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();
128 return internal::rigid_body_data().quaternion_;
135 if (
get_model()->get_has_attribute(internal::rigid_body_data().members_,
160 return get_member_particle_indexes() + get_body_member_particle_indexes();
183 static void teardown_particle(
RigidBody rb);
185 IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(
RigidBody);
190 return internal::get_has_required_attributes_for_body(m, pi);
201 return get_reference_frame().get_transformation_to().get_rotation();
209 get_model()->get_attribute(internal::rigid_body_data().quaternion_[0],
211 get_model()->get_attribute(internal::rigid_body_data().quaternion_[1],
213 get_model()->get_attribute(internal::rigid_body_data().quaternion_[2],
215 get_model()->get_attribute(internal::rigid_body_data().quaternion_[3],
218 "Rotation is not a unit vector: " << v);
224 bool assume_normalized =
true;
241 inline void set_reference_frame_lazy
246 get_particle()->set_value(internal::rigid_body_data().quaternion_[0], v[0]);
247 get_particle()->set_value(internal::rigid_body_data().quaternion_[1], v[1]);
248 get_particle()->set_value(internal::rigid_body_data().quaternion_[2], v[2]);
249 get_particle()->set_value(internal::rigid_body_data().quaternion_[3], v[3]);
257 inline void set_rotation_lazy_using_internal_tables
259 double* quaternion_tables[])
264 quaternion_tables[0][pi]=v[0];
265 quaternion_tables[1][pi]=v[1];
266 quaternion_tables[2][pi]=v[2];
267 quaternion_tables[3][pi]=v[3];
272 inline void apply_rotation_lazy_using_internal_tables
274 double* quaternion_tables[])
278 ( quaternion_tables[0][pi],
279 quaternion_tables[1][pi],
280 quaternion_tables[2][pi],
281 quaternion_tables[3][pi] );
283 (cur_rot*rot).get_quaternion();;
284 quaternion_tables[0][pi]=v[0];
285 quaternion_tables[1][pi]=v[1];
286 quaternion_tables[2][pi]=v[2];
287 quaternion_tables[3][pi]=v[3];
290 #endif // IMP_DOXYGEN
308 void set_reference_frame_from_members(
const ParticleIndexes &members);
324 void pull_back_members_adjoints(DerivativeAccumulator &da);
332 DerivativeAccumulator &da);
347 const algebra::Transformation3D &T,
351 algebra::Transformation3DAdjoint &DT,
353 DerivativeAccumulator &da);
362 DerivativeAccumulator &da);
381 const algebra::Transformation3D &TA,
382 algebra::Transformation3D &TB,
383 algebra::Transformation3DAdjoint &DTC,
384 algebra::Transformation3DAdjoint &DTA,
385 algebra::Transformation3DAdjoint &DTB,
387 DerivativeAccumulator &da);
403 IMPCORE_DEPRECATED_METHOD_DECL(2.12)
404 void add_to_derivatives(const algebra::
Vector3D &local_derivative,
405 const algebra::
Vector3D &local_location,
406 DerivativeAccumulator &da);
419 IMPCORE_DEPRECATED_METHOD_DECL(2.12)
420 void add_to_derivatives(const algebra::
Vector3D &local_derivative,
421 const algebra::
Vector3D &global_derivative,
422 const algebra::
Vector3D &local_location,
423 const algebra::Rotation3D &rot_local_to_global,
424 DerivativeAccumulator &da);
441 IMPCORE_DEPRECATED_METHOD_DECL(2.12)
442 void add_to_rotational_derivatives(const algebra::
Vector4D &other_qderiv,
443 const algebra::Rotation3D &rot_other_to_local,
444 const algebra::Rotation3D &rot_local_to_global,
445 DerivativeAccumulator &da);
454 inline
void add_to_rotational_derivatives(const algebra::
Vector4D &qderiv,
455 DerivativeAccumulator &da);
465 inline
void add_to_torque(const algebra::
Vector3D &torque_local,
466 DerivativeAccumulator &da);
472 for (
unsigned int i = 0; i < 3; ++i) {
479 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
482 static double const* access_torque_i_data
487 internal::rigid_body_data().torque_[i];
488 double const* ret=m->access_derivative_data(k);
494 static double* access_torque_i_data
499 internal::rigid_body_data().torque_[i];
500 double* ret=m->access_derivative_data(k);
505 static double const* access_quaternion_i_data
