281691908937, 40.011730483685835, 0.0) * angstroms
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cc = Vec3(-14.146281691908937, -20.0058628205162, 34.651176446201672) * angstroms
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a, b, c = inpcrd.getBoxVectors()
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diffa = ac - a
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diffb = bc - b
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diffc = cc - c
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self.assertAlmostEqual(norm(diffa)/angstroms, 0)
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self.assertAlmostEqual(norm(diffb)/angstroms, 0)
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self.assertAlmostEqual(norm(diffc)/angstroms, 0)
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# Make sure angles and lengths come out about right
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la = norm(a).in_units_of(angstroms)
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lb = norm(b).in_units_of(angstroms)
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lc = norm(c).in_units_of(angstroms)
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self.assertAlmostEqual(la/angstroms, 42.4388485, 6)
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self.assertAlmostEqual(lb/angstroms, 42.4388485, 6)
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self.assertAlmostEqual(lc/angstroms, 42.4388485, 6)
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self.assertAlmostEqual(dot(a,b)/la/lb, cos(109.4712190*degrees), 6)
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self.assertAlmostEqual(dot(a,c)/la/lc, cos(109.4712190*degrees), 6)
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self.assertAlmostEqual(dot(b,c)/lc/lb, cos(109.4712190*degrees), 6)
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if __name__ == '__main__':
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unittest.main()
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