simon_darc_minimize.cc File Reference

#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/Pose.hh>
#include <basic/MetricValue.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/after_opts.hh>
#include <utility/excn/Exceptions.hh>
#include <protocols/simple_moves/ScoreMover.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculator.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/pose_metric_calculators/PackstatCalculator.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <ostream>
#include <string>
#include <sstream>
#include <cmath>
#include <map>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>

Functions
void	define_interface (core::pose::Pose &ref_pose)
bool	is_interface_heavyatom (core::pose::Pose const &pose, core::pose::Pose const &, core::Size resno, core::Size atomno)
Real	calpha_pdb_superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose)
Real	interface_rmsd (pose::Pose &mod_pose, pose::Pose const &ref_pose)
Real	get_lig_rmsd (pose::Pose &mod_pose, pose::Pose const &ref_pose, Size lig_res_num)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.ragul_darc_minimize.main")
std::set< std::string >	interface
core::Size	lig_res_num

Function Documentation

calpha_pdb_superimpose_pose()

Real calpha_pdb_superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose
	)

References create_a3b_hbs::ii, beta_nonlocal::jj, and superimpose_pose().

Referenced by main().

define_interface()

void define_interface

(

core::pose::Pose &

ref_pose

)

References test.T200_Scoring::emap, utility::options::OptionKeys::options::exit, utility::graph::Edge::get_node(), interface, create_a3b_hbs::j, lig_res_num, utility::graph::Node::lower_edge_list_end(), predPRE::resnum, and TR.

Referenced by main().

get_lig_rmsd()

Real get_lig_rmsd	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		Size	lig_res_num
	)

References create_a3b_hbs::i, create_a3b_hbs::k, lig_res_num, natoms(), and numeric::model_quality::rms_wrapper().

Referenced by main().

interface_rmsd()

Real interface_rmsd	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, is_interface_heavyatom(), create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, natoms(), and numeric::model_quality::rms_wrapper().

Referenced by main().

is_interface_heavyatom()

bool is_interface_heavyatom	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	,
		core::Size	resno,
		core::Size	atomno
	)

References interface, and beta_nonlocal::pose.

Referenced by interface_rmsd().

main()

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

References argv, utility::vectorL< L, T, A >::at(), calpha_pdb_superimpose_pose(), utility::io::ozstream::clear(), utility::io::ozstream::close(), utility::io::oc::cout, define_interface(), test.T009_Exceptions::e, basic::options::OptionKeys::score::empty, create_a3b_hbs::f, get_lig_rmsd(), create_a3b_hbs::i, create_a3b_hbs::ii, basic::init(), interface_rmsd(), lig_res_num, NEW_OPT, create_a3b_hbs::nres, utility::io::ozstream::open(), option, erraser_single_res_analysis::out, drrafter_rna::output_tag, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::carbohydrates::glycopeptide_docking::score_only, oop_conformations::scorefxn, basic::options::start_files(), tag, TR, pna::trans_mover, and basic::MetricValue< T >::value().

Variable Documentation

interface

std::set<std::string> interface

Referenced by define_interface(), and is_interface_heavyatom().

lig_res_num

core::Size lig_res_num

Referenced by define_interface(), get_lig_rmsd(), and main().

TR

basic::Tracer TR("apps.pilot.ragul_darc_minimize.main") ( "apps.pilot.ragul_darc_minimize.main"  )

static

Referenced by define_interface(), and main().