1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
|
# Energy tests
#
# Written by Konrad Hinsen
#
import unittest
from subsets import SubsetTest
from MMTK import *
from MMTK.MoleculeFactory import MoleculeFactory
from MMTK.ForceFields import Amber99ForceField, LennardJonesForceField
from MMTK_forcefield import NonbondedList
from MMTK.Random import randomPointInBox
from MMTK.Geometry import SCLattice
from MMTK.Utility import pairs
from Scientific.Geometry import ex, ey, ez
from Scientific import N
from cStringIO import StringIO
import itertools
factory = MoleculeFactory()
factory.createGroup('dihedral_test')
factory.addAtom('dihedral_test', 'C1', 'C')
factory.addAtom('dihedral_test', 'C2', 'C')
factory.addAtom('dihedral_test', 'C3', 'C')
factory.addAtom('dihedral_test', 'C4', 'C')
factory.addBond('dihedral_test', 'C1', 'C2')
factory.addBond('dihedral_test', 'C2', 'C3')
factory.addBond('dihedral_test', 'C3', 'C4')
factory.setAttribute('dihedral_test', 'C1.amber_atom_type', 'D1')
factory.setAttribute('dihedral_test', 'C2.amber_atom_type', 'D2')
factory.setAttribute('dihedral_test', 'C3.amber_atom_type', 'D3')
factory.setAttribute('dihedral_test', 'C4.amber_atom_type', 'D4')
factory.setAttribute('dihedral_test', 'C1.amber_charge', 0.)
factory.setAttribute('dihedral_test', 'C2.amber_charge', 0.)
factory.setAttribute('dihedral_test', 'C3.amber_charge', 0.)
factory.setAttribute('dihedral_test', 'C4.amber_charge', 0.)
factory.setPosition('dihedral_test', 'C1', Vector(1., 0., 0.))
factory.setPosition('dihedral_test', 'C2', Vector(0., 0., 0.))
factory.setPosition('dihedral_test', 'C3', Vector(0., 0., 1.))
factory.setPosition('dihedral_test', 'C4', Vector(1., 0., 1.))
def sorted_tuple(pair):
if pair[0] < pair[1]:
return (pair[0], pair[1])
else:
return (pair[1], pair[0])
class DihedralTest(unittest.TestCase):
def setUp(self):
self.universe = InfiniteUniverse()
self.universe.addObject(factory.retrieveMolecule('dihedral_test'))
self.mod_template = """Amber parameters
MASS
D1 12.0
D2 12.0
D3 12.0
D4 12.0
BOND
D1-D2 0.0 1.000
D2-D3 0.0 1.000
D3-D4 0.0 1.000
ANGL
D1-D2-D3 0.0 90.0
D2-D3-D4 0.0 90.0
DIHEDRAL
D1-D2-D3-D4 1%15.6f%15.6f%15.6f
NONB
D1 1.0000 0.0000 0.00000
D2 1.0000 0.0000 0.00000
D3 1.0000 0.0000 0.00000
D4 1.0000 0.0000 0.00000
"""
def _gradientTest(self, delta = 0.0001):
e0, grad = self.universe.energyAndGradients()
atoms = self.universe.atomList()
for a in atoms:
num_grad = []
for v in [ex, ey, ez]:
x = a.position()
a.setPosition(x+delta*v)
eplus = self.universe.energy()
a.setPosition(x-delta*v)
eminus = self.universe.energy()
a.setPosition(x)
num_grad.append(0.5*(eplus-eminus)/delta)
self.assert_((Vector(num_grad)-grad[a]).length() < 1.e-2)
def _forceConstantTest(self, delta = 0.0001):
e0, grad0, fc = self.universe.energyGradientsAndForceConstants()
atoms = self.universe.atomList()
for a1, a2 in itertools.chain(itertools.izip(atoms, atoms),
pairs(atoms)):
num_fc = []
for v in [ex, ey, ez]:
x = a1.position()
a1.setPosition(x+delta*v)
e_plus, grad_plus = self.universe.energyAndGradients()
a1.setPosition(x-delta*v)
e_minus, grad_minus = self.universe.energyAndGradients()
a1.setPosition(x)
num_fc.append(0.5*(grad_plus[a2]-grad_minus[a2])/delta)
num_fc = N.array([a.array for a in num_fc])
diff = N.fabs(N.ravel(num_fc-fc[a1, a2].array))
error = N.maximum.reduce(diff)
self.assert_(error < 5.e-2)
def _dihedralTerm(self, n, phase, V):
mod_file = self.mod_template % \
(V/(Units.kcal/Units.mol), phase/Units.deg, n)
ff = Amber99ForceField(mod_files=[StringIO(mod_file)])
self.universe.setForceField(ff)
param = self.universe.energyEvaluatorParameters()
i1, i2, i3, i4, n_test, phase_test, V_test = \
param['cosine_dihedral_term'][0]
self.assertEqual(n_test, n)
