iterhybrid_selector.cc File Reference

#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/util.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/scoring/rms_util.hh>
#include <protocols/wum/SilentStructStore.hh>
#include <protocols/mpi_refinement/util.hh>
#include <protocols/mpi_refinement/MultiObjective.hh>
#include <core/types.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/io/ozstream.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <cstdio>

Functions
void	get_gremlin_d_and_width (std::string const &aa1, std::string const &aa2, core::Real &d0, core::Real &width)
bool	check_silent_error (core::io::silent::SilentStructOP ss)
core::Size	get_min_index (utility::vector1< core::Real > const &scores, utility::vector1< bool > const &redundant)
core::Real	distance (core::io::silent::SilentStructCOP ss1, core::io::silent::SilentStructCOP ss2, std::string const &mode="Score", core::Real const dbase2=4.0)
core::Size	check_redundant (core::Size iss, protocols::wum::SilentStructStore const &library_in, utility::vector1< bool > &redundant, core::Real const dcut)
void	retag (protocols::wum::SilentStructStore &library_inout, std::string const &scorename)
protocols::wum::SilentStructStore	read_library_simple (std::string const &silentfile)
protocols::wum::SilentStructStore	read_library_w_simpose (std::string const &silentfile, core::pose::Pose const &pose0)
protocols::wum::SilentStructStore	read_silent_input_as_library (std::string const &silentfile, core::pose::Pose const &pose0, utility::vector1< core::Real > &scores, core::Real const dcut_ref, std::string const &scorename, core::Size const keep_topn)
utility::vector1< core::Real >	get_quota_per_silent (core::Size const nsilent, core::Size const nout)
protocols::wum::SilentStructStore	energy_cluster (protocols::wum::SilentStructStore const &library_in, core::Size const npick, utility::vector1< core::Real > const &scores, core::Real const dcut_in, std::string const &scorename)
utility::vector1< std::pair < core::Size, core::Size > >	get_contact_list (core::pose::Pose const &pose, utility::vector1< std::pair< core::Real, core::Real > > &d0ws)
void	get_contact_devs (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &contacts, utility::vector1< std::pair< core::Real, core::Real > > const &d0ws, utility::vector1< utility::vector1< core::Real > > &contact_devs)
void	report_and_dump (protocols::wum::SilentStructStore const &library_inout, core::pose::Pose const &pose0, bool const dump_cst, bool const is_iterative_selection)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("app.public.iterhybrid_selector")

Function Documentation

core::Size check_redundant	(	core::Size	iss,
		protocols::wum::SilentStructStore const &	library_in,
		utility::vector1< bool > &	redundant,
		core::Real const	dcut
	)

References distance(), basic::options::OptionKeys::mh::match::ss1, and basic::options::OptionKeys::mh::match::ss2.

Referenced by energy_cluster().

bool check_silent_error

(

core::io::silent::SilentStructOP

ss

)

References ObjexxFCL::abs(), and basic::options::OptionKeys::in::file::xyz.

Referenced by read_silent_input_as_library().

core::Real distance	(	core::io::silent::SilentStructCOP	ss1,
		core::io::silent::SilentStructCOP	ss2,
		std::string const &	mode = "Score",
		core::Real const	dbase2 = 4.0
	)

References basic::options::OptionKeys::dna::specificity::mode, clean_pdb_keep_ligand::nres, basic::options::OptionKeys::AnchoredDesign::rmsd, and ObjexxFCL::FArray< T >::size().

Referenced by calculate_burial(), check_redundant(), find_residues_around_mutation(), utility::vector1< bool, A >::index(), utility::vector1< numeric::urs_Quat >::index(), utility::graph::RingDetection< Graph >::LengthOfSmallestCycleWithVertex(), main(), FragmentAssemblyMover::run(), utility::keys::ClassKeyVector< K, T, C >::sort(), sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), sphere_FA_nc_calculator(), PhProtocol::titrate_pH(), utility::graph::RingSizeVisitor< Graph, DistanceMap, LabelMap >::tree_edge(), and apps::public1::scenarios::chemically_conjugated_docking::ubq_ras_distance().

protocols::wum::SilentStructStore energy_cluster	(	protocols::wum::SilentStructStore const &	library_in,
		core::Size const	npick,
		utility::vector1< core::Real > const &	scores,
		core::Real const	dcut_in,
		std::string const &	scorename
	)

References check_redundant(), get_min_index(), utility::vectorL< SSize, T, A >::has(), test.T008_Serialization::iss, basic::options::OptionKeys::mh::match::ss, and basic::options::TR.

