8 #ifndef IMPCORE_RIGID_BODIES_H
9 #define IMPCORE_RIGID_BODIES_H
11 #include <IMP/core/core_config.h>
12 #include "internal/rigid_bodies.h"
23 #include <Eigen/Dense>
25 IMPCORE_BEGIN_NAMESPACE
27 IMP_DECORATORS_DECL(RigidMember, RigidMembers);
28 IMP_DECORATORS_DECL(RigidBodyMember, RigidBodyMembers);
90 void add_member_internal(
Particle *p,
99 static void teardown_constraints(
Particle *p);
114 void setup_score_states();
130 if (
get_model()->get_has_attribute(internal::rigid_body_data().members_,
155 return get_member_particle_indexes() + get_body_member_particle_indexes();
178 static void teardown_particle(
RigidBody rb);
180 IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(
RigidBody);
185 return internal::get_has_required_attributes_for_body(m, pi);
196 return get_reference_frame().get_transformation_to().get_rotation();
204 get_model()->get_attribute(internal::rigid_body_data().quaternion_[0],
206 get_model()->get_attribute(internal::rigid_body_data().quaternion_[1],
208 get_model()->get_attribute(internal::rigid_body_data().quaternion_[2],
210 get_model()->get_attribute(internal::rigid_body_data().quaternion_[3],
213 "Rotation is not a unit vector: " << v);
219 bool assume_normalized =
true;
236 inline void set_reference_frame_lazy
241 get_particle()->set_value(internal::rigid_body_data().quaternion_[0], v[0]);
242 get_particle()->set_value(internal::rigid_body_data().quaternion_[1], v[1]);
243 get_particle()->set_value(internal::rigid_body_data().quaternion_[2], v[2]);
244 get_particle()->set_value(internal::rigid_body_data().quaternion_[3], v[3]);
252 inline void set_rotation_lazy_using_internal_tables
254 double* quaternion_tables[])
259 quaternion_tables[0][pi]=v[0];
260 quaternion_tables[1][pi]=v[1];
261 quaternion_tables[2][pi]=v[2];
262 quaternion_tables[3][pi]=v[3];
267 inline void apply_rotation_lazy_using_internal_tables
269 double* quaternion_tables[])
273 ( quaternion_tables[0][pi],
274 quaternion_tables[1][pi],
275 quaternion_tables[2][pi],
276 quaternion_tables[3][pi] );
278 (cur_rot*rot).get_quaternion();;
279 quaternion_tables[0][pi]=v[0];
280 quaternion_tables[1][pi]=v[1];
281 quaternion_tables[2][pi]=v[2];
282 quaternion_tables[3][pi]=v[3];
285 #endif // IMP_DOXYGEN
303 void set_reference_frame_from_members(
const ParticleIndexes &members);
320 DerivativeAccumulator &da);
336 const algebra::Rotation3D &rot_local_to_global,
337 DerivativeAccumulator &da);
355 const algebra::Rotation3D &rot_other_to_local,
356 const algebra::Rotation3D &rot_local_to_global,
357 DerivativeAccumulator &da);
367 DerivativeAccumulator &da);
378 DerivativeAccumulator &da);
384 for (
unsigned int i = 0; i < 3; ++i) {
391 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
394 static double const* access_torque_i_data
399 internal::rigid_body_data().torque_[i];
400 double const* ret=m->access_derivative_data(k);
406 static double* access_torque_i_data
411 internal::rigid_body_data().torque_[i];
412 double* ret=m->access_derivative_data(k);
417 static double const* access_quaternion_i_data
422 internal::rigid_body_data().quaternion_[i];
423 double const* ret=m->FloatAttributeTable::access_attribute_data(k);
428 static double* access_quaternion_i_data
433 internal::rigid_body_data().quaternion_[i];
434 double* ret=m->FloatAttributeTable::access_attribute_data(k);
450 void normalize_rotation();
454 void update_members();
457 algebra::VectorD<4> get_rotational_derivatives()
const;
460 unsigned int get_number_of_members()
const {
461 return get_body_member_particle_indexes().size() +
462 get_member_particle_indexes().size();
465 RigidBodyMember get_member(
unsigned int i)
const;
480 void add_member(ParticleIndexAdaptor p);
487 void add_non_rigid_member(ParticleIndexAdaptor p);
501 DerivativeAccumulator &da) {
502 for (
unsigned int i = 0; i < 4; ++i) {
503 get_model()->add_to_derivative(internal::rigid_body_data().quaternion_[i],
504 get_particle_index(), qderiv[i], da);
511 DerivativeAccumulator &da) {
512 for (
unsigned int i = 0; i < 3; ++i) {
513 get_model()->add_to_derivative(internal::rigid_body_data().torque_[i],
514 get_particle_index(), torque_local[i], da);
523 const algebra::Rotation3D &rot_local_to_global,
524 DerivativeAccumulator &da) {
