/
ProteinLocalizationRestraint.h
986 lines (809 loc) · 31.5 KB
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ProteinLocalizationRestraint.h
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/**
* \file IMP/npc/ProteinLocalizationRestraint.h
* \brief protein localization restraints
*
* Restrict max distance between at least one pair of particles of any
* two distinct types. It also handles multiple copies of the same particles.
*
* Copyright 2007-2022 IMP Inventors. All rights reserved.
*
*/
#ifndef IMPNPC_PROTEIN_LOCALIZATION_RESTRAINT_H
#define IMPNPC_PROTEIN_LOCALIZATION_RESTRAINT_H
#include <IMP/Pointer.h>
#include <IMP/Restraint.h>
#include <IMP/npc/npc_config.h>
#include <IMP/SingletonContainer.h>
#include <cereal/access.hpp>
#include <cereal/types/base_class.hpp>
IMPNPC_BEGIN_NAMESPACE
//! Restrain particles by their z coordinate
/** Each particle's z coordinate is harmonically restrained to lie between
the given lower and upper bounds.
*/
class IMPNPCEXPORT ZAxialPositionRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(ZAxialPositionRestraint);
public:
ZAxialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
ZAxialPositionRestraint(Model *m,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
ZAxialPositionRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(ZAxialPositionRestraint);;
};
//! Restrain particles by their z coordinate
/** Each particle's z coordinate is harmonically restrained to lie above
the given lower bound.
*/
class IMPNPCEXPORT ZAxialPositionLowerRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(ZAxialPositionLowerRestraint);
public:
ZAxialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, bool consider_radius, double sigma=1);
ZAxialPositionLowerRestraint(Model *m,
double lower_bound, bool consider_radius, double sigma=1);
ZAxialPositionLowerRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(ZAxialPositionLowerRestraint);;
};
//! Restrain particles by their z coordinate
/** Each particle's z coordinate is harmonically restrained to lie below
the given upper bound.
*/
class IMPNPCEXPORT ZAxialPositionUpperRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(ZAxialPositionUpperRestraint);
public:
ZAxialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
double upper_bound, bool consider_radius, double sigma=1);
ZAxialPositionUpperRestraint(Model *m,
double upper_bound, bool consider_radius, double sigma=1);
ZAxialPositionUpperRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(ZAxialPositionUpperRestraint);;
};
//! Restrain particles by their y coordinate
/** Each particle's y coordinate is harmonically restrained to lie between
the given lower and upper bounds.
*/
class IMPNPCEXPORT YAxialPositionRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(YAxialPositionRestraint);
public:
YAxialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
YAxialPositionRestraint(Model *m,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
YAxialPositionRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(YAxialPositionRestraint);;
};
//! Restrain particles by their y coordinate
/** Each particle's y coordinate is harmonically restrained to lie above
the given lower bound.
*/
class IMPNPCEXPORT YAxialPositionLowerRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(YAxialPositionLowerRestraint);
public:
YAxialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, bool consider_radius, double sigma=1);
YAxialPositionLowerRestraint(Model *m,
double lower_bound, bool consider_radius, double sigma=1);
YAxialPositionLowerRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(YAxialPositionLowerRestraint);;
};
//! Restrain particles by their y coordinate
/** Each particle's y coordinate is harmonically restrained to lie below
the given upper bound.
*/
class IMPNPCEXPORT YAxialPositionUpperRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(YAxialPositionUpperRestraint);
public:
YAxialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
double upper_bound, bool consider_radius, double sigma=1);
YAxialPositionUpperRestraint(Model *m,
double upper_bound, bool consider_radius, double sigma=1);
YAxialPositionUpperRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(YAxialPositionUpperRestraint);;
};
//! Restrain particles by their distance from the z axis in the xy plane
/** Each particle's distance to the z axis is harmonically restrained to
lie between the given lower and upper bounds.
*/
class IMPNPCEXPORT XYRadialPositionRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(XYRadialPositionRestraint);
public:
XYRadialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
XYRadialPositionRestraint(Model *m,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
XYRadialPositionRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(XYRadialPositionRestraint);;
};
//! Restrain particles by their distance from the z axis in the xy plane
/** Each particle's distance to the z axis is harmonically restrained to
lie above the given lower bound.
