backrub_pilot.cc File Reference

#include <protocols/branch_angle/BranchAngleOptimizer.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/backrub/BackrubMover.hh>
#include <protocols/simple_moves/DOFHistogramRecorder.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/canonical_sampling/PDBTrajectoryRecorder.hh>
#include <protocols/viewer/viewers.hh>
#include <core/chemical/ResidueType.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/DOF_ID_Range.hh>
#include <devel/init.hh>
#include <core/scoring/mm/MMBondAngleResidueTypeParamSet.fwd.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <numeric/random/random.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/backrub.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Functions
void *	my_main (void *)
int	main (int argc, char *argv[])
bool	read_fold_tree_from_file (core::kinematics::FoldTree &foldtree, std::string filepath)
bool	read_fold_tree_from_file (core::pose::Pose &pose, std::string filepath)
void	append_fold_tree_to_file (core::kinematics::FoldTree const &foldtree, std::string file_path)
utility::vector1< core::Size >	positions_incompatible_with_task (core::pose::Pose &pose, core::pack::task::PackerTask &packertask)

Variables
static basic::Tracer	TR ("apps.backrub")

Function Documentation

append_fold_tree_to_file()

void append_fold_tree_to_file	(	core::kinematics::FoldTree const &	foldtree,
		std::string	file_path
	)

References job_manager::app, erraser::file_path, erraser_single_res_analysis::out, and TR.

Referenced by my_main().

main()

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

References argv, constraints::cst_fa_file(), constraints::cst_fa_weight(), in::path::database(), test.T009_Exceptions::e, in::ignore_unrecognized_res(), basic::init(), in::file::l(), backrub::max_atoms(), backrub::min_atoms(), in::file::movemap(), my_main(), NEW_OPT, out::nstruct(), OPT, backrub::pivot_atoms(), backrub::pivot_residues(), packing::resfile(), in::file::s(), and viewer_main().

my_main()

void* my_main

(

void *

)

References append_fold_tree_to_file(), basic::options::OptionKeys::in::file::centroid_input, utility::io::ozstream::close(), basic::Tracer::flush(), create_a3b_hbs::i, basic::options::OptionKeys::backrub::initial_pack, mc, basic::options::OptionKeys::backrub::mc_kt, basic::options::OptionKeys::backrub::minimize_movemap, test.T400_Refinement::minmover, basic::options::OptionKeys::backrub::mm_bend_weight, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::backrub::ntrials, basic::options::option, drrafter_rna::output_tag, basic::options::OptionKeys::backrub::pivot_atoms, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, positions_incompatible_with_task(), read_fold_tree_from_file(), basic::options::OptionKeys::packing::resfile, numeric::random::rg(), basic::options::OptionKeys::backrub::sc_prob, basic::options::OptionKeys::backrub::sc_prob_uniform, basic::options::OptionKeys::backrub::sc_prob_withinrot, beta_nonlocal::score_fxn, basic::options::OptionKeys::backrub::sm_prob, test.T400_Refinement::smallmover, vancomycin::task, basic::options::TR, gaussian-sampling::trajectory, basic::options::OptionKeys::backrub::trajectory, basic::options::OptionKeys::backrub::trajectory_gz, basic::options::OptionKeys::backrub::trajectory_stride, numeric::random::uniform(), numeric::random::RandomGenerator::uniform(), basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.

Referenced by main().

positions_incompatible_with_task()

utility::vector1<core::Size> positions_incompatible_with_task	(	core::pose::Pose &	pose,
		core::pack::task::PackerTask &	packertask
	)

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

Referenced by my_main().

read_fold_tree_from_file() [1/2]

bool read_fold_tree_from_file	(	core::kinematics::FoldTree &	foldtree,
		std::string	filepath
	)

References getline(), subloop_histogram::key, line, and TR.

Referenced by my_main(), and read_fold_tree_from_file().

read_fold_tree_from_file() [2/2]

bool read_fold_tree_from_file	(	core::pose::Pose &	pose,
		std::string	filepath
	)

References beta_nonlocal::pose, read_fold_tree_from_file(), and TR.

Variable Documentation

TR

basic::Tracer TR("apps.backrub") ( "apps.backrub"  )

static

Referenced by append_fold_tree_to_file(), and read_fold_tree_from_file().