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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
Diffusion.h
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1 /**
2  * \file IMP/atom/Diffusion.h
3  * \brief A decorator for a diffusing particle.
4  *
5  * Copyright 2007-2021 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPATOM_DIFFUSION_H
10 #define IMPATOM_DIFFUSION_H
11 
12 #include <IMP/atom/atom_config.h>
13 
14 #include <IMP/core/XYZR.h>
15 #include <IMP/algebra/Vector3D.h>
16 #include <IMP/internal/constants.h>
17 
18 #include <vector>
19 #include <limits>
20 
21 IMPATOM_BEGIN_NAMESPACE
22 
23 //! A decorator for a diffusing particle with a diffusion coefficient.
24 /** \ingroup helper
25  \ingroup decorators
26  \see BrownianDynamics
27 
28  Diffusion is used to decorate a diffusing particle with a diffusion
29  coefficient D. D is assumed to be in units of \f$A^2/fs\f$.
30 
31  \see RigidBodyDiffusion
32  */
33 class IMPATOMEXPORT Diffusion : public IMP::core::XYZ {
34  static void do_setup_particle(Model *m, ParticleIndex pi,
35  Float D) {
36  IMP_USAGE_CHECK(XYZ::get_is_setup(m, pi),
37  "Particle must already be an XYZ particle");
38  m->add_attribute(get_diffusion_coefficient_key(), pi, D);
39  }
40  static void do_setup_particle(Model *m, ParticleIndex pi,
41  const algebra::Vector3D &v, Float D) {
42  XYZ::setup_particle(m, pi, v);
43  do_setup_particle(m, pi, D);
44  }
45 
46  /**
47  Same as do_setup_particle(m, pi, D) but D is automatically set
48  to IMP::atom::get_einstein_diffusion_coefficient(radius) for radius
49  IMP::core::XYZR(m, pi).get_radius().
50 
51  Note a different D should probably be set manually if the temperature is
52  not the default IMP temperature (297.15).
53  */
54  static void do_setup_particle(Model *m, ParticleIndex pi);
55 
56  public:
60  /** Assume particle is already a core::XYZR particle. */
62 
63  //! Return true if the particle is an instance of Diffusion
64  static bool get_is_setup(Model *m, ParticleIndex p) {
65  return m->get_has_attribute(get_diffusion_coefficient_key(), p);
66  }
67  //! set diffusion coefficient in \f$A^2/fs\f$
68  void set_diffusion_coefficient(double d) {
69  get_particle()->set_value(get_diffusion_coefficient_key(), d);
70 
71  }
72  //! get diffusion coefficient in \f$A^2/fs\f$
73  double get_diffusion_coefficient() const {
74  return get_model()->get_attribute(get_diffusion_coefficient_key(),
76  }
77  //! Get the D key
78  static FloatKey get_diffusion_coefficient_key();
79 };
80 
81 IMPATOMEXPORT double get_diffusion_coefficient_from_cm2_per_second(double din);
82 
83 IMP_DECORATORS(Diffusion, Diffusions, core::XYZs);
84 
85 /** A rigid body that is diffusing, so it also has a rotation diffusion
86  coefficient. The units on the rotational coefficient are
87  \f$radians^2/fs\f$.
88 
89  The translational and rotational diffusion coefficients are set automatically
90  using IMP::atom::get_einstein_diffusion_coefficient(radius) and
91  IMP::atom::get_einstein_rotational_diffusion_coefficient(radius) for radius
92  IMP::core::XYZR(m, pi).get_radius().
93 
94  Note that different translational and rotational coefficients should probably
95  be set manually if the temperature is not the default IMP temperature.
96 */
97 class IMPATOMEXPORT RigidBodyDiffusion : public Diffusion {
98  static void do_setup_particle(Model *m, ParticleIndex pi);
99 
100  public:
102  /** All diffusion coefficients are determined from the radius */
104 
105  //! returns the rotational diffusion coefficient in \f$radians^2/fs\f$
107  return get_model()->get_attribute
108  (get_rotational_diffusion_coefficient_key(),
110  }
111 
112 
113  //! sets the rotational diffusion coefficient in \f$radians^2/fs\f$
115  return get_particle()->set_value(get_rotational_diffusion_coefficient_key(),
116  d);
117  }
118 
119  //! Return true if the particle is an instance of an Diffusion
120  static bool get_is_setup(Model *m, ParticleIndex p) {
121  return m->get_has_attribute(get_rotational_diffusion_coefficient_key(), p);
122  }
123 
124  //! Get the D key
125  static FloatKey get_rotational_diffusion_coefficient_key();
126 };
127 
128 IMP_DECORATORS(RigidBodyDiffusion, RigidBodyDiffusions, Diffusions);
129 
130 IMPATOM_END_NAMESPACE
131 
132 #endif /* IMPATOM_DIFFUSION_H */
ParticleIndex get_particle_index() const
Returns the particle index decorated by this decorator.
Definition: Decorator.h:188
static bool get_is_setup(Model *m, ParticleIndex p)
Return true if the particle is an instance of an Diffusion.
Definition: Diffusion.h:120
#define IMP_DECORATOR_SETUP_1(Name, FirstArgumentType, first_argument_name)
Model * get_model() const
Returns the Model containing the particle.
Definition: Decorator.h:191
static XYZ setup_particle(Model *m, ParticleIndex pi)
Definition: XYZ.h:51
double get_diffusion_coefficient() const
get diffusion coefficient in
Definition: Diffusion.h:73
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:73
void set_rotational_diffusion_coefficient(double d) const
sets the rotational diffusion coefficient in
Definition: Diffusion.h:114
void set_diffusion_coefficient(double d)
set diffusion coefficient in
Definition: Diffusion.h:68
void add_attribute(TypeKey attribute_key, ParticleIndex particle, Type value)
add particle atribute with the specied key and initial value
#define IMP_DECORATOR_SETUP_2(Name, FirstArgumentType, first_argument_name,SecondArgumentType, second_argument_name)
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
#define IMP_DECORATOR_SETUP_0(Name)
static bool get_is_setup(Model *m, ParticleIndex p)
Return true if the particle is an instance of Diffusion.
Definition: Diffusion.h:64
Particle * get_particle() const
Returns the particle decorated by this decorator.
Definition: Decorator.h:171
#define IMP_DECORATOR_METHODS(Name, Parent)
VectorD< 3 > Vector3D
Definition: VectorD.h:421
double get_rotational_diffusion_coefficient() const
returns the rotational diffusion coefficient in
Definition: Diffusion.h:106
double Float
Basic floating-point value (could be float, double...)
Definition: types.h:20
Simple 3D vector class.
#define IMP_USAGE_CHECK(expr, message)
A runtime test for incorrect usage of a class or method.
Definition: check_macros.h:168
#define IMP_DECORATORS(Name, PluralName, Parent)
Define the types for storing sets of decorators.
bool get_has_attribute(TypeKey attribute_key, ParticleIndex particle) const
return true if particle has attribute with the specified key
A decorator for a diffusing particle with a diffusion coefficient.
Definition: Diffusion.h:33
Type get_attribute(TypeKey attribute_key, ParticleIndex particle)
get the value of the particle attribute with the specified key
Decorator for a sphere-like particle.