sidechain_min.cc File Reference

Minimizes non-disulfide-bonded side-chains in the input structure. More...

#include <protocols/loops/Loops.hh>
#include <protocols/viewer/viewers.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/id/TorsionID.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/options/option.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <utility/io/izstream.hh>
#include <iostream>
#include <map>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Functions
void	loops_set_move_map (protocols::loops::Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm)
void	get_tenA_neighbor_residues (pose::Pose const &pose, utility::vector1< bool > &residue_positions)
void	fold_tree_from_loops (Size const total_residue, protocols::loops::Loops const &loops, kinematics::FoldTree &f)
bool	set_secstruct_from_psipred_ss2 (pose::Pose &pose)
void	select_loop_residues (pose::Pose const &pose, protocols::loops::Loops const &loops, bool const include_neighbors, utility::vector1< bool > &map)
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("procotols.looprelax")

Detailed Description

Minimizes non-disulfide-bonded side-chains in the input structure.

Author

Daniel J. Mandell

Function Documentation

fold_tree_from_loops()

void fold_tree_from_loops	(	Size const	total_residue,
		protocols::loops::Loops const &	loops,
		kinematics::FoldTree &	f
	)

References create_a3b_hbs::f, make_symmdef_file_denovo::jump_num, make_symmdef_file_denovo::jump_start, make_symmdef_file_denovo::jump_stop, and basic::options::OptionKeys::cluster::loops.

get_tenA_neighbor_residues()

void get_tenA_neighbor_residues	(	pose::Pose const &	pose,
		utility::vector1< bool > &	residue_positions
	)

use TenANeighborGraph. As input, residue_positions[i] is true for residues to be counted. As output, residue_position[i] is true for all neighbor residues including orginal input residues. The function is used to find all neighboring residues of the loop residues in case they need to be repacked or minimized in fullatom refinement.

References utility::graph::Node::const_edge_list_begin(), utility::graph::Node::const_edge_list_end(), create_a3b_hbs::i, enumerate_junctions::int, and beta_nonlocal::pose.

Referenced by select_loop_residues().

loops_set_move_map()

void loops_set_move_map	(	protocols::loops::Loops const &	loops,
		bool const	fix_template_sc,
		core::kinematics::MoveMap &	mm
	)

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable.

References create_a3b_hbs::i, and beta_nonlocal::mm.

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().

my_main()

void* my_main

(

void *

)

References basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::i, if(), rna_decompose::input_pdb, create_a3b_hbs::nres, option, options, erraser_single_res_analysis::out, drrafter_rna::output_tag, closure_error::path, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T500_Packing::rotamer_trials, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main().

select_loop_residues()

void select_loop_residues	(	pose::Pose const &	pose,
		protocols::loops::Loops const &	loops,
		bool const	include_neighbors,
		utility::vector1< bool > &	map
	)

use 10A CB distance cutoff as neighboring residue defintion. The function is used for conveniently setting up sidechain movable residues in loop modeling.

References get_tenA_neighbor_residues(), create_a3b_hbs::i, and beta_nonlocal::pose.

set_secstruct_from_psipred_ss2()

bool set_secstruct_from_psipred_ss2

(

pose::Pose &

pose

)

read in secondary structure definition from a psipred_ss2 file and set that to a Pose. A temporary setup since there is very limited ss support in Pose right now.

References aa, count, data, basic::Tracer::Error, lactamize::filename, getline(), create_a3b_hbs::i, line, option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::options::OptionKeys::in::file::psipred_ss2, numeric::sec(), and TR.

Variable Documentation

TR

basic::Tracer TR("procotols.looprelax") ( "procotols.looprelax"  )

static

Referenced by set_secstruct_from_psipred_ss2().