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util.cc File Reference

utility functions for defining constraints. Maybe better placed in src/numeric? More...

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <basic/options/option.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AmbiguousNMRConstraint.hh>
#include <core/conformation/Residue.hh>
#include <numeric/random/random_permutation.hh>
#include <numeric/random/random.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::scoring
 
 core::scoring::constraints
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::scoring
 
 core::scoring::constraints
 

Functions

static
numeric::random::RandomGenerator 
core::scoring::constraints::RG (42015512)
 
static basic::Tracer core::scoring::constraints::tr ("core.scoring.constraints")
 
Real core::scoring::constraints::logdgaussian (Real x, Real mean, Real sd, Real weight)
 Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real core::scoring::constraints::logdgaussian_deriv (Real x, Real mean, Real sd, Real)
 Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real core::scoring::constraints::dgaussian (Real x, Real mean, Real sd, Real weight)
 Returns the weighted value of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real core::scoring::constraints::gaussian_deriv (Real x, Real mean, Real sd, Real weight)
 Returns the weighted derivative of a normal distribution evaluated with the given mean, sd, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real core::scoring::constraints::dexponential (Real x, Real anchor, Real rate, Real weight)
 Returns the weighted value of an exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real core::scoring::constraints::exponential_deriv (Real x, Real anchor, Real rate, Real weight)
 Returns the weighted derivative of a log-exponential distribution evaluated with the given anchor, rate, and x values. Returns zero if the weight is less than 1e-10. More...
 
Real core::scoring::constraints::linear_interpolate (Real const x_val, Real const x1, Real const x2, Real const y1, Real const y2)
 Estimates the y-value of the given x-value by interpolating between the given points (x1,y1) and (x2,y2) by using linear interpolation between the two points. More...
 
void core::scoring::constraints::cull_violators (ConstraintCOPs const &target_list, ConstraintCOPs &culled_list, pose::Pose const &filter_pose, core::Real threshold)
 
std::string core::scoring::constraints::get_cst_file_option ()
 
void core::scoring::constraints::add_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
 
void core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
 
void core::scoring::constraints::add_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
 
std::string core::scoring::constraints::get_cst_fa_file_option ()
 
void core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
 add constraints if specified by user using the -constraints::cst_fa_file flag. Setting appropriate weights for ScoreFunction is done elsewhere. More...
 
void core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
 add constraints if specified by user. More...
 
void core::scoring::constraints::add_fa_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
 add constraints if specified by user. More...
 
void core::scoring::constraints::add_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev=10.0)
 handy function for tethering pose to starting coordinates. More...
 
bool core::scoring::constraints::combinable (Constraint const &cst, utility::vector1< Size > exclude_res)
 
void core::scoring::constraints::choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, ConstraintCOPs &in)
 combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint More...
 
core::Size core::scoring::constraints::bin_by_seq_separation (core::Size sep)
 
void core::scoring::constraints::combine_constraints (ConstraintCOPs &in, core::Size combine_ratio, utility::vector1< bool > exclude_res, core::kinematics::ShortestPathInFoldTree const &sp_in)
 combine constraints randomly into AmbiguousConstraints N -> 1 this greatly decreases the odds to have a wrong constraint More...
 
void core::scoring::constraints::count_constraint (ConstraintCOP cst, bool redundant, ObjexxFCL::FArray2D_int &count_matrix, Size influence_width, Size total_residue)
 
bool core::scoring::constraints::keep_constraint (ConstraintCOP cst, bool redundant, ObjexxFCL::FArray2D_int &count_matrix, Size influence_width, Size total_residue)
 
void core::scoring::constraints::skip_redundant_constraints (ConstraintCOPs &in, core::Size total_residue, core::Size influence_width=1)
 have at most one constraint per residue pair... More...
 
void core::scoring::constraints::drop_constraints (ConstraintCOPs &in, core::Real drop_rate)
 

Detailed Description

utility functions for defining constraints. Maybe better placed in src/numeric?

Author
James Thompson