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density_force.hh
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1 #ifndef OPENMM_DENSITYFORCE_H_
2 #define OPENMM_DENSITYFORCE_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) 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/Context.h>
36 #include <openmm/Force.h>
37 #include <ost/img/image.hh>
38 
39 namespace ost { namespace mol{ namespace mm{
40 
41 
42 class DensityForce : public OpenMM::Force {
43 public:
49  //since the density is scaled in Angstrom, the resolution is also in Angstrom
50  DensityForce(const ost::img::ImageHandle& d, Real r, Real s): density_(d),
51  resolution_(r),
52  scaling_(s) { }
53 
54  void addParticle(Real mass);
55 
56  int getNumParticles() const { return masses_.size(); }
57 
58  int getNumBodies() const { return bodies_.size(); }
59 
60  Real getParticleMass(int idx) const;
61 
62  bool isInBody(int idx) const;
63 
64  void defineBody(const std::vector<int>& indices);
65 
66  const std::vector<int>& getBody(int idx) const;
67 
68  void setScaling(Real scaling) { scaling_ = scaling; }
69 
70  Real getScaling() const { return scaling_; }
71 
72  ost::img::ImageHandle getDensity() const { return density_; }
73 
74  Real getResolution() const { return resolution_; }
75 
76  void updateParametersInContext(OpenMM::Context& context);
77 
78  bool usesPeriodicBoundaryConditions() const { return false; }
79 
80 protected:
81  OpenMM::ForceImpl* createImpl() const;
82 private:
83 
84  ost::img::ImageHandle density_;
85  std::vector<Real> masses_;
86  std::vector<bool> in_body_;
87  std::vector<std::vector<int> > bodies_;
88  Real resolution_;
89  Real scaling_;
90 };
91 
92 }}} // ns
93 
94 #endif /*OPENMM_DENSITYFORCE_H_*/
detail::quantity< detail::force_dimension > Force
void defineBody(const std::vector< int > &indices)
float Real
Definition: base.hh:44
void updateParametersInContext(OpenMM::Context &context)
const std::vector< int > & getBody(int idx) const
bool isInBody(int idx) const
void addParticle(Real mass)
Manage shared instances of images.
Real getParticleMass(int idx) const
void setScaling(Real scaling)
bool usesPeriodicBoundaryConditions() const
OpenMM::ForceImpl * createImpl() const
DensityForce(const ost::img::ImageHandle &d, Real r, Real s)
ost::img::ImageHandle getDensity() const