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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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#include <IMP/atom/TAMDCentroid.h>
Inheritance diagram for IMP::atom::TAMDCentroid:A decorator for a center of mass particle that is part of a TAMD simulation (so simulators can recognize it as such)
TAMDCentroid is almost identical to IMP::core::Centroid, used to decorate particles that represent centers of mass of their children. It also contains some flags that are useful for TAMD simulations (Temperature-Accelerated MD).
Definition at line 38 of file TAMDCentroid.h.
Public Member Functions | |
| TAMDCentroid (::IMP::Model *m,::IMP::ParticleIndex id) | |
| TAMDCentroid (const IMP::ParticleAdaptor &d) | |
| void | show (std::ostream &out=std::cout) const |
| Public Member Functions inherited from IMP::core::Centroid | |
| Centroid (const IMP::ParticleAdaptor &d) | |
| Centroid (::IMP::Model *m,::IMP::ParticleIndex id) | |
| Constraint * | get_constraint () const |
| void | show (std::ostream &out=std::cout) const |
| Public Member Functions inherited from IMP::core::XYZ | |
| XYZ (::IMP::Model *m,::IMP::ParticleIndex id) | |
| XYZ (const IMP::ParticleAdaptor &d) | |
| void | add_to_derivative (int i, Float v, DerivativeAccumulator &d) |
| Add something to the derivative of the ith coordinate. More... | |
| void | add_to_derivatives (const algebra::Vector3D &v, DerivativeAccumulator &d) |
| Add something to the derivative of the coordinates. More... | |
| Float | get_coordinate (int i) const |
| Get the ith coordinate. More... | |
| const algebra::Vector3D & | get_coordinates () const |
| Convert it to a vector. More... | |
| bool | get_coordinates_are_optimized () const |
| Get whether the coordinates are optimized. More... | |
| Float | get_derivative (int i) const |
| Get the ith coordinate derivative. More... | |
| algebra::Vector3D | get_derivatives () const |
| Get the vector of derivatives. More... | |
| algebra::Vector3D | get_vector_to (const XYZ &b) const |
| Get the vector from this particle to another. More... | |
| Float | get_x () const |
| Float | get_y () const |
| Float | get_z () const |
| void | set_coordinate (unsigned int i, Float v) |
| set the ith coordinate More... | |
| void | set_coordinates (const algebra::Vector3D &v) |
| set all coordinates from a vector More... | |
| void | set_coordinates_are_optimized (bool tf) const |
| Set whether the coordinates are optimized. More... | |
| void | set_x (Float t) |
| void | set_y (Float t) |
| void | set_z (Float t) |
| void | show (std::ostream &out=std::cout) const |
| 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 bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static TAMDCentroid | setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members) |
| static TAMDCentroid | setup_particle (IMP::ParticleAdaptor decorator, ParticleIndexesAdaptor members) |
| static TAMDCentroid | setup_particle (Model *m, ParticleIndex pi, Refiner *refiner) |
| static TAMDCentroid | setup_particle (IMP::ParticleAdaptor decorator, Refiner *refiner) |
| Static Public Member Functions inherited from IMP::core::Centroid | |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static Centroid | setup_particle (IMP::ParticleAdaptor decorator, Refiner *refiner) |
| static Centroid | setup_particle (Model *m, ParticleIndex pi, Refiner *refiner) |
| static Centroid | setup_particle (IMP::ParticleAdaptor decorator, ParticleIndexesAdaptor members) |
| static Centroid | setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor members) |
| Static Public Member Functions inherited from IMP::core::XYZ | |
| static FloatKey | get_coordinate_key (unsigned int i) |
| static bool | get_is_setup (const IMP::ParticleAdaptor &p) |
| static bool | get_is_setup (Model *m, ParticleIndex pi) |
| static const FloatKeys & | get_xyz_keys () |
| Get a vector containing the keys for x,y,z. More... | |
| static XYZ | setup_particle (IMP::ParticleAdaptor decorator) |
| static XYZ | setup_particle (Model *m, ParticleIndex pi) |
| static XYZ | setup_particle (IMP::ParticleAdaptor decorator, algebra::Vector3D v) |
| static XYZ | setup_particle (Model *m, ParticleIndex pi, algebra::Vector3D v) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::Decorator | |
| Decorator (Model *m, ParticleIndex pi) | |
| Decorator (ParticleAdaptor p) | |
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Definition at line 63 of file TAMDCentroid.h.
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Sets up TAMDCentroid over members, and constrains TAMDCentroid to be computed before model evaluation and to propagate derivatives following model evaluation. SetupDocSetup the particle so that it can be used with this decorator
Definition at line 63 of file TAMDCentroid.h.
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Definition at line 71 of file TAMDCentroid.h.
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Sets up TAMDCentroid over particles passed by applying the refiner over the particle pi, and constrains TAMDCentroid to be computed before model evaluation and to propagate derivatives following model evaluation. SetupDocSetup the particle so that it can be used with this decorator
Definition at line 71 of file TAMDCentroid.h.
