doc/developer/example_protocol.cc File Reference

#include <core/pose/Pose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskOperation.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/moves/MinMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/PackRotamersMover.hh>
#include <protocols/moves/RotamerTrialsMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/ReturnSidechainMover.hh>
#include <protocols/moves/TaskAwareMinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/BackboneMover.hh>
#include <protocols/loops/CcdLoopClosureMover.hh>
#include <protocols/loops/LoopClass.hh>
#include <protocols/geometry/RB_geometry.hh>
#include <protocols/docking/DockingProtocol.hh>
#include <protocols/toolbox/TaskOperations/RestrictToInterfaceOperation.hh>
#include <core/init.hh>
#include <core/options/util.hh>
#include <core/options/option.hh>
#include <core/util/tracer.hh>
#include <utility/exit.hh>
#include <string>
#include <sstream>

Namespaces
namespace	dddm
Functions
static util::Tracer	TR ("apps.demonstration")
RealOptionKey const	dddm::pert_mc_temp ("dddm::pert_mc_temp")
RealOptionKey const	dddm::pert_dock_rot_mag ("dddm::pert_dock_rot_mag")
RealOptionKey const	dddm::pert_dock_trans_mag ("dddm::pert_dock_trans_mag")
RealOptionKey const	dddm::pert_loop_temp ("dddm::pert_loop_temp")
RealOptionKey const	dddm::pert_pep_small_temp ("dddm::pert_pep_small_temp")
RealOptionKey const	dddm::pert_pep_small_H ("dddm::pert_pep_small_H")
RealOptionKey const	dddm::pert_pep_small_L ("dddm::pert_pep_small_L")
RealOptionKey const	dddm::pert_pep_small_E ("dddm::pert_pep_small_E")
RealOptionKey const	dddm::pert_pep_shear_temp ("dddm::pert_pep_shear_temp")
RealOptionKey const	dddm::pert_pep_shear_H ("dddm::pert_pep_shear_H")
RealOptionKey const	dddm::pert_pep_shear_L ("dddm::pert_pep_shear_L")
RealOptionKey const	dddm::pert_pep_shear_E ("dddm::pert_pep_shear_E")
RealOptionKey const	dddm::pert_ter_small_temp ("dddm::pert_ter_small_temp")
RealOptionKey const	dddm::pert_ter_small_H ("dddm::pert_ter_small_H")
RealOptionKey const	dddm::pert_ter_small_L ("dddm::pert_ter_small_L")
RealOptionKey const	dddm::pert_ter_small_E ("dddm::pert_ter_small_E")
RealOptionKey const	dddm::pert_ter_shear_temp ("dddm::pert_ter_shear_temp")
RealOptionKey const	dddm::pert_ter_shear_H ("dddm::pert_ter_shear_H")
RealOptionKey const	dddm::pert_ter_shear_L ("dddm::pert_ter_shear_L")
RealOptionKey const	dddm::pert_ter_shear_E ("dddm::pert_ter_shear_E")
RealOptionKey const	dddm::pert_pep_num_rep ("dddm::pert_pep_num_rep")
RealOptionKey const	dddm::pert_ter_num_rep ("dddm::pert_pep_num_rep")
IntegerOptionKey const	dddm::pert_num ("dddm::pert_num")
RealOptionKey const	dddm::desn_mc_temp ("dddm::desn_mc_temp")
FileOptionKey const	dddm::loops_file ("dddm:loops_file")
void	setup_pert_foldtree (core::pose::Pose &pose, protocols::loops::Loops &myloops)
int	main (int argc, char *argv[])

---

Function Documentation

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

References utility::io::oc::cout, dddm::desn_mc_temp(), color_pdb::i, src::init(), dddm::loops_file(), basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::MonteCarlo::MonteCarlo, out::nstruct(), option, pep_end(), dddm::pert_dock_rot_mag(), dddm::pert_dock_trans_mag(), dddm::pert_loop_temp(), dddm::pert_mc_temp(), dddm::pert_num(), dddm::pert_pep_num_rep(), dddm::pert_pep_shear_E(), dddm::pert_pep_shear_H(), dddm::pert_pep_shear_L(), dddm::pert_pep_shear_temp(), dddm::pert_pep_small_E(), dddm::pert_pep_small_H(), dddm::pert_pep_small_L(), dddm::pert_pep_small_temp(), dddm::pert_ter_num_rep(), dddm::pert_ter_shear_E(), dddm::pert_ter_shear_H(), dddm::pert_ter_shear_L(), dddm::pert_ter_shear_temp(), dddm::pert_ter_small_E(), dddm::pert_ter_small_H(), dddm::pert_ter_small_L(), dddm::pert_ter_small_temp(), PyMOL_demo::pose, backrub::score_fxn, setup_pert_foldtree(), basic::options::start_file(), and value.

void setup_pert_foldtree	(	core::pose::Pose &	pose,
		protocols::loops::Loops &	myloops
	)

References utility::io::oc::cout, make_table_of_pilot_apps::f, basic::options::OptionKeys::chunk::loop2, basic::options::OptionKeys::cluster::loops, and pep_end().

Referenced by main().

static util::Tracer TR

(

"apps.demonstration"

)

[static]