# The accuracy is no better than five digits because the
# parameters pass through a text representation.
self.assertAlmostEqual(phase_test, phase, 5)
self.assertAlmostEqual(V_test, V, 5)
two_pi = 2.*N.pi
m = self.universe[0]
for angle in N.arange(0., two_pi, 0.1):
m.C4.setPosition(Vector(N.cos(angle), N.sin(angle), 1.))
e = self.universe.energyTerms()['cosine dihedral angle']
da = self.universe.dihedral(m.C1, m.C2, m.C3, m.C4)
e_ref = V*(1.+N.cos(n*angle-phase))
self.assertAlmostEqual(angle % two_pi, da % two_pi, 14)
self.assertAlmostEqual(e, e_ref, 5)
self._gradientTest()
self._forceConstantTest()
def test_dihedral(self):
for n in [1, 2, 3, 4]:
for phase in N.arange(0., 6., 0.5):
for V in [-10., 2.]:
self._dihedralTerm(n, phase, V)
class NonbondedListTest:
def test_nonbondedList(self):
self.universe.configuration()
atoms = self.universe.atomList()
atom_indices = N.array([a.index for a in self.universe.atomList()])
empty = N.zeros((0, 2), N.Int)
for cutoff in [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.]:
nblist = NonbondedList(empty, empty, atom_indices,
self.universe._spec, cutoff)
nblist.update(self.universe.configuration().array)
distances = nblist.pairDistances()
pairs1 = nblist.pairIndices()
pairs1 = [sorted_tuple(pairs1[i]) for i in range(len(pairs1))
if distances[i] < cutoff]
pairs1.sort(lambda a, b: cmp(a[0], b[0]) or cmp(a[1], b[1]))
pairs2 = []
for i in range(len(atoms)):
for j in range(i+1, len(atoms)):
d = self.universe.distance(atoms[i], atoms[j])
if d < cutoff:
pairs2.append(sorted_tuple((atoms[i].index,
atoms[j].index)))
pairs2.sort(lambda a, b: cmp(a[0], b[0]) or cmp(a[1], b[1]))
self.assertEqual(pairs1, pairs2)
class InfiniteUniverseNonbondedListTest(unittest.TestCase,
NonbondedListTest):
def setUp(self):
self.universe = InfiniteUniverse()
for i in range(100):
p = randomPointInBox(1.)
self.universe.addObject(Atom('C', position = p))
class OrthorhombicUniverseNonbondedListTest(unittest.TestCase,
NonbondedListTest):
def setUp(self):
self.universe = OrthorhombicPeriodicUniverse((1.5, 0.8, 1.1))
for i in range(100):
p = self.universe.boxToRealCoordinates(randomPointInBox(1.))
self.universe.addObject(Atom('C', position = p))
class ParallelepipedicUniverseNonbondedListTest(unittest.TestCase,
NonbondedListTest):
def setUp(self):
a = Vector(1.5, 0.3, 0.)
b = Vector(-0.1, 0.8, 0.2)
c = Vector(0., -0.2, 1.1)
self.universe = ParallelepipedicPeriodicUniverse((a, b, c))
for i in range(100):
p = self.universe.boxToRealCoordinates(randomPointInBox(1.))
self.universe.addObject(Atom('C', position = p))
class LennardJonesSubsetTest(unittest.TestCase,
SubsetTest):
def setUp(self):
self.universe = OrthorhombicPeriodicUniverse((2., 2., 2.),
LennardJonesForceField())
for point in SCLattice(0.5, 4):
self.universe.addObject(Atom('Ar', position=point))
self.subset1 = Collection(self.universe.atomList()[:10])
self.subset2 = Collection(self.universe.atomList()[20:30])
def suite():
loader = unittest.TestLoader()
s = unittest.TestSuite()
s.addTest(loader.loadTestsFromTestCase(DihedralTest))
s.addTest(loader.loadTestsFromTestCase(InfiniteUniverseNonbondedListTest))
s.addTest(loader.loadTestsFromTestCase(OrthorhombicUniverseNonbondedListTest))
s.addTest(loader.loadTestsFromTestCase(ParallelepipedicUniverseNonbondedListTest))
s.addTest(loader.loadTestsFromTestCase(LennardJonesSubsetTest))
return s
if __name__ == '__main__':
unittest.main()
|
