Rosetta Core  2014.35
Namespaces | Functions
util.hh File Reference

Utility functions for defining and using constraints. More...

#include <core/types.hh>
#include <core/scoring/constraints/Constraint.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/kinematics/ShortestPathInFoldTree.fwd.hh>
#include <utility/vector1.hh>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::scoring
 
 core::scoring::constraints
 

Functions

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::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::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. 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::merge_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
 merge cmdline constraints to pre-existing constraints More...
 
void core::scoring::constraints::merge_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
 merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued More...
 
void core::scoring::constraints::merge_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
 merge cmdline constraints to pre-existing constraints More...
 
void core::scoring::constraints::merge_fa_constraints_from_cmdline_to_pose (core::pose::Pose &pose)
 merge cmdline constraints to pre-existing constraints More...
 
void core::scoring::constraints::merge_fa_constraints_from_cmdline_to_scorefxn (core::scoring::ScoreFunction &scorefxn_)
 merge cmdline constraints to pre-existing constraints - only adds to ZERO weights; previously nonzero constraint weights are unmodified and a warning is issued More...
 
void core::scoring::constraints::merge_fa_constraints_from_cmdline (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_)
 merge cmdline constraints to pre-existing constraints More...
 
void core::scoring::constraints::add_coordinate_constraints (core::pose::Pose &pose, core::Real const coord_sdev=10.0, bool include_sc=true)
 handy function for tethering pose to starting coordinates. More...
 
void core::scoring::constraints::add_coordinate_constraints (core::pose::Pose &pose, core::Size const start_res, core::Size const end_res, core::Real const coord_sdev=10.0, bool include_sc=true)
 Add coordinate constraints for starting coordinates, start:end residues, inclusive. More...
 
void core::scoring::constraints::remove_constraints_of_type (core::pose::Pose &pose, std::string const type)
 Remove all constraints of a given type from a pose. More...
 
void core::scoring::constraints::remove_constraints_of_type (core::pose::Pose &pose, std::string const type, core::Size const start_res, core::Size const end_res)
 Remove all constraints of a given type from a pose that involve start_res to end_res. Useful for coordinate/dihedral constraints. More...
 
void core::scoring::constraints::remove_nonbb_constraints (pose::Pose &pose)
 
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...
 
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::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 and using constraints.

Author
James Thompson
Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om (merge_constraints_from_cmdline...)