sweep_respair_energies.cc File Reference

#include <devel/init.hh>
#include <core/chemical/AtomType.fwd.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/scoring/EnergyGraph.fwd.hh>
#include <core/scoring/MinimizationGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreTypeManager.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/optimization/MinimizerMap.hh>
#include <protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.hh>
#include <protocols/toolbox/match_enzdes_util/ExternalGeomSampler.hh>
#include <protocols/toolbox/match_enzdes_util/LigandConformer.hh>
#include <numeric/random/random.hh>
#include <numeric/constants.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/database/sql_utils.hh>
#include <basic/database/schema_generator/DbDataType.hh>
#include <basic/database/schema_generator/PrimaryKey.hh>
#include <basic/database/schema_generator/ForeignKey.hh>
#include <basic/database/schema_generator/Column.hh>
#include <basic/database/schema_generator/Schema.hh>
#include <utility/sql_database/DatabaseSessionManager.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/LexicographicalIterator.hh>
#include <fstream>
#include <cppdb/frontend.h>
#include <boost/uuid/uuid.hpp>
#include <ObjexxFCL/format.hh>
#include <boost/uuid/random_generator.hpp>

Classes
class	hbgeom_to_measure
class	local_minimum
struct	sort_minima_by_scores

Typedefs
using	hbgeoms_to_measure = utility::vector1< hbgeom_to_measure >
using	HTReal = numeric::HomogeneousTransform< core::Real >

Functions
void	create_schema (utility::sql_database::sessionOP db_session)
void	write_score_types_to_database (utility::sql_database::sessionOP db_session)
void	write_hbgeom_types_to_database (utility::sql_database::sessionOP db_session)
boost::uuids::uuid	write_new_respair_to_database (utility::sql_database::sessionOP db_session, protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo const &mcfi)
	return the new respair_id uuid created by this insertion More...
void	write_hbgeom_to_db (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, std::string const &geom_name, core::Real geometry)
void	write_ahdist_to_db (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, core::conformation::Residue const &acc_res, core::conformation::Residue const &don_res, core::Size acc_ind, core::Size hdon_ind)
void	write_AHD_to_db (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, core::conformation::Residue const &acc_res, core::conformation::Residue const &don_res, core::Size acc_ind, core::Size hdon_ind, core::Size don_ind)
void	write_BAH_to_db (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, core::conformation::Residue const &acc_res, core::conformation::Residue const &don_res, core::Size acc_base, core::Size acc_ind, core::Size hdon_ind)
void	write_chi_to_db (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, core::conformation::Residue const &acc_res, core::conformation::Residue const &don_res, core::Size acc_base2, core::Size acc_base, core::Size acc_ind, core::Size hdon_ind)
void	write_hbgeoms_to_database (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, core::pose::Pose const &pose, hbgeoms_to_measure const &geoms, core::Size res1ind, core::Size res2ind)
void	write_respair_scores_to_database (utility::sql_database::sessionOP db_session, boost::uuids::uuid const conf_id, core::scoring::ScoreFunction const &sfxn, core::pose::Pose &pose, core::Size res1ind, core::Size res2ind)
void	write_scores_and_hbond_geoms_to_database (utility::sql_database::sessionOP db_session, boost::uuids::uuid const respair_id, core::scoring::ScoreFunction const &sfxn, core::pose::Pose &pose, hbgeoms_to_measure const &geoms, core::Size res1ind, core::Size res2ind)
void	populate_database_with_dummy_data (utility::sql_database::sessionOP db_session)
hbgeoms_to_measure	create_fullcoverage_hbgeoms_to_measure (core::pose::Pose const &pose, protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo const &mcfi, core::Size acc_id, core::Size don_id)
	assumes that the geometry is specified between the donor and the acceptor; this is not necessarily true! FIX THIS so that the hbond geometry can be defined independently of the mat More...
core::Real	score_residue_pair (core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::Size const res1_index, core::Size const res2_index)
core::Real	build_and_score_res1_against_res2 (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, HTReal const &htend, core::Size res1_index, core::Size res2_index, protocols::toolbox::match_enzdes_util::LigandConformer const &res1_geom)
bool	determine_if_at_local_minimum_numeric (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, protocols::toolbox::match_enzdes_util::ExternalGeomSamplerCOP exgeom, HTReal const &launch, core::Size res1_index, core::Size res2_index, utility::LexicographicalIterator const &lex, protocols::toolbox::match_enzdes_util::LigandConformer const &res1_geom, core::Real &score)
void	create_mingraph_for_focused_residue_pair (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::Size res1_index, core::Size res2_index, core::optimization::MinimizerMapOP &minimizer_map, core::scoring::MinimizationGraphOP &mingraph)
core::Real	gradient_magnitude_for_conformation (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::Size res1_index, core::Size res2_index, core::optimization::MinimizerMapOP &minimizer_map, core::scoring::MinimizationGraphOP &mingraph)
bool	determine_if_at_local_minimum_analytic (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, protocols::toolbox::match_enzdes_util::ExternalGeomSamplerCOP exgeom, HTReal const &launch, core::Size res1_index, core::Size res2_index, utility::LexicographicalIterator const &lex, protocols::toolbox::match_enzdes_util::LigandConformer const &res1_geom, core::optimization::MinimizerMapOP minimizer_map, core::scoring::MinimizationGraphOP mingraph, core::Real &score)
bool	same_coordinates (core::conformation::Residue const &r1, core::conformation::Residue const &r2, core::Real tolerance)
std::list< local_minimum >	trim_redundant_local_minima (std::list< local_minimum > const &input_minima, core::Real tolerance)
void	output_local_minima (core::pose::Pose &pose, std::list< local_minimum > &local_minima, std::string const &acc3let, std::string const &don3let, core::Size res1_index)
void	sweep_params_from_match_constraint_file (utility::sql_database::sessionOP db_session, core::scoring::ScoreFunction const &sfxn, std::string const &cst_fname)
int	main (int argc, char *argv[])

