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VirtualSite.h
1 #ifndef OPENMM_VIRTUALSITE_H_
2 #define OPENMM_VIRTUALSITE_H_
3
4 /* -------------------------------------------------------------------------- *
5 * OpenMM *
6 * -------------------------------------------------------------------------- *
7 * This is part of the OpenMM molecular simulation toolkit originating from *
8 * Simbios, the NIH National Center for Physics-Based Simulation of *
9 * Biological Structures at Stanford, funded under the NIH Roadmap for *
10 * Medical Research, grant U54 GM072970. See https://simtk.org. *
11 * *
12 * Portions copyright (c) 2012-2014 Stanford University and the Authors. *
13 * Authors: Peter Eastman *
14 * Contributors: *
15 * *
16 * Permission is hereby granted, free of charge, to any person obtaining a *
17 * copy of this software and associated documentation files (the "Software"), *
18 * to deal in the Software without restriction, including without limitation *
19 * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
20 * and/or sell copies of the Software, and to permit persons to whom the *
21 * Software is furnished to do so, subject to the following conditions: *
22 * *
23 * The above copyright notice and this permission notice shall be included in *
24 * all copies or substantial portions of the Software. *
25 * *
26 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
27 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
28 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
29 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
30 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
31 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
32 * USE OR OTHER DEALINGS IN THE SOFTWARE. *
33 * -------------------------------------------------------------------------- */
34
35 #include <openmm/Vec3.h>
36 #include "internal/windowsExport.h"
37 #include <vector>
38
39 namespace OpenMM {
40
48 class OPENMM_EXPORT VirtualSite {
49 public:
50 virtual ~VirtualSite() {
51 }
55 int getNumParticles() const;
62 int getParticle(int particle) const;
63 protected:
64 VirtualSite() {
65 }
66 void setParticles(const std::vector<int>& particleIndices);
67 private:
68 std::vector<int> particles;
69 };
70
76 class OPENMM_EXPORT TwoParticleAverageSite : public VirtualSite {
77 public:
87 TwoParticleAverageSite(int particle1, int particle2, double weight1, double weight2);
94 double getWeight(int particle) const;
95 private:
96 double weight1, weight2;
97 };
98
104 class OPENMM_EXPORT ThreeParticleAverageSite : public VirtualSite {
105 public:
117 ThreeParticleAverageSite(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3);
124 double getWeight(int particle) const;
125 private:
126 double weight1, weight2, weight3;
127 };
128
141 class OPENMM_EXPORT OutOfPlaneSite : public VirtualSite {
142 public:
153 OutOfPlaneSite(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross);
157 double getWeight12() const;
161 double getWeight13() const;
165 double getWeightCross() const;
166 private:
167 double weight12, weight13, weightCross;
168 };
169
195 class OPENMM_EXPORT LocalCoordinatesSite : public VirtualSite {
196 public:
208 LocalCoordinatesSite(int particle1, int particle2, int particle3, const Vec3& originWeights, const Vec3& xWeights, const Vec3& yWeights, const Vec3& localPosition);
212 const Vec3& getOriginWeights() const;
216 const Vec3& getXWeights() const;
220 const Vec3& getYWeights() const;
224 const Vec3& getLocalPosition() const;
225 private:
226 Vec3 originWeights, xWeights, yWeights, localPosition;
227 };
228
229 } // namespace OpenMM
230
231 #endif /*OPENMM_VIRTUALSITE_H_*/
OpenMM::ThreeParticleAverageSite
This is a VirtualSite that computes the particle location as a weighted average of three other partic...
Definition: VirtualSite.h:104
OpenMM::VirtualSite::~VirtualSite
virtual ~VirtualSite()
Definition: VirtualSite.h:50
OpenMM::VirtualSite::VirtualSite
VirtualSite()
Definition: VirtualSite.h:64
OpenMM::VirtualSite
A VirtualSite describes the rules for computing a particle's position based on other particles...
Definition: VirtualSite.h:48
OpenMM::OutOfPlaneSite
This is a VirtualSite that computes the particle location based on three other particles' locations...
Definition: VirtualSite.h:141
OpenMM::Vec3
This class represents a three component vector.
Definition: Vec3.h:45
OpenMM::LocalCoordinatesSite
This is a VirtualSite that uses the locations of three other particles to compute a local coordinate ...
Definition: VirtualSite.h:195
OpenMM::TwoParticleAverageSite
This is a VirtualSite that computes the particle location as a weighted average of two other particle...
Definition: VirtualSite.h:76
OpenMM
Definition: AndersenThermostat.h:40