heme_binding.cc File Reference

Application to redesign an enzyme to bind an alternative ligand. More...

#include <protocols/moves/Mover.hh>
#include <protocols/backrub/BackrubMover.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/PointGraph.hh>
#include <core/conformation/find_neighbors.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/MultiConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/conversions.hh>
#include <numeric/random/random.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/database/open.hh>

Classes
class	HemeBindingMover

Namespaces
	local

Typedefs
typedef utility::pointer::shared_ptr< HemeBindingMover >	HemeBindingMoverOP
typedef utility::pointer::shared_ptr< HemeBindingMover const >	HemeBindingMoverCOP

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

Variables
static basic::Tracer	TR ("apps.pilot.guffysl.heme_binding")
basic::options::IntegerOptionKey const	local::num_iterations ("num_iterations")
basic::options::RealOptionKey const	local::prob_br_move ("prob_br_move")
basic::options::BooleanOptionKey const	local::add_ligand_constraints ("add_ligand_constraints")
basic::options::StringVectorOptionKey const	local::ligand_cst_atoms ("ligand_cst_atoms")
basic::options::RealOptionKey const	local::dist_cst_weight ("dist_cst_weight")
basic::options::RealOptionKey const	local::dihedral_cst_weight ("dihedral_cst_weight")
basic::options::RealOptionKey const	local::mc_temperature ("mc_temperature")

Detailed Description

Application to redesign an enzyme to bind an alternative ligand.

Mover to replace heme alternative ligand with heme of the appropriate variant and rescore the pose.

Author

Sharon Guffy

Typedef Documentation

HemeBindingMoverCOP

typedef utility::pointer::shared_ptr< HemeBindingMover const > HemeBindingMoverCOP

HemeBindingMoverOP

typedef utility::pointer::shared_ptr< HemeBindingMover > HemeBindingMoverOP

Function Documentation

main()

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

References utility::options::OptionCollection::add(), local::add_ligand_constraints, argv, utility::options::ScalarOption_T_< K, T >::def(), local::dihedral_cst_weight, local::dist_cst_weight, test.T009_Exceptions::e, basic::init(), local::ligand_cst_atoms, local::mc_temperature, local::num_iterations, basic::options::option, local::prob_br_move, and TR.

Variable Documentation

TR

basic::Tracer TR("apps.pilot.guffysl.heme_binding") ( "apps.pilot.guffysl.heme_binding"  )

static

Referenced by HemeBindingMover::add_initial_constraints(), HemeBindingMover::apply(), HemeBindingMover::HemeBindingMover(), HemeBindingMover::initialize_from_options(), and main().