Typedef Documentation

hbgeoms_to_measure

using hbgeoms_to_measure = utility::vector1<hbgeom_to_measure>

HTReal

using HTReal = numeric::HomogeneousTransform<core::Real>

Function Documentation

build_and_score_res1_against_res2()

core::Real build_and_score_res1_against_res2	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		HTReal const &	htend,
		core::Size	res1_index,
		core::Size	res2_index,
		protocols::toolbox::match_enzdes_util::LigandConformer const &	res1_geom
	)

References create_a3b_hbs::ii, beta_nonlocal::pose, score_residue_pair(), and test.T120_core::sfxn.

Referenced by determine_if_at_local_minimum_analytic(), and determine_if_at_local_minimum_numeric().

create_fullcoverage_hbgeoms_to_measure()

hbgeoms_to_measure create_fullcoverage_hbgeoms_to_measure	(	core::pose::Pose const &	pose,
		protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo const &	mcfi,
		core::Size	acc_id,
		core::Size	don_id
	)

assumes that the geometry is specified between the donor and the acceptor; this is not necessarily true! FIX THIS so that the hbond geometry can be defined independently of the mat

References hbgeom_to_measure::hbgeoms_, beta_nonlocal::pose, hbgeom_to_measure::r1atind, and hbgeom_to_measure::r2atind.

Referenced by sweep_params_from_match_constraint_file().

create_mingraph_for_focused_residue_pair()

void create_mingraph_for_focused_residue_pair	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::Size	res1_index,
		core::Size	res2_index,
		core::optimization::MinimizerMapOP &	minimizer_map,
		core::scoring::MinimizationGraphOP &	mingraph
	)

References beta_nonlocal::mm, beta_nonlocal::pose, and test.T120_core::sfxn.

Referenced by sweep_params_from_match_constraint_file().

create_schema()

void create_schema

(

utility::sql_database::sessionOP

db_session

)

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), erraser_analysis::res1, erraser_analysis::res2, and basic::database::schema_generator::Schema::write().

Referenced by main().

determine_if_at_local_minimum_analytic()

bool determine_if_at_local_minimum_analytic	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		protocols::toolbox::match_enzdes_util::ExternalGeomSamplerCOP	exgeom,
		HTReal const &	launch,
		core::Size	res1_index,
		core::Size	res2_index,
		utility::LexicographicalIterator const &	lex,
		protocols::toolbox::match_enzdes_util::LigandConformer const &	res1_geom,
		core::optimization::MinimizerMapOP	minimizer_map,
		core::scoring::MinimizationGraphOP	mingraph,
		core::Real &	score
	)

References build_and_score_res1_against_res2(), gradient_magnitude_for_conformation(), beta_nonlocal::pose, test.T120_core::sfxn, and numeric::HomogeneousTransform< T >::walk_along_z().

Referenced by sweep_params_from_match_constraint_file().

determine_if_at_local_minimum_numeric()

bool determine_if_at_local_minimum_numeric	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		protocols::toolbox::match_enzdes_util::ExternalGeomSamplerCOP	exgeom,
		HTReal const &	launch,
		core::Size	res1_index,
		core::Size	res2_index,
		utility::LexicographicalIterator const &	lex,
		protocols::toolbox::match_enzdes_util::LigandConformer const &	res1_geom,
		core::Real &	score
	)

References build_and_score_res1_against_res2(), utility::LexicographicalIterator::dimsize(), beta_nonlocal::pose, test.T120_core::sfxn, and numeric::HomogeneousTransform< T >::walk_along_z().

gradient_magnitude_for_conformation()

core::Real gradient_magnitude_for_conformation	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::Size	res1_index,
		core::Size	res2_index,
		core::optimization::MinimizerMapOP &	minimizer_map,
		core::scoring::MinimizationGraphOP &	mingraph
	)

References create_a3b_hbs::ii, beta_nonlocal::pose, and test.T120_core::sfxn.

