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IMP Reference Guide
2.9.0
The Integrative Modeling Platform
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#include <IMP/atom/TAMDParticle.h>
Inheritance diagram for IMP::atom::TAMDParticle:A decorator for a diffusing particle that is simulated in a TAMD BD simulation.
TAMDParticle is used to decorate diffusing particle that are simulated as part of a TAMD simulation (Temperature-Accelerated MD), and exhibit elevated temperature and elevated friction coefficient (=actual diffusion coefficient reduced during TAMD BD simulation).
See: Maragliano and Vanden-Eijden, 2006; Abrams and Vanden-Eijden, PNAS 2011
Definition at line 39 of file TAMDParticle.h.
Public Member Functions | |
| TAMDParticle (::IMP::Model *m,::IMP::ParticleIndex id) | |
| TAMDParticle (const IMP::ParticleAdaptor &d) | |
| double | get_friction_scale_factor () const |
| ParticleIndex | get_reference_particle_index () const |
| double | get_temperature_scale_factor () const |
| void | set_friction_scale_factor (float tsf) |
| void | set_temperature_scale_factor (float tsf) |
| void | show (std::ostream &out=std::cout) const |
| void | update_coordinates_from_ref () |
| Public Member Functions inherited from IMP::Decorator | |
| bool | get_is_valid () const |
| Returns true if constructed with a non-default constructor. More... | |
| Model * | get_model () const |
| Returns the Model containing the particle. More... | |
| Particle * | get_particle () const |
| Returns the particle decorated by this decorator. More... | |
| ParticleIndex | get_particle_index () const |
| Returns the particle index decorated by this decorator. More... | |
| operator Particle * () const | |
| operator ParticleIndex () const | |
| Particle * | operator-> () const |
Static Public Member Functions | |
| static FloatKey | get_friction_scale_factor_key () |
| Get the temperature scale factor key. More... | |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex p) |
| Return true if the particle is an instance of an TAMDParticle. More... | |
| static ParticleIndexKey | get_reference_particle_index_key () |
| Get the temperature scale factor key. More... | |
| static FloatKey | get_temperature_scale_factor_key () |
| Get the temperature scale factor key. More... | |
| static TAMDParticle | setup_particle (Model *m, ParticleIndex pi, ParticleIndex pi_ref, Float tsf, Float fsf) |
| static TAMDParticle | setup_particle (IMP::ParticleAdaptor decorator, ParticleIndex pi_ref, Float tsf, Float fsf) |
| static TAMDParticle | setup_particle (Model *m, ParticleIndex pi, Particle *p_ref, Float tsf, Float fsf) |
| static TAMDParticle | setup_particle (IMP::ParticleAdaptor decorator, Particle *p_ref, Float tsf, Float fsf) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::Decorator | |
| Decorator (Model *m, ParticleIndex pi) | |
| Decorator (ParticleAdaptor p) | |
| double IMP::atom::TAMDParticle::get_friction_scale_factor | ( | ) | const |
get friction factoring for particle relative to particle diffusion coefficient / rotational diffusion coefficient
Definition at line 138 of file TAMDParticle.h.
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Get the temperature scale factor key.
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Return true if the particle is an instance of an TAMDParticle.
Definition at line 102 of file TAMDParticle.h.
Here is the call graph for this function:| ParticleIndex IMP::atom::TAMDParticle::get_reference_particle_index | ( | ) | const |
returns the particle associated with this TAMD variable (eg, centroid of some particles)
Definition at line 112 of file TAMDParticle.h.
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Get the temperature scale factor key.
| double IMP::atom::TAMDParticle::get_temperature_scale_factor | ( | ) | const |
get temperature factoring for particle relative to simulation temperature
Definition at line 125 of file TAMDParticle.h.
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Get the temperature scale factor key.
| void IMP::atom::TAMDParticle::set_friction_scale_factor | ( | float | tsf | ) |
set friction factoring for particle relative to particle diffusion coefficient / rotational diffusion coefficient
Definition at line 132 of file TAMDParticle.h.
Here is the call graph for this function:| void IMP::atom::TAMDParticle::set_temperature_scale_factor | ( | float | tsf | ) |
set temperature factoring for particle relative to simulation temperature
Definition at line 119 of file TAMDParticle.h.
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setup a TAMD variable associated with pi_ref, with temperature scaled by tsf and friction scaled by fsf.
| m | the particle model |
| pi | the particle index to be setup |
| pi_ref | - reference particle index in same model with which this tamd particle is associate |
| tsf | - temperature scale factor |
| fsf | - friction scale factorSetup the particle so it can be used with this decorator. |
Definition at line 80 of file TAMDParticle.h.
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setup a TAMD variable associated with pi_ref, with temperature scaled by tsf and friction scaled by fsf
| m | the particle model |
| pi | the particle index to be setup |
| p_ref | - reference particle with which this tamd particle is associate |
| tsf | - temperature scale factor |
| fsf | - friction scale factorSetup the particle so it can be used with this decorator. |
Definition at line 97 of file TAMDParticle.h.
| void IMP::atom::TAMDParticle::update_coordinates_from_ref | ( | ) |
copy x,y,z coordinates from reference particle.
