a3b_hbs_creator.cc File Reference

#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/pose/ncbb/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/util.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/RandomTorsionMover.hh>
#include <protocols/ncbb/hbs/HbsPatcher.hh>
#include <protocols/ncbb/a3b_hbs/A3BHbsPatcher.hh>
#include <protocols/simple_moves/chiral/ChiralMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/minimization_packing/TaskAwareMinMover.hh>
#include <numeric/random/random.hh>
#include <devel/init.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <utility/pointer/owning_ptr.hh>
#include <string>

Classes
class	A3BHbsCreatorMover

Namespaces
	a3b_hbs_creator

Typedefs
using	A3BHbsCreatorMoverOP = utility::pointer::shared_ptr< A3BHbsCreatorMover >
using	A3BHbsCreatorMoverCOP = utility::pointer::shared_ptr< const A3BHbsCreatorMover >

Functions
void	setup_pert_foldtree (core::pose::Pose &pose)
std::string	alpha_to_beta (std::string const &alpha)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("A3BHBS_Creator")
StringOptionKey const	a3b_hbs_creator::hbs_chain ("a3b_hbs_creator::hbs_chain")
IntegerOptionKey const	a3b_hbs_creator::hbs_final_res ("a3b_hbs_creator::hbs_final_res")
IntegerOptionKey const	a3b_hbs_creator::hbs_length ("a3b_hbs_creator::hbs_length")
IntegerOptionKey const	a3b_hbs_creator::hbs_offset ("a3b_hbs_creator::hbs_offset")
IntegerOptionKey const	a3b_hbs_creator::change_resnums ("a3b_hbs_creator::change_resnums")
BooleanOptionKey const	a3b_hbs_creator::bridgehead_gly ("a3b_hbs_creator::bridgehead_gly")
BooleanOptionKey const	a3b_hbs_creator::final_repack ("a3b_hbs_creator::final_repack")
BooleanOptionKey const	a3b_hbs_creator::final_minimize ("a3b_hbs_creator::final_minimize")
BooleanOptionKey const	a3b_hbs_creator::final_mc ("a3b_hbs_creator::final_mc")

Typedef Documentation

A3BHbsCreatorMoverCOP

using A3BHbsCreatorMoverCOP = utility::pointer::shared_ptr<const A3BHbsCreatorMover>

A3BHbsCreatorMoverOP

using A3BHbsCreatorMoverOP = utility::pointer::shared_ptr<A3BHbsCreatorMover>

Function Documentation

alpha_to_beta()

std::string alpha_to_beta

(

std::string const &

alpha

)

References compute_difference::alpha, create_a3b_hbs::postfix, create_a3b_hbs::prefix, and TR.

Referenced by A3BHbsCreatorMover::make_a3b_pose().

main()

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

References A3BHbsCreatorMover::A3BHbsCreatorMover(), argv, a3b_hbs_creator::bridgehead_gly, a3b_hbs_creator::change_resnums, test.T009_Exceptions::e, a3b_hbs_creator::final_mc, a3b_hbs_creator::final_minimize, a3b_hbs_creator::final_repack, a3b_hbs_creator::hbs_chain, a3b_hbs_creator::hbs_final_res, a3b_hbs_creator::hbs_length, a3b_hbs_creator::hbs_offset, basic::init(), and option.

setup_pert_foldtree()

void setup_pert_foldtree

(

core::pose::Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::f, pep_end(), and beta_nonlocal::pose.

Referenced by DougsDockDesignMinimizeMagicMover::apply(), A3BHbsCreatorMover::apply(), A3BHbsDockDesignMinimizeMover::apply(), TrizaolamerDockDesignMinimizeMover::apply(), HotspotPlacementMover::apply(), HbsDesignMover::apply(), OopDesignMover::apply(), and PeptoidDesignMover::apply().

Variable Documentation

TR

basic::Tracer TR("A3BHBS_Creator") ( "A3BHBS_Creator"  )

static

Referenced by A3BHbsCreatorMover::add_hbond_and_omega_constraints_starting_at_seqpos(), alpha_to_beta(), A3BHbsCreatorMover::apply(), A3BHbsCreatorMover::do_mc(), A3BHbsCreatorMover::make_a3b_pose(), and A3BHbsCreatorMover::scan().