526 XYZ::add_to_derivatives(deriv_global, da);
528 Eigen::RowVector4d q =
529 Eigen::RowVector3d(deriv_global.get_data()) *
530 rot_local_to_global.get_gradient(Eigen::Vector3d(local.get_data()));
532 for (
unsigned int i = 0; i < 4; ++i) {
533 get_model()->add_to_derivative(internal::rigid_body_data().quaternion_[i],
534 get_particle_index(), q[i], da);
537 add_to_torque(torque, da);
543 DerivativeAccumulator &da) {
544 algebra::Rotation3D rot_local_to_global =
545 get_reference_frame().get_transformation_to().get_rotation();
547 add_to_derivatives(deriv_local, deriv_global, local,
548 rot_local_to_global, da);
552 void RigidBody::add_to_rotational_derivatives(
const algebra::Vector4D &other_qderiv,
553 const algebra::Rotation3D &rot_other_to_local,
554 const algebra::Rotation3D &rot_local_to_global,
555 DerivativeAccumulator &da) {
556 Eigen::MatrixXd derivs =
558 rot_local_to_global, rot_other_to_local);
559 Eigen::RowVector4d qderiv = Eigen::RowVector4d(other_qderiv.get_data()) * derivs;
560 for (
unsigned int i = 0; i < 4; ++i) {
561 get_model()->add_to_derivative(internal::rigid_body_data().quaternion_[i],
562 get_particle_index(), qderiv[i], da);
603 "Can only set the internal transformation if member is"
604 <<
" a rigid body itself.");
631 "Can only set the internal transformation if member is a "
632 <<
"rigid body itself.");
636 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[0],
638 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[1],
640 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[2],
642 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[3],
661 IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(RigidBodyMember);
665 return internal::get_has_required_attributes_for_member(m, p);
668 static FloatKeys get_internal_coordinate_keys() {
669 return internal::rigid_body_data().child_keys_;
672 static FloatKeys get_internal_rotation_keys() {
673 return internal::rigid_body_data().lquaternion_;
697 return internal::get_has_required_attributes_for_rigid_member(m, p);
717 return internal::get_has_required_attributes_for_non_member(m, p);
727 for (
unsigned int i = 0; i < 3; ++i) {
728 get_model()->add_to_derivative(get_internal_coordinate_keys()[i],
749 Eigen::MatrixXd derivs =
751 rot_parent_to_global, rot_local_to_parent);
752 Eigen::RowVector4d qderiv = Eigen::RowVector4d(local_qderiv.get_data()) * derivs;
753 for (
unsigned int i = 0; i < 4; ++i) {
754 get_model()->add_to_derivative(get_internal_rotation_keys()[i],
770 "Can only set derivatives of internal rotation if member is a "
771 <<
"rigid body itself.");
772 for (
unsigned int i = 0; i < 4; ++i) {
773 get_model()->add_to_derivative(get_internal_rotation_keys()[i],
782 for (
unsigned int i = 0; i < 3; ++i) {
792 for (
unsigned int i = 0; i < 4; ++i) {
802 class IMPCOREEXPORT RigidMembersRefiner :
public Refiner {
804 RigidMembersRefiner(std::string name =
"RigidMembersRefiner%d")
810 virtual const ParticlesTemp
get_refined(Particle *) const
813 Model *m, const ParticleIndexes &pis) const
IMP_OVERRIDE;
818 IMPCOREEXPORT RigidMembersRefiner *get_rigid_members_refiner();
844 return get_initial_reference_frame(ps[0]->get_model(),
861 IMP_DECORATORS_DEF(RigidMember, RigidMembers);
867 TextOutput(std::cout));
873 IMPCORE_END_NAMESPACE
void add_to_derivatives(const algebra::Vector3D &v, DerivativeAccumulator &d)
Add the vector v to the derivative vector of the x,y,z coordinates.
void set_internal_coordinates(const algebra::Vector3D &v) const
set the internal (local) coordinates for this member
A Modifier on ParticlesTemp.
ParticleIndex get_particle_index() const
Returns the particle index decorated by this decorator.
algebra::Vector3D get_internal_derivatives() const
Get derivatives wrt translation component of internal transformation.
algebra::Vector4D get_internal_rotational_derivatives() const
Get derivatives wrt quaternion component of internal transformation.
Key< 0 > FloatKey
The type used to identify float attributes in the Particles.
A member of a rigid body, it has internal (local) coordinates.
A container for Singletons.
ParticleIndex get_root_rigid_body(RigidMember m)
Return the index of the outer-most rigid body containing the member.
