matdes_dock.cc File Reference

#include <basic/database/open.hh>
#include <basic/options/keys/holes.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/Jump.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/packing/HolesParams.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <fstream>
#include <iostream>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <protocols/docking/util.hh>
#include <protocols/moves/Mover.hh>
#include <sstream>
#include <string>
#include <utility/io/izstream.hh>
#include <utility/io/mpistream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat

Functions
int	count_int_CBs_clashes (pose::Pose const &pose, Size i, Size j, Real contact_dist, Real clash_dist)
void	move_pose (pose::Pose &pose, Size sym_jump, Vec dt, Real dr=0.0)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("matdes::dock")

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

count_int_CBs_clashes()

int count_int_CBs_clashes	(	pose::Pose const &	pose,
		Size	i,
		Size	j,
		Real	contact_dist,
		Real	clash_dist
	)

References basic::options::OptionKeys::matdes::design::contact_dist, numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, make_symmdef_file_denovo::nsub, beta_nonlocal::pose, and utility_exit_with_message.

Referenced by main().

main()

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

References matdes::angle(), oop_conformations::angles, argv, count_int_CBs_clashes(), matdes::dock::dump_chainA_only(), matdes::dock::dump_pdb(), test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, basic::init(), subloop_histogram::iterator, create_a3b_hbs::j, make_symmdef_file_denovo::jump_num, move_pose(), matdes::dock::neg_r(), matdes::num_subs_building_block(), matdes::num_subs_total(), offset, option, erraser_single_res_analysis::out, matdes::pdbID(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, matdes::prefix(), create_a3b_hbs::r, basic::options::OptionKeys::matdes::radial_disp, matdes::radial_disp(), in::file::s(), ObjexxFCL::string_of(), basic::options::OptionKeys::symmetry::symmetry, TR, and utility_exit_with_message.

move_pose()

void move_pose	(	pose::Pose &	pose,
		Size	sym_jump,
		Vec	dt,
		Real	dr = 0.0
	)

References create_a3b_hbs::j, beta_nonlocal::pose, create_a3b_hbs::r, predPRE::t, and numeric::x_rotation_matrix_degrees().

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("matdes::dock") ( "matdes::dock"  )

static

Referenced by main().