*/
class IMPNPCEXPORT XYRadialPositionLowerRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(XYRadialPositionLowerRestraint);
public:
XYRadialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, bool consider_radius, double sigma=1);
XYRadialPositionLowerRestraint(Model *m,
double lower_bound, bool consider_radius, double sigma=1);
XYRadialPositionLowerRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(XYRadialPositionLowerRestraint);;
};
//! Restrain particles by their distance from the z axis in the xy plane
/** Each particle's distance to the z axis is harmonically restrained to
lie below the given upper bound.
*/
class IMPNPCEXPORT XYRadialPositionUpperRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(XYRadialPositionUpperRestraint);
public:
XYRadialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
double upper_bound, bool consider_radius, double sigma=1);
XYRadialPositionUpperRestraint(Model *m,
double upper_bound, bool consider_radius, double sigma=1);
XYRadialPositionUpperRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(XYRadialPositionUpperRestraint);;
};
//! Try to keep all particle surfaces in contact
/** The particles (each of which should be a core::XYZR) are harmonically
restrained such that each particle's sphere surface is in contact
with every other surface.
*/
class IMPNPCEXPORT ProteinContactRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double tolerance_factor_;
double sigma_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, tolerance_factor_, sigma_);
}
IMP_OBJECT_SERIALIZE_DECL(ProteinContactRestraint);
public:
ProteinContactRestraint(Model *m, SingletonContainerAdaptor sc,
double tolerance_factor, double sigma=0.1);
ProteinContactRestraint(Model *m,
double tolerance_factor, double sigma=0.1);
ProteinContactRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(ProteinContactRestraint);;
};
//! Try to keep particle surfaces in contact in a chain
/** The particles (each of which should be a core::XYZR) are harmonically
restrained such that each particle's sphere surface is in contact
with the surface of the previous particle.
*/
class IMPNPCEXPORT ProteinChainRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double sigma_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, sigma_);
}
IMP_OBJECT_SERIALIZE_DECL(ProteinChainRestraint);
public:
ProteinChainRestraint(Model *m, SingletonContainerAdaptor sc,
double sigma=0.1);
ProteinChainRestraint(Model *m,
double sigma=0.1);
ProteinChainRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(ProteinChainRestraint);;
};
//! Try to keep particles localized on a membrane surface
/** The membrane is defined in this case to be a half torus in the xy
plane with center at the origin.
*/
class IMPNPCEXPORT MembraneSurfaceLocationRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double R_;
double r_;
double sigma_;
double thickness_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, R_, r_, sigma_, thickness_);
}
IMP_OBJECT_SERIALIZE_DECL(MembraneSurfaceLocationRestraint);
public:
MembraneSurfaceLocationRestraint(Model *m, SingletonContainerAdaptor sc,
double R, double r, double thickness, double sigma=2);
MembraneSurfaceLocationRestraint(Model *m,
double R, double r, double thickness, double sigma=2);
MembraneSurfaceLocationRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(MembraneSurfaceLocationRestraint);;
};
//! Try to keep one set of particles localized on a membrane surface
/** The membrane is defined in this case to be a half torus in the xy
plane with center at the origin. One of the two sets of particles
(whichever is closer) is restrained to the membrane surface.
*/
class IMPNPCEXPORT MembraneSurfaceLocationConditionalRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc1_;
IMP::PointerMember<IMP::SingletonContainer> sc2_;
double R_;
double r_;
double sigma_;
double thickness_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc1_, sc2_, R_, r_, sigma_, thickness_);
}
IMP_OBJECT_SERIALIZE_DECL(MembraneSurfaceLocationConditionalRestraint);
public:
MembraneSurfaceLocationConditionalRestraint(Model *m, SingletonContainerAdaptor sc1, SingletonContainerAdaptor sc2,
double R, double r, double thickness, double sigma=2);
MembraneSurfaceLocationConditionalRestraint(Model *m,
double R, double r, double thickness, double sigma=2);
MembraneSurfaceLocationConditionalRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle1(Particle *p);
void add_particle2(Particle *p);
void add_particles1(const ParticlesTemp &ps);
void add_particles2(const ParticlesTemp &ps);
void set_particles1(const ParticlesTemp &ps);
void set_particles2(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(MembraneSurfaceLocationConditionalRestraint);;
};
//! Try to keep particles away from a membrane
/** The membrane is defined in this case to be a half torus in the xy
plane with center at the origin.
