util.hh File Reference

#include <core/types.hh>
#include <core/chemical/VariantType.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/full_model_info/FullModelInfo.fwd.hh>
#include <core/kinematics/Edge.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.fwd.hh>
#include <utility/vector1.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <map>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::stepwise
	protocols::stepwise::modeler

Typedefs
typedef std::map< std::string, core::pose::PoseOP >	protocols::stepwise::modeler::PoseList

Functions
Size	protocols::stepwise::modeler::make_cut_at_moving_suite (pose::Pose &pose, core::Size const &moving_suite)
Size	protocols::stepwise::modeler::make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, core::Size const &moving_suite)
Size	protocols::stepwise::modeler::find_jump_number_at_suite (kinematics::FoldTree const &fold_tree, core::Size const &moving_suite)
Size	protocols::stepwise::modeler::look_for_unique_jump_to_moving_res (kinematics::FoldTree const &fold_tree, core::Size const &i)
bool	protocols::stepwise::modeler::is_cutpoint_closed (pose::Pose const &pose, core::Size const seq_num)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_cutpoint_closed (pose::Pose const &pose)
utility::vector1< core::Size >	protocols::stepwise::modeler::merge_vectors (utility::vector1< core::Size > const &vec1, utility::vector1< core::Size > const &vec2)
void	protocols::stepwise::modeler::merge_in_other_pose_by_bond (pose::Pose &pose, pose::Pose const &pose2, core::Size const merge_res)
void	protocols::stepwise::modeler::merge_in_other_pose_by_jump (pose::Pose &pose, pose::Pose const &pose2, core::Size const lower_merge_res, core::Size const upper_merge_res)
void	protocols::stepwise::modeler::merge_in_other_pose (pose::Pose &pose, pose::Pose const &pose2, core::Size const lower_merge_res, core::Size const upper_merge_res, bool const connect_residues_by_bond)
utility::vector1< core::Size >	protocols::stepwise::modeler::merge_two_poses_using_full_model_info (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, core::Size const lower_merge_res, core::Size const upper_merge_res, bool const connect_residues_by_bond)
utility::vector1< core::Size >	protocols::stepwise::modeler::merge_two_poses (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< core::Size > const &working_res1, utility::vector1< core::Size > const &working_res2, core::Size const lower_merge_res, core::Size const upper_merge_res, bool const connect_residues_by_bond, bool const fix_first_pose)
void	protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints (pose::Pose &pose, pose::Pose const &source_pose, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &source_working_res)
void	protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints (pose::Pose &pose, pose::Pose const &source_pose, utility::vector1< core::Size > const &working_res)
void	protocols::stepwise::modeler::slice (pose::Pose &sliced_out_pose, pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)
void	protocols::stepwise::modeler::slice_out_pose (pose::Pose &pose, pose::Pose &sliced_out_pose, utility::vector1< core::Size > const &residues_to_delete)
Size	protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element)
Size	protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, FullModelInfo const &full_model_info)
Size	protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &chains_in_full_model)
Size	protocols::stepwise::modeler::check_jump_to_next_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element)
Size	protocols::stepwise::modeler::check_jump_to_next_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, FullModelInfo const &full_model_info)
Size	protocols::stepwise::modeler::check_jump_to_next_residue_in_chain (pose::Pose const &pose, core::Size const i, utility::vector1< core::Size > const &current_element, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &chains_in_full_model)
void	protocols::stepwise::modeler::switch_focus_to_other_pose (pose::Pose &pose, core::Size const &focus_pose_idx, core::scoring::ScoreFunctionCOP scorefxn)
bool	protocols::stepwise::modeler::switch_focus_among_poses_randomly (pose::Pose &pose, core::scoring::ScoreFunctionCOP scorefxn, bool force_switch)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_chain_break_res (pose::Pose const &pose, kinematics::MoveMap const &mm)
	TODO: generalize to cyclized chainbreaks. More...
bool	protocols::stepwise::modeler::check_for_input_domain (pose::Pose const &pose, utility::vector1< core::Size > const &partition_res)