Referenced by main().

void get_contact_devs	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	contacts,
		utility::vector1< std::pair< core::Real, core::Real > > const &	d0ws,
		utility::vector1< utility::vector1< core::Real > > &	contact_devs
	)

References basic::options::OptionKeys::frags::contacts::contacts, assign_charges::first, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by report_and_dump().

utility::vector1< std::pair< core::Size, core::Size > > get_contact_list	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Real, core::Real > > &	d0ws
	)

References basic::options::OptionKeys::frags::contacts::contacts, get_gremlin_d_and_width(), erraser_analysis::res1, erraser_analysis::res2, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and basic::options::OptionKeys::mp::visualize::width.

Referenced by report_and_dump().

void get_gremlin_d_and_width	(	std::string const &	aa1,
		std::string const &	aa2,
		core::Real &	d0,
		core::Real &	width
	)

References basic::options::OptionKeys::score::fiber_diffraction::a, and basic::options::OptionKeys::score::fiber_diffraction::b.

Referenced by get_contact_list().

core::Size get_min_index	(	utility::vector1< core::Real > const &	scores,
		utility::vector1< bool > const &	redundant
	)

Referenced by energy_cluster(), and read_silent_input_as_library().

utility::vector1< core::Real > get_quota_per_silent	(	core::Size const	nsilent,
		core::Size const	nout
	)

References basic::options::option, basic::options::OptionKeys::cm::quota_per_silent, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

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

References utility::io::oc::cout, basic::options::OptionKeys::constraints::dump_cst_set, test.T009_Exceptions::e, energy_cluster(), get_quota_per_silent(), devel::init(), utility::excn::Exception::msg(), basic::options::OptionKeys::cm::nremain_reset, basic::options::OptionKeys::out::nstruct, basic::options::option, pyrosetta.distributed.io::pose_from_file, erraser_single_res_analysis::prefix, basic::options::OptionKeys::out::prefix, read_library_simple(), read_library_w_simpose(), read_silent_input_as_library(), basic::options::OptionKeys::cm::refsimilarity_cut, report_and_dump(), retag(), basic::options::OptionKeys::mh::path::scores, basic::options::OptionKeys::cm::seeds, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::cm::similarity_cut, amino_acids::size, basic::options::OptionKeys::in::file::template_pdb, basic::options::OptionKeys::in::file::template_silent, and basic::options::OptionKeys::inout::dbms::user.

protocols::wum::SilentStructStore read_library_simple

(

std::string const &

silentfile

)

References basic::options::OptionKeys::mh::match::ss.

Referenced by main().

protocols::wum::SilentStructStore read_library_w_simpose	(	std::string const &	silentfile,
		core::pose::Pose const &	pose0
	)

References demo.D010_Pose_structure::pose, and basic::options::OptionKeys::mh::match::ss.

Referenced by main().

protocols::wum::SilentStructStore read_silent_input_as_library	(	std::string const &	silentfile,
		core::pose::Pose const &	pose0,
		utility::vector1< core::Real > &	scores,
		core::Real const	dcut_ref,
		std::string const &	scorename,
		core::Size const	keep_topn
	)

References check_silent_error(), utility::options::BooleanOptionKey::clone(), utility::vectorL< SSize, T, A >::contains(), pyrosetta::create_score_function, get_min_index(), basic::options::option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, erraser_single_res_analysis::score, basic::options::OptionKeys::out::scorecut, test.T220_AtomAtomPairEnergies::sfxn, basic::options::OptionKeys::mh::match::ss, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::score::weights.

Referenced by main().

void report_and_dump	(	protocols::wum::SilentStructStore const &	library_inout,
		core::pose::Pose const &	pose0,
		bool const	dump_cst,
		bool const	is_iterative_selection
	)

References ObjexxFCL::format::A(), basic::options::OptionKeys::frags::contacts::contacts, basic::options::OptionKeys::constraints::dump_cst_set, ObjexxFCL::format::F(), test.G202_Module_PythonPDB::filename, assign_charges::first, get_contact_devs(), get_contact_list(), test.T110_Numeric::I, local::nstruct, basic::options::option, clean_pdb_keep_ligand::pdbname, erraser_single_res_analysis::prefix, basic::options::OptionKeys::out::prefix, erraser_analysis::res1, erraser_analysis::res2, basic::options::OptionKeys::out::file::silent, basic::options::OptionKeys::mh::match::ss, loops_kic::tol, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and numeric::statistics::w().

Referenced by main().

void retag	(	protocols::wum::SilentStructStore &	library_inout,
		std::string const &	scorename
	)

References test.T008_Serialization::iss, basic::options::option, erraser_single_res_analysis::prefix, basic::options::OptionKeys::out::prefix, basic::options::OptionKeys::mh::match::ss, and numeric::interpolation::to_string().

Referenced by main().

Variable Documentation

basic::Tracer TR("app.public.iterhybrid_selector")

static