*/
class IMPNPCEXPORT MembraneExclusionRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double R_;
double r_;
double sigma_;
double thickness_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, R_, r_, sigma_, thickness_);
}
IMP_OBJECT_SERIALIZE_DECL(MembraneExclusionRestraint);
public:
MembraneExclusionRestraint(Model *m, SingletonContainerAdaptor sc,
double R, double r, double thickness, double sigma=2);
MembraneExclusionRestraint(Model *m,
double R, double r, double thickness, double sigma=2);
MembraneExclusionRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(MembraneExclusionRestraint);;
};
//! Try to keep particles on the pore side of a membrane
/** The membrane is defined in this case to be a half torus in the xy
plane with center at the origin.
*/
class IMPNPCEXPORT PoreSideVolumeLocationRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double R_;
double r_;
double sigma_;
double thickness_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, R_, r_, sigma_, thickness_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(PoreSideVolumeLocationRestraint);
public:
PoreSideVolumeLocationRestraint(Model *m, SingletonContainerAdaptor sc,
double R, double r, double thickness, bool consider_radius, double sigma=2);
PoreSideVolumeLocationRestraint(Model *m,
double R, double r, double thickness, bool consider_radius, double sigma=2);
PoreSideVolumeLocationRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(PoreSideVolumeLocationRestraint);;
};
//! Try to keep particles on the perinuclear side of a membrane
/** The membrane is defined in this case to be a half torus in the xy
plane with center at the origin.
*/
class IMPNPCEXPORT PerinuclearVolumeLocationRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double R_;
double r_;
double sigma_;
double thickness_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, R_, r_, sigma_, thickness_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(PerinuclearVolumeLocationRestraint);
public:
PerinuclearVolumeLocationRestraint(Model *m, SingletonContainerAdaptor sc,
double R, double r, double thickness, bool consider_radius, double sigma=2);
PerinuclearVolumeLocationRestraint(Model *m,
double R, double r, double thickness, bool consider_radius, double sigma=2);
PerinuclearVolumeLocationRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(PerinuclearVolumeLocationRestraint);;
};
//! Restrain two interparticle distances to be the same
/** This restraint must be given 4 particles. They are restrained to
be symmetric, by enforcing a harmonic penalty on the difference
between the distance between the first 2 particles and the distance
between the last two.
*/
class IMPNPCEXPORT AssemblySymmetryByDistanceRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double sigma_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, sigma_);
}
IMP_OBJECT_SERIALIZE_DECL(AssemblySymmetryByDistanceRestraint);
public:
AssemblySymmetryByDistanceRestraint(Model *m, SingletonContainerAdaptor sc,
double sigma=4);
AssemblySymmetryByDistanceRestraint(Model *m,
double sigma=4);
AssemblySymmetryByDistanceRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(AssemblySymmetryByDistanceRestraint);;
};
//! Restrain two interparticle dihedrals to be the same
/** This restraint must be given 8 particles. They are restrained to
be symmetric, by enforcing a harmonic penalty on the difference
between the dihedral angle between the first 4 particles and the dihedral
between the last 4.
*/
class IMPNPCEXPORT AssemblySymmetryByDihedralRestraint
: public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double sigma_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, sigma_);
}
IMP_OBJECT_SERIALIZE_DECL(AssemblySymmetryByDihedralRestraint);
public:
AssemblySymmetryByDihedralRestraint(Model *m, SingletonContainerAdaptor sc,
double sigma=0.1);
AssemblySymmetryByDihedralRestraint(Model *m,
double sigma=0.1);
AssemblySymmetryByDihedralRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(AssemblySymmetryByDihedralRestraint);;
};
//! Restrain a set of particles to be proximate to each other
/** Each particle is harmonically restrained to be no more than
`max_dist` away from every other particle.
