cxdesign.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <basic/options/keys/matdes.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/func/XYZ_Func.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sc/ShapeComplementarityCalculator.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <numeric/conversions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <sys/stat.h>
#include <utility/excn/Exceptions.hh>
#include <apps/pilot/will/sicfast.ihh>

Classes
struct	Hit

Typedefs
typedef numeric::xyzVector< Real >	Vecf
typedef numeric::xyzMatrix< Real >	Matf

Functions
	OPT_1GRP_KEY (Integer, cxdock, sphere) void register_options()
bool	cmp (Hit i, Hit j)
void	new_sc (core::pose::Pose &pose, int nmono, Real &int_area, Real &sc)
Real	average_degree (Pose const &pose, Size nmono, vector1< Size > mutalyze_pos, Real distance_threshold=8.0)
vector1< Size >	design (Pose &p, Size nmono, Size nsym)
void	repack (Pose &p, Size nmono, vector1< Size > const &iface)
void	minimize (Pose &pose, utility::vector1< Size > const &iface)
Real	get_ddg (Pose p, Size nmono, vector1< Size > const &iface)
void	cxdock_design (Pose const init, std::string const &fn, vector1< xyzVector< double > > const &ssamp, int iss, int irt, int ic, Real cbc)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("pentcb")
static core::io::silent::SilentFileData	sfd

Typedef Documentation

Matf

typedef numeric::xyzMatrix<Real> Matf

Vecf

typedef numeric::xyzVector<Real> Vecf

Function Documentation

average_degree()

Real average_degree	(	Pose const &	pose,
		Size	nmono,
		vector1< Size >	mutalyze_pos,
		Real	distance_threshold = 8.0
	)

References count_neighbors(), build_jacobian::distance, create_a3b_hbs::i, beta_nonlocal::pose, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by cxdock_design().

cmp()

bool cmp	(	Hit	i,
		Hit	j
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by arls_impl.DockingFile::__cmp__(), compare_cartesian_rmsd(), compare_frags_pose(), best_ifaceE::main(), and prune_atdiff_top5pct::main().

cxdock_design()

void cxdock_design	(	Pose const	init,
		std::string const &	fn,
		vector1< xyzVector< double > > const &	ssamp,
		int	iss,
		int	irt,
		int	ic,
		Real	cbc
	)

References average_degree(), design(), basic::options::OptionKeys::magnesium::montecarlo::dump, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_ddg(), has, create_a3b_hbs::i, basic::init(), test.T008_Serialization::iss, subloop_histogram::iterator, minimize(), new_sc(), basic::options::OptionKeys::out::file::o, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::constants::d::pi, pi, docking::R, rot, rot_pose(), numeric::rotation_matrix_degrees(), basic::options::OptionKeys::canonical_sampling::probabilities::sc, sfd, sicfast(), basic::options::OptionKeys::out::file::silent, str(), predPRE::t, tag, tan, trans_pose(), and utility_exit_with_message.

Referenced by main().

design()

vector1<Size> design	(	Pose &	p,
		Size	nmono,
		Size	nsym
	)

References create_a3b_hbs::i, min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by cxdock_design().

get_ddg()

Real get_ddg	(	Pose	p,
		Size	nmono,
		vector1< Size > const &	iface
	)

References create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, make_symmdef_file_denovo::jump_num, minimize(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, repack(), basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::out::sf, and utility_exit_with_message.

Referenced by cxdock_design().

main()

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

References argv, cxdock_design(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, basic::init(), test.T008_Serialization::iss, basic::options::OptionKeys::in::file::l, NSS, basic::database::open(), basic::options::option, pyrosetta.distributed.io::pose_from_file, register_options(), res, str(), basic::options::OptionKeys::symmetry::symmetry_definition, basic::options::TR, trans_pose(), utility_exit_with_message, x, predPRE::y, and predPRE::z.

minimize()

void minimize	(	Pose &	pose,
		utility::vector1< Size > const &	iface
	)

References test.T009_Exceptions::e, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by cxdock_design(), and get_ddg().

new_sc()

void new_sc	(	core::pose::Pose &	pose,
		int	nmono,
		Real &	int_area,
		Real &	sc
	)

References create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::OptionKeys::canonical_sampling::probabilities::sc.

Referenced by cxdock_design().

OPT_1GRP_KEY()

OPT_1GRP_KEY	(	Integer	,
		cxdock	,
		sphere
	)

References basic::options::OptionKeys::crossmatch::clash_dis, basic::options::OptionKeys::sicdock::contact_dis, basic::options::OptionKeys::magnesium::montecarlo::dump, NEW_OPT, OPT, and basic::options::OptionKeys::in::file::s.

repack()

void repack	(	Pose &	p,
		Size	nmono,
		vector1< Size > const &	iface
	)

References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by design(), and get_ddg().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

Referenced by ConstraintMinimizer::apply(), LoopHashRelax_Sampler::apply(), apply_all_frags(), apply_filter_base_stack_direction(), calc_rmsf_and_avrg(), calc_scores(), cluster_rigid_body_settings_test(), cluster_silent_file_data(), cxdock_design(), define_states_test(), dinucleotide_test(), distribute_jobs(), protocols::abinitio::JumpSpecificAbrelax::do_distributed_rerun(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), do_the_match(), doit(), dostuff(), expand_chi_for_silent_structs(), extract_replica(), flxbb_nobu(), initialize_rigid_body_sampler(), main(), make_fragments(), make_sf(), minimize_with_constraints(), my_main(), output_centroid_silent_struct(), ThisApplication::pick_frags(), pose_to_string(), printScoreTermsPose(), processChildren(), processChildrenIntensification(), read_library_simple(), read_library_w_simpose(), read_occupancy_data(), read_silent_input_as_library(), read_structures(), rebuild_centroid_test(), report_and_dump(), rescore_pose(), RotamerAnalysis(), run(), ScoreFragmentSetMover::run(), FragmentAssemblyMover::run(), ConsensusFragmentMover::run(), SolutionRescoreMover::run(), myspace::Scheduler::run_combine(), run_parallel_docking(), save_cluster_tree_lite(), search_translations(), split_silent_file_data(), string_to_pose(), SymmSilentFileTest(), write_for_resnum(), write_output_files(), and myspace::write_silent().

TR

basic::Tracer TR("pentcb") ( "pentcb"  )

static