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Rosetta
2021.16
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Rosetta
2021.16
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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... | |
Utility functions for defining and using constraints.
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