*/
class IMPNPCEXPORT ProteinProximityRestraint
: public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double sigma_;
double max_dist_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this), sc_, sigma_, max_dist_);
}
IMP_OBJECT_SERIALIZE_DECL(ProteinProximityRestraint);
public:
ProteinProximityRestraint(Model *m, SingletonContainerAdaptor sc,
double max_dist, double sigma=0.1);
ProteinProximityRestraint(Model *m,
double max_dist, double sigma=0.1);
ProteinProximityRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
IMP_OBJECT_METHODS(ProteinProximityRestraint);;
};
//! Restrain particles by their x coordinate
/** Each particle's x coordinate is harmonically restrained to lie between
the given lower and upper bounds.
*/
class IMPNPCEXPORT XAxialPositionRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(XAxialPositionRestraint);
public:
XAxialPositionRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
XAxialPositionRestraint(Model *m,
double lower_bound, double upper_bound, bool consider_radius, double sigma=1);
XAxialPositionRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(XAxialPositionRestraint);;
};
//! Restrain particles by their x coordinate
/** Each particle's x coordinate is harmonically restrained to lie above
the given lower bound.
*/
class IMPNPCEXPORT XAxialPositionLowerRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double lower_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, lower_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(XAxialPositionLowerRestraint);
public:
XAxialPositionLowerRestraint(Model *m, SingletonContainerAdaptor sc,
double lower_bound, bool consider_radius, double sigma=1);
XAxialPositionLowerRestraint(Model *m,
double lower_bound, bool consider_radius, double sigma=1);
XAxialPositionLowerRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(XAxialPositionLowerRestraint);;
};
//! Restrain particles by their x coordinate
/** Each particle's x coordinate is harmonically restrained to lie below
the given upper bound.
*/
class IMPNPCEXPORT XAxialPositionUpperRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double upper_bound_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, upper_bound_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(XAxialPositionUpperRestraint);
public:
XAxialPositionUpperRestraint(Model *m, SingletonContainerAdaptor sc,
double upper_bound, bool consider_radius, double sigma=1);
XAxialPositionUpperRestraint(Model *m,
double upper_bound, bool consider_radius, double sigma=1);
XAxialPositionUpperRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(XAxialPositionUpperRestraint);;
};
//! Restrain particle to a specific position
/** All distances are in Angstrom
While SphereDistanceToSingletonScore creates a score based on a UnaryFunction object,
OverallPositionRestraint assumes a harmonic restraint.
\param[in] x_start x position to restrain to
\param[in] y_start y position to restrain to
\param[in] z_start z position to restrain to
\param[in] tolerance range of distances where restraint=0
\param[in] consider_radius bool, consider the radius of the particle
\param[in] sigma inverse strength of harmonic potential
*/
class IMPNPCEXPORT OverallPositionRestraint : public Restraint
{
IMP::PointerMember<IMP::SingletonContainer> sc_;
double x_start_;
double y_start_;
double z_start_;
double tolerance_;
double sigma_;
bool consider_radius_;
friend class cereal::access;
template<class Archive> void serialize(Archive &ar) {
ar(cereal::base_class<Restraint>(this),
sc_, x_start_, y_start_, z_start_, tolerance_, sigma_, consider_radius_);
}
IMP_OBJECT_SERIALIZE_DECL(OverallPositionRestraint);
public:
OverallPositionRestraint(Model *m,
SingletonContainerAdaptor sc,
double x_start, double y_start, double z_start, double tolerance, bool consider_radius, double sigma=1);
OverallPositionRestraint(Model *m,
double x_start, double y_start, double z_start, double tolerance, bool consider_radius, double sigma=1);
OverallPositionRestraint() {}
#ifndef IMP_DOXYGEN
void add_particle(Particle *p);
void add_particles(const ParticlesTemp &ps);
void set_particles(const ParticlesTemp &ps);
#endif
double unprotected_evaluate(
IMP::DerivativeAccumulator *accum) const override;
ModelObjectsTemp do_get_inputs() const override;
//! \return Information for writing to RMF files
RestraintInfo *get_static_info() const override;
IMP_OBJECT_METHODS(OverallPositionRestraint);;
};
IMPNPC_END_NAMESPACE
#endif /* IMPNPC_PROTEIN_LOCALIZATION_RESTRAINT_H */