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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>
#include <utility/options/OptionCollection.fwd.hh>
#include <utility/options/keys/OptionKeyList.fwd.hh>
#include <iostream>

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 ()
 
std::string core::scoring::constraints::get_cst_file_option (utility::options::OptionCollection const &options)
 
void core::scoring::constraints::options_for_get_cst_file_option (utility::options::OptionKeyList &opts)
 companion function for get_cst_file_option More...
 
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 ()
 
std::string core::scoring::constraints::get_cst_fa_file_option (utility::options::OptionCollection const &options)
 
void core::scoring::constraints::options_for_get_cst_fa_file_option (utility::options::OptionKeyList &opts)
 companion function for get_cst_file_option More...
 
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)
 
void core::scoring::constraints::print_atom_pair_constraints (pose::Pose const &pose, std::ostream &out=std::cout)
 example of how to go through a pose constraint set and print out stuff. More...
 
void core::scoring::constraints::map_constraints_from_original_pose (core::pose::Pose const &original_pose, core::pose::Pose &pose)
 map constraints to new atom numbers after, e.g. variants change. requires pose to have same number of residues. More...
 

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...)