bool	protocols::stepwise::modeler::check_for_input_domain (pose::Pose const &pose)
void	protocols::stepwise::modeler::make_variants_match (pose::Pose &pose, pose::Pose const &reference_pose, core::Size const n, chemical::VariantType const variant_type)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_cutpoints_closed (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, core::Size const moving_res)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
void	protocols::stepwise::modeler::figure_out_moving_chain_breaks (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res, utility::vector1< core::Size > &cutpoints_closed, utility::vector1< core::Size > &five_prime_chain_breaks, utility::vector1< core::Size > &three_prime_chain_breaks, utility::vector1< core::Size > &chain_break_gap_sizes)
	TODO: generalize to cyclized chainbreaks. More...
Size	protocols::stepwise::modeler::figure_out_reference_res_for_suite (pose::Pose const &pose, core::Size const moving_res)
utility::vector1< bool >	protocols::stepwise::modeler::get_partition_definition (pose::Pose const &pose, core::Size const &moving_suite)
utility::vector1< bool >	protocols::stepwise::modeler::get_partition_definition_by_jump (pose::Pose const &pose, core::Size const &jump_nr)
utility::vector1< bool >	protocols::stepwise::modeler::get_partition_definition_by_chemical_edge (pose::Pose const &pose, core::kinematics::Edge const &edge)
void	protocols::stepwise::modeler::reroot_based_on_full_model_info (pose::Pose &pose)
void	protocols::stepwise::modeler::reroot_based_on_full_model_info (pose::Pose &pose, utility::vector1< core::Size > const &root_partition_res)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_partition_res_for_suite (pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_partition_res_for_jump (pose::Pose const &pose, core::Size const jump_nr)
void	protocols::stepwise::modeler::figure_out_root_and_moving_partition_res (pose::Pose const &pose, core::Size const moving_res, utility::vector1< core::Size > &root_partition_res, utility::vector1< core::Size > &moving_partition_res)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_partition_res (pose::Pose const &pose, core::Size const moving_res)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_moving_partition_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
utility::vector1< core::Size >	protocols::stepwise::modeler::figure_out_root_partition_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
bool	protocols::stepwise::modeler::revise_root_and_moving_res (pose::Pose &pose, core::Size &moving_res)
bool	protocols::stepwise::modeler::revise_root_and_moving_res_list (pose::Pose &pose, utility::vector1< core::Size > &moving_res_list)
Size	protocols::stepwise::modeler::find_downstream_connection_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res)
Size	protocols::stepwise::modeler::split_pose (pose::Pose &pose, core::Size const moving_res, core::Size const reference_res)
void	protocols::stepwise::modeler::split_pose (pose::Pose &pose, utility::vector1< core::Size > const &moving_res_list)
void	protocols::stepwise::modeler::fix_up_jump_atoms (pose::Pose &pose)
void	protocols::stepwise::modeler::fix_up_jump_atoms_and_residue_type_variants (pose::Pose &pose_to_fix)
void	protocols::stepwise::modeler::fix_protein_jump_atom (pose::Pose &pose, core::Size const res, std::string const &atom_name)
void	protocols::stepwise::modeler::add_to_pose_list (utility::vector1< core::pose::PoseOP > &pose_list, pose::Pose const &pose, std::string const &pose_tag)
bool	protocols::stepwise::modeler::is_protein (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_domain_boundary_suites (pose::Pose const &pose)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_domain_boundary_res (pose::Pose const &pose)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_moving_res_including_domain_boundaries (pose::Pose const &pose, utility::vector1< core::Size > const &moving_res_list)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_all_working_moving_res (working_parameters::StepWiseWorkingParametersCOP working_parameters)
void	protocols::stepwise::modeler::virtualize_side_chains (pose::Pose &pose)
utility::vector1< core::Size >	protocols::stepwise::modeler::get_all_residues (pose::Pose const &pose)
Size	protocols::stepwise::modeler::get_unique_connection_res (pose::Pose const &pose, utility::vector1< core::Size > const &moving_partition_res)

Detailed Description

Author

Rhiju Das