9 #ifndef IMPISD_GAUSSIAN_EM_RESTRAINT_H
10 #define IMPISD_GAUSSIAN_EM_RESTRAINT_H
12 #include "isd_config.h"
24 #include <Eigen/Dense>
25 #include <boost/unordered_map.hpp>
27 IMPISD_BEGIN_NAMESPACE
65 Float model_cutoff_dist,
Float density_cutoff_dist,
67 bool update_model=
true,
bool backbone_slope=
false,
69 std::string name=
"GaussianEMRestraint%1%");
73 return exp(-unprotected_evaluate(NULL));
82 return cross_correlation_;
98 void compute_initial_scores();
108 void show(std::ostream &out)
const { out <<
"GEM restraint"; }
119 double model_cutoff_dist_, density_cutoff_dist_;
123 bool update_model_,local_;
125 Float normalization_;
127 Float self_mm_score_;
128 PointerMember<container::CloseBipartitePairContainer> md_container_;
131 std::
string density_fn_;
138 mutable
double cross_correlation_;
Declare an efficient stl-compatible map.
Decorator to hold Gaussian3D.
A decorator for particles with mass.
virtual RestraintInfo * get_static_info() const
Store a list of ParticleIndexes.
Return all pairs from a SingletonContainer.
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Float get_slope()
Get restraint slope.
void set_density_filename(std::string density_fn)
Set the filename corresponding to the density GMM particles.
Handling of file input/output.
void set_slope(Float s)
Set restraint slope.
Macros to define containers of objects.
Class for storing model, its restraints, constraints, and particles.
double get_probability() const
Returns exp(score)
double get_cross_correlation_coefficient() const
Get cross correlation between the model and the map.
Restraint between two Gaussian Mixture Models, "model" and "density".
Return all pairs from a SingletonContainer.
A smart pointer to a ref-counted Object that is a class member.
Report key:value information on restraints.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
std::string get_absolute_path(std::string file)
Convert a possibly relative path to an absolute path.
double Float
Basic floating-point value (could be float, double...)
virtual ModelObjectsTemp do_get_inputs() const =0
#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.
A restraint is a term in an IMP ScoringFunction.