minimize_ppi.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/SasaCalculatorLegacy.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 <core/scoring/constraints/ConstraintSet.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/kinematics/FoldTree.hh>
#include <core/scoring/func/HarmonicFunc.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 <protocols/simple_moves/SuperimposeMover.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	ligand_rmsd (pose::Pose const &pose1, pose::Pose const &pose2)
int	main (int argc, char *argv[])

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

Function Documentation

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

References test.T200_Scoring::ii.

Referenced by main().

void define_interface

(

core::pose::Pose &

ref_pose

)

References test.T200_Scoring::emap, utility::options::OptionKeys::options::exit, utility::graph::Edge::get_node(), basic::options::OptionKeys::frags::j, utility::graph::Node::lower_edge_list_end(), clean_pdb_keep_ligand::resnum, and TR.

Referenced by main().

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

References debug_assert, test.T200_Scoring::ii, is_interface_heavyatom(), basic::options::OptionKeys::frags::j, and numeric::model_quality::rms_wrapper().

Referenced by main().

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

References interface.

Referenced by interface_rmsd().

Real ligand_rmsd	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2
	)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::frags::j, clean_pdb_keep_ligand::resnum, and basic::options::OptionKeys::AnchoredDesign::rmsd.

Referenced by main(), and DockGlycansProtocol::record_pose_metrics().

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

References utility::vectorL< SSize, T, A >::at(), calpha_pdb_superimpose_pose(), utility::io::ozstream::clear(), utility::io::ozstream::close(), utility::io::oc::cout, basic::options::OptionKeys::templates::cst::cst, basic::options::OptionKeys::constraints::cst_weight, define_interface(), test.T009_Exceptions::e, basic::options::OptionKeys::score::empty, demo.D060_Folding::f, basic::options::OptionKeys::in::file::fold_tree, test.T200_Scoring::ii, devel::init(), interface_rmsd(), ligand_rmsd(), utility::excn::Exception::msg(), NEW_OPT, clean_pdb_keep_ligand::nres, utility::io::ozstream::open(), option, erraser_single_res_analysis::out, basic::options::OptionKeys::out::output_tag, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::out::file::score_only, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::start_files(), tag, TR, and basic::MetricValue< T >::value().

Variable Documentation

std::set<std::string> interface

Referenced by is_interface_heavyatom().

core::Size lig_res_num

Referenced by main().

basic::Tracer TR("apps.pilot.minimize_ppi")

static

Referenced by define_interface(), and main().