mirror of
https://github.com/openmm/openmm
synced 2026-06-03 06:39:48 +09:00
e53bdc5eab
* Top level Python module is now "openmm" * Updated module names in examples * Updated module names in documentation * Updated module in CI scripts * Added deprecation warning
105 lines
4.4 KiB
Python
105 lines
4.4 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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import openmm.app.forcefield as forcefield
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import math
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try:
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from cStringIO import StringIO
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except ImportError:
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from io import StringIO
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import os
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import warnings
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class TestGenerators(unittest.TestCase):
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"""Test the various generators found in forcefield.py."""
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def setUp(self):
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# alanine dipeptide with implicit water
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self.pdb1 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
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def test_CustomHbondGenerator(self):
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"""Test the generator for CustomHbondForce."""
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for bondCutoff in range(4):
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xml = """
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<ForceField>
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<CustomHbondForce energy="a*b*distance(a1,d1)" particlesPerDonor="3" particlesPerAcceptor="2" bondCutoff="%d">
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<PerDonorParameter name="a"/>
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<PerAcceptorParameter name="b"/>
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<Donor class1="C" class2="N" class3="H" a="3"/>
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<Acceptor class1="C" class2="O" b="2"/>
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<Function name="test" min="1" max="2" type="Continuous1D">
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0 1 2 3 4 5
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</Function>
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</CustomHbondForce>
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</ForceField>""" % bondCutoff
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ff = ForceField('amber99sb.xml', StringIO(xml))
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system = ff.createSystem(self.pdb1.topology)
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hbond = [f for f in system.getForces() if isinstance(f, CustomHbondForce)][0]
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self.assertEqual(1, hbond.getNumPerDonorParameters())
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self.assertEqual(1, hbond.getNumPerAcceptorParameters())
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self.assertEqual('a', hbond.getPerDonorParameterName(0))
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self.assertEqual('b', hbond.getPerAcceptorParameterName(0))
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self.assertEqual(1, hbond.getNumTabulatedFunctions())
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expectedDonors = [(4,6,7), (14,16,17)]
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expectedAcceptors = [(4,5,-1), (14,15,-1)]
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self.assertEqual(len(expectedDonors), hbond.getNumDonors())
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self.assertEqual(len(expectedAcceptors), hbond.getNumAcceptors())
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for i in range(hbond.getNumDonors()):
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atom1, atom2, atom3, params = hbond.getDonorParameters(i)
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self.assertTrue((atom1, atom2, atom3) in expectedDonors)
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self.assertEqual((3.0,), params)
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for i in range(hbond.getNumAcceptors()):
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atom1, atom2, atom3, params = hbond.getAcceptorParameters(i)
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self.assertTrue((atom1, atom2, atom3) in expectedAcceptors)
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self.assertEqual((2.0,), params)
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expectedExclusions = [(0,0), (1,1)]
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if bondCutoff >= 2:
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expectedExclusions.append((0,1))
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if bondCutoff >= 3:
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expectedExclusions.append((1,0))
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self.assertEqual(len(expectedExclusions), hbond.getNumExclusions())
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for i in range(hbond.getNumExclusions()):
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self.assertTrue(tuple(hbond.getExclusionParticles(i)) in expectedExclusions)
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def test_CustomHbondGenerator2(self):
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"""Test the generator for CustomHbondForce with different parameters."""
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xml = """
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<ForceField>
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<CustomHbondForce energy="a*b*distance(a1,d1)" particlesPerDonor="2" particlesPerAcceptor="1" bondCutoff="0">
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<PerDonorParameter name="a"/>
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<PerAcceptorParameter name="b"/>
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<Donor class1="N" class2="H" a="3"/>
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<Acceptor class1="O" b="2"/>
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</CustomHbondForce>
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</ForceField>"""
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ff = ForceField('amber99sb.xml', StringIO(xml))
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system = ff.createSystem(self.pdb1.topology)
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hbond = [f for f in system.getForces() if isinstance(f, CustomHbondForce)][0]
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self.assertEqual(1, hbond.getNumPerDonorParameters())
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self.assertEqual(1, hbond.getNumPerAcceptorParameters())
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self.assertEqual('a', hbond.getPerDonorParameterName(0))
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self.assertEqual('b', hbond.getPerAcceptorParameterName(0))
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expectedDonors = [(6,7,-1), (16,17,-1)]
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expectedAcceptors = [(5,-1,-1), (15,-1,-1)]
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self.assertEqual(len(expectedDonors), hbond.getNumDonors())
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self.assertEqual(len(expectedAcceptors), hbond.getNumAcceptors())
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for i in range(hbond.getNumDonors()):
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atom1, atom2, atom3, params = hbond.getDonorParameters(i)
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self.assertTrue((atom1, atom2, atom3) in expectedDonors)
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self.assertEqual((3.0,), params)
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for i in range(hbond.getNumAcceptors()):
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atom1, atom2, atom3, params = hbond.getAcceptorParameters(i)
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self.assertTrue((atom1, atom2, atom3) in expectedAcceptors)
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self.assertEqual((2.0,), params)
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if __name__ == '__main__':
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unittest.main()
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