9 #ifndef IMPSPB_SPB_RESTRAINT_H
10 #define IMPSPB_SPB_RESTRAINT_H
16 #include <IMP/spb/spb_config.h>
18 IMPSPB_BEGIN_NAMESPACE
24 get_sphere_pair_score(
FloatRange dist,
double kappa);
27 get_sphere_pair_score(
double dist,
double kappa);
29 IMPSPBEXPORT
void add_SPBexcluded_volume(Model *m, RestraintSet *allrs,
30 atom::Hierarchies &hs,
34 IMPSPBEXPORT
void add_internal_restraint(Model *m, RestraintSet *allrs,
36 atom::Molecule protein_a,
37 atom::Molecule protein_b,
38 double kappa,
double dist);
40 IMPSPBEXPORT
void add_my_connectivity(Model *m, RestraintSet *allrs,
42 atom::Molecule protein,
45 IMPSPBEXPORT
void add_restrain_protein_length(
46 RestraintSet *allrs,
const atom::Hierarchy &hs,
47 std::string protein_a, Particle *dist,
double sigma0_dist);
49 IMPSPBEXPORT
void add_restrain_coiledcoil_to_cterm(
50 Model *m, RestraintSet *allrs,
const atom::Hierarchy &hs,
51 std::string protein_a, Particle *dist,
double sigma0_dist);
54 do_bipartite_mindist(Model *m, Particles p1, Particles p2,
59 do_bipartite_mindist(Model *m, Particles p1, Particles p2,
63 IMPSPBEXPORT
void add_layer_restraint(
64 RestraintSet *allrs, container::ListSingletonContainer *lsc,
67 IMPSPBEXPORT
void add_bayesian_layer_restraint(
68 RestraintSet *allrs, container::ListSingletonContainer *lsc,
69 Particle *a, Particle *b);
72 atom::Hierarchies &hs, std::string protein_a,
73 std::string residues_a, std::string protein_b, std::string residues_b,
74 double fexp, FretParameters Fret, std::string cell_type,
bool use_GFP,
75 Particle *Kda, Particle *Ida, Particle *R0, Particle *Sigma0,
79 atom::Hierarchies &hs, std::string protein_a,
80 std::string residues_a, std::string protein_b,
int residues_b,
double fexp,
81 FretParameters Fret, std::string cell_type,
bool use_GFP, Particle *Kda,
82 Particle *Ida, Particle *R0, Particle *Sigma0, Particle *pBl);
85 atom::Hierarchies &hs, std::string protein_a,
int residues_a,
86 std::string protein_b, std::string residues_b,
double fexp,
87 FretParameters Fret, std::string cell_type,
bool use_GFP, Particle *Kda,
88 Particle *Ida, Particle *R0, Particle *Sigma0, Particle *pBl);
91 Model *m,
const atom::Hierarchy &ha, std::string protein_a,
92 IntRange residues_a, atom::Hierarchies &hb, std::string protein_b,
93 IntRange residues_b,
double kappa);
96 Model *m,
const atom::Hierarchy &ha, std::string protein_a,
97 std::string residues_a, atom::Hierarchies &hb, std::string protein_b,
98 std::string residues_b,
double kappa);
101 Model *m,
const atom::Hierarchy &ha, std::string protein_a,
102 IntRange residues_a, atom::Hierarchies &hb, std::string protein_b,
103 std::string residues_b,
double kappa);
106 Model *m,
const atom::Hierarchy &ha, std::string protein_a,
107 std::string residues_a, atom::Hierarchies &hb, std::string protein_b,
108 IntRange residues_b,
double kappa);
110 IMPSPBEXPORT
void add_symmetry_restraint(
112 Particle *SideXY, Particle *SideZ);
114 IMPSPBEXPORT
void add_link(Model *m, RestraintSet *allrs,
115 const atom::Hierarchy &h, std::string protein_a,
116 std::string residues_a, atom::Hierarchies &hs,
117 std::string protein_b, IntRange residues_b,
120 IMPSPBEXPORT
void add_link(Model *m, RestraintSet *allrs,
121 const atom::Hierarchy &h, std::string protein_a,
122 std::string residues_a, atom::Hierarchies &hs,
123 std::string protein_b, std::string residues_b,
126 IMPSPBEXPORT std::vector<core::RigidBody> get_rigid_bodies(Particles ps);
128 IMPSPBEXPORT
void add_tilt_restraint(Model *m, RestraintSet *allrs,
132 IMPSPBEXPORT
void add_tilt(Model *m, RestraintSet *allrs,
133 const atom::Hierarchy &h, std::string name,
134 IntRange range,
double tilt,
double kappa);
136 IMPSPBEXPORT
void add_GFP_restraint(Model *m, RestraintSet *allrs,
137 const atom::Hierarchy &h,
140 IMPSPBEXPORT
void add_stay_close_restraint(Model *m, RestraintSet *allrs,
141 const atom::Hierarchy &h,
145 IMPSPBEXPORT
void add_stay_close_restraint(Model *m, RestraintSet *allrs,
146 const atom::Hierarchy &h,
148 int residue,
double kappa);
150 IMPSPBEXPORT
void add_stay_on_plane_restraint(Model *m,
152 const atom::Hierarchy &h,
154 int residue,
double kappa);
156 IMPSPBEXPORT
void add_diameter_rgyr_restraint(
157 RestraintSet *allrs,
const atom::Hierarchy &h,
158 std::string protein,
double diameter,
double rgyr,
double kappa);
161 atom::Hierarchies &hs, std::string protein, EM2DParameters EM2D,
165 atom::Hierarchies &hs, std::string protein, EM2DParameters EM2D,
IMP::Vector< Float > Floats
Standard way to pass a bunch of Float values.
Include all non-deprecated headers in IMP.
Include all non-deprecated headers in IMP.core.
std::pair< Float, Float > FloatRange
A pair representing the allowed range for a Float attribute.
A smart pointer to a reference counted object.
Include all non-deprecated headers in IMP.isd.
Include all non-deprecated headers in IMP.em2d.
IMP::Vector< Transformation3D > Transformation3Ds
Include all non-deprecated headers in IMP.atom.