510 internal::rigid_body_data().quaternion_[i];
511 double const* ret=m->FloatAttributeTable::access_attribute_data(k);
516 static double* access_quaternion_i_data
521 internal::rigid_body_data().quaternion_[i];
522 double* ret=m->FloatAttributeTable::access_attribute_data(k);
538 void normalize_rotation();
542 void update_members();
545 algebra::VectorD<4> get_rotational_derivatives()
const;
548 unsigned int get_number_of_members()
const {
549 return get_body_member_particle_indexes().size() +
550 get_member_particle_indexes().size();
553 RigidBodyMember get_member(
unsigned int i)
const;
568 void add_member(ParticleIndexAdaptor p);
575 void add_non_rigid_member(ParticleIndexAdaptor p);
589 DerivativeAccumulator &da) {
590 for (
unsigned int i = 0; i < 4; ++i) {
591 get_model()->add_to_derivative(internal::rigid_body_data().quaternion_[i],
592 get_particle_index(), qderiv[i], da);
599 DerivativeAccumulator &da) {
600 for (
unsigned int i = 0; i < 3; ++i) {
601 get_model()->add_to_derivative(internal::rigid_body_data().torque_[i],
602 get_particle_index(), torque_local[i], da);
644 "Can only set the internal transformation if member is"
645 <<
" a rigid body itself.");
672 "Can only set the internal transformation if member is a "
673 <<
"rigid body itself.");
677 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[0],
679 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[1],
681 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[2],
683 get_model()->get_attribute(internal::rigid_body_data().lquaternion_[3],
702 IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(RigidBodyMember);
706 return internal::get_has_required_attributes_for_member(m, p);
709 static FloatKeys get_internal_coordinate_keys() {
710 return internal::rigid_body_data().child_keys_;
713 static FloatKeys get_internal_rotation_keys() {
714 return internal::rigid_body_data().lquaternion_;
738 return internal::get_has_required_attributes_for_rigid_member(m, p);
758 return internal::get_has_required_attributes_for_non_member(m, p);
768 for (
unsigned int i = 0; i < 3; ++i) {
769 get_model()->add_to_derivative(get_internal_coordinate_keys()[i],
786 IMPCORE_DEPRECATED_METHOD_DECL(2.12)
787 void add_to_internal_rotational_derivatives(
788 const algebra::
Vector4D &local_qderiv,
789 const algebra::Rotation3D &rot_local_to_parent,
790 const algebra::Rotation3D &rot_parent_to_global,
799 void add_to_internal_rotational_derivatives(const algebra::
Vector4D &qderiv,
804 "Can only set derivatives of internal rotation if member is a "
805 <<
"rigid body itself.");
806 for (
unsigned int i = 0; i < 4; ++i) {
807 get_model()->add_to_derivative(get_internal_rotation_keys()[i],
816 for (
unsigned int i = 0; i < 3; ++i) {
826 for (
unsigned int i = 0; i < 4; ++i) {
836 class IMPCOREEXPORT RigidMembersRefiner :
public Refiner {
838 RigidMembersRefiner(std::string name =
"RigidMembersRefiner%d")
844 virtual const ParticlesTemp
get_refined(Particle *) const
847 Model *m, const ParticleIndexes &pis) const
IMP_OVERRIDE;
852 IMPCOREEXPORT RigidMembersRefiner *get_rigid_members_refiner();
878 return get_initial_reference_frame(ps[0]->get_model(),
895 IMP_DECORATORS_DEF(RigidMember, RigidMembers);
901 TextOutput(std::cout));
907 IMPCORE_END_NAMESPACE
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.
Model * get_model() const
Returns the Model containing the particle.
ParticlesTemp create_rigid_bodies(Model *m, unsigned int n, bool no_members=false)
Index< ParticleIndexTag > ParticleIndex
bool get_coordinates_are_optimized() const
Get whether the coordinates are optimized.
static FloatKeys get_rotation_keys()
Get keys for rotation quaternion.
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.
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.
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.
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