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
|
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using namespace OpenMM;
using namespace std;
void testSerialization() {
// Create a Force.
CMAPTorsionForce force;
force.setForceGroup(3);
force.setName("custom name");
vector<double> map1(9);
for (int i = 0; i < 9; i++)
map1[i] = 0.1*i;
force.addMap(3, map1);
vector<double> map2(16);
for (int i = 0; i < 16; i++)
map2[i] = 0.2*i;
force.addMap(4, map2);
force.addTorsion(0, 0, 1, 2, 3, 2, 3, 4, 5);
force.addTorsion(0, 0, 2, 3, 4, 5, 6, 7, 8);
force.addTorsion(1, 2, 3, 4, 7, 1, 2, 3, 4);
force.addTorsion(1, 5, 1, 2, 3, 2, 3, 4, 8);
force.setUsesPeriodicBoundaryConditions(true);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<CMAPTorsionForce>(&force, "Force", buffer);
CMAPTorsionForce* copy = XmlSerializer::deserialize<CMAPTorsionForce>(buffer);
// Compare the two forces to see if they are identical.
CMAPTorsionForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getName(), force2.getName());
ASSERT_EQUAL(force.usesPeriodicBoundaryConditions(), force2.usesPeriodicBoundaryConditions());
ASSERT_EQUAL(force.getNumMaps(), force2.getNumMaps());
for (int i = 0; i < force.getNumMaps(); i++) {
int size1, size2;
vector<double> energy1, energy2;
force.getMapParameters(i, size1, energy1);
force2.getMapParameters(i, size2, energy2);
ASSERT_EQUAL(size1, size2);
ASSERT_EQUAL(energy1.size(), energy2.size());
for (int j = 0; j < (int) energy1.size(); j++)
ASSERT_EQUAL(energy1[j], energy2[j]);
}
ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
for (int i = 0; i < force.getNumTorsions(); i++) {
int map1, map2;
int a11, a21, a31, a41, a12, a22, a32, a42;
int b11, b21, b31, b41, b12, b22, b32, b42;
force.getTorsionParameters(i, map1, a11, a21, a31, a41, b11, b21, b31, b41);
force2.getTorsionParameters(i, map2, a12, a22, a32, a42, b12, b22, b32, b42);
ASSERT_EQUAL(map1, map2);
ASSERT_EQUAL(a11, a12);
ASSERT_EQUAL(a21, a22);
ASSERT_EQUAL(a31, a32);
ASSERT_EQUAL(a41, a42);
ASSERT_EQUAL(b11, b12);
ASSERT_EQUAL(b21, b22);
ASSERT_EQUAL(b31, b32);
ASSERT_EQUAL(b41, b42);
}
}
int main() {
try {
testSerialization();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
|