#define IMP_USAGE_CHECK_FLOAT_EQUAL(expra, exprb, message)
algebra::Vector3D get_coordinates() const
IMP::algebra::Rotation3D get_rotation() const
#define IMP_DECORATOR_SETUP_1(Name, FirstArgumentType, first_argument_name)
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
void add_to_internal_rotational_derivatives(const algebra::Vector4D &local_qderiv, const algebra::Rotation3D &rot_local_to_parent, const algebra::Rotation3D &rot_parent_to_global, DerivativeAccumulator &da)
Model * get_model() const
Returns the Model containing the particle.
void add_to_internal_rotational_derivatives(const algebra::Vector4D &qderiv, DerivativeAccumulator &da)
ParticlesTemp create_rigid_bodies(Model *m, unsigned int n, bool no_members=false)
Index< ParticleIndexTag > ParticleIndex
Eigen::MatrixXd get_gradient_of_composed_with_respect_to_second(const Rotation3D &q, const Rotation3D &p, bool projected=true)
Get gradient of quaternion product with respect to second quaternion.
bool get_coordinates_are_optimized() const
Get whether the coordinates are optimized.
void add_rigid_body_cache_key(ObjectKey k)
A more IMP-like version of the std::vector.
const Vector4D & get_quaternion() const
Return the quaternion so that it can be stored.
void show_rigid_body_hierarchy(RigidBody rb, TextOutput out=TextOutput(std::cout))
void clear_particle_caches(ParticleIndex pi)
Clear all the cache attributes of a given particle.
IMP::Vector< IMP::WeakPointer< ModelObject > > ModelObjectsTemp
Class for storing model, its restraints, constraints, and particles.
algebra::Vector3D get_torque() const
static bool get_is_setup(Model *m, ParticleIndexAdaptor p)
return true if it is a rigid member
virtual bool get_can_refine(Particle *) const
Return true if this refiner can refine that particle.
Vector3D get_vector_product(const Vector3D &p1, const Vector3D &p2)
Return the vector product (cross product) of two vectors.
void set_reference_frame(const IMP::algebra::ReferenceFrame3D &tr)
Set the current reference frame.
A Cartesian vector in D-dimensions.
Refine a particle into a list of particles.
void set_coordinates(const algebra::Vector3D &v)
set all coordinates from a vector
const Transformation3D & get_transformation_to() const
Return transformation from local to global coordinates.
static bool get_is_setup(Model *m, ParticleIndex pi)
Return true if the particle is a rigid body.
const ParticleIndexes & get_member_particle_indexes() const
static bool get_is_setup(Model *m, ParticleIndexAdaptor p)
return true if it is a rigid member
Represent an XYZR particle with a sphere.
void set_attribute(TypeKey attribute_key, ParticleIndex particle, Type value)
set the value of particle attribute with the specified key
void add_to_internal_derivatives(const algebra::Vector3D &deriv_parent, DerivativeAccumulator &da)
Add to derivatives of local coordinates.
A decorator for a particle with x,y,z coordinates.
const algebra::Vector3D & get_coordinates() const
Convert it to a vector.
virtual const ParticlesTemp get_refined(Particle *a) const =0
Refine the passed particle into a set of particles.
A decorator for a particle that is part of a rigid body but not rigid.
Simple 3D rotation class.
void set_internal_transformation(const algebra::Transformation3D &v)
Particle * get_particle() const
Returns the particle decorated by this decorator.
Key< 4 > ObjectKey
The type used to identify an Object attribute.
void set_coordinates_are_optimized(bool tf) const
Set whether the coordinates are optimized.
void set_coordinates(const algebra::Vector3D ¢er)
sets the global coordinates of this member using XYZ::set_coordinates()
#define IMP_DECORATOR_METHODS(Name, Parent)
Abstract class to implement hierarchical methods.
Class to handle individual particles of a Model object.
#define IMP_USAGE_CHECK(expr, message)
A runtime test for incorrect usage of a class or method.
#define IMP_DECORATORS(Name, PluralName, Parent)
Define the types for storing sets of decorators.
void transform(RigidBody a, const algebra::Transformation3D &tr)
Transform a rigid body.
Eigen::MatrixXd get_gradient_of_composed_with_respect_to_first(const Rotation3D &q, const Rotation3D &p, bool projected=true)
Get gradient of quaternion product with respect to first quaternion.
ParticleIndexes get_member_indexes() const
const ParticleIndexes & get_body_member_particle_indexes() const
A decorator for a rigid body.
algebra::Transformation3D get_internal_transformation() const
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.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
static bool get_is_setup(Model *m, ParticleIndex p)
return true if it is a rigid member
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Class for adding derivatives from restraints to the model.
const algebra::Vector3D & get_internal_coordinates() const
Return the internal (local) coordinates of this member.
IMP::algebra::ReferenceFrame3D get_reference_frame() const