Referenced by determine_if_at_local_minimum_analytic().

main()

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

References argv, basic::options::OptionKeys::chemical::chemical, create_schema(), test.T009_Exceptions::e, PREcst::fname, basic::database::get_db_session(), create_a3b_hbs::ii, basic::init(), in::file::l(), NEW_OPT, basic::options::option, option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::database::set_cache_size(), test.T120_core::sfxn, sweep_params_from_match_constraint_file(), write_hbgeom_types_to_database(), and write_score_types_to_database().

output_local_minima()

void output_local_minima	(	core::pose::Pose &	pose,
		std::list< local_minimum > &	local_minima,
		std::string const &	acc3let,
		std::string const &	don3let,
		core::Size	res1_index
	)

References count, ObjexxFCL::format::I(), create_a3b_hbs::ii, natoms(), erraser_single_res_analysis::out, beta_nonlocal::pose, and trim_redundant_local_minima().

Referenced by sweep_params_from_match_constraint_file().

populate_database_with_dummy_data()

void populate_database_with_dummy_data

(

utility::sql_database::sessionOP

db_session

)

A function to populate the database with fake data in order to write the R scripts that will be necessary to visualize the data that will be generated by this program.

References dist(), create_a3b_hbs::ii, beta_nonlocal::jj, max(), min(), numeric::constants::d::pi, ObjexxFCL::pow(), numeric::random::rg(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), and basic::options::OptionKeys::blivens::score_type.

same_coordinates()

bool same_coordinates	(	core::conformation::Residue const &	r1,
		core::conformation::Residue const &	r2,
		core::Real	tolerance
	)

References create_a3b_hbs::ii, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by trim_redundant_local_minima().

score_residue_pair()

core::Real score_residue_pair	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::Size const	res1_index,
		core::Size const	res2_index
	)

References test.T200_Scoring::emap, beta_nonlocal::pose, and test.T120_core::sfxn.

Referenced by build_and_score_res1_against_res2().

sweep_params_from_match_constraint_file()

void sweep_params_from_match_constraint_file	(	utility::sql_database::sessionOP	db_session,
		core::scoring::ScoreFunction const &	sfxn,
		std::string const &	cst_fname
	)

References utility::LexicographicalIterator::at_end(), utility::LexicographicalIterator::begin(), create_a3b_hbs::best_pose, create_a3b_hbs::best_score, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, create_fullcoverage_hbgeoms_to_measure(), create_mingraph_for_focused_residue_pair(), determine_if_at_local_minimum_analytic(), test.T200_Scoring::emap, create_a3b_hbs::ii, utility::LexicographicalIterator::num_states_total(), basic::options::option, output_local_minima(), beta_nonlocal::pose, res, local_minimum::res1_conformation, erraser_analysis::res2, basic::options::OptionKeys::in::file::residue_type_set, create_a3b_hbs::score, local_minimum::score_, test.T120_core::sfxn, utility::to_string(), numeric::HomogeneousTransform< T >::walk_along_z(), write_new_respair_to_database(), and write_scores_and_hbond_geoms_to_database().

Referenced by main().

trim_redundant_local_minima()

std::list< local_minimum > trim_redundant_local_minima	(	std::list< local_minimum > const &	input_minima,
		core::Real	tolerance
	)

References erraser_util::copy(), create_a3b_hbs::ii, beta_nonlocal::jj, same_coordinates(), and basic::options::OptionKeys::loops::ccd::tolerance.

Referenced by output_local_minima().

write_AHD_to_db()

void write_AHD_to_db	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		core::conformation::Residue const &	acc_res,
		core::conformation::Residue const &	don_res,
		core::Size	acc_ind,
		core::Size	hdon_ind,
		core::Size	don_ind
	)

References numeric::angle_radians(), and write_hbgeom_to_db().

Referenced by write_hbgeoms_to_database().

write_ahdist_to_db()

void write_ahdist_to_db	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		core::conformation::Residue const &	acc_res,
		core::conformation::Residue const &	don_res,
		core::Size	acc_ind,
		core::Size	hdon_ind
	)

References dist(), and write_hbgeom_to_db().

Referenced by write_hbgeoms_to_database().

write_BAH_to_db()

void write_BAH_to_db	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		core::conformation::Residue const &	acc_res,
		core::conformation::Residue const &	don_res,
		core::Size	acc_base,
		core::Size	acc_ind,
		core::Size	hdon_ind
	)

References numeric::angle_radians(), and write_hbgeom_to_db().

Referenced by write_hbgeoms_to_database().

write_chi_to_db()

void write_chi_to_db	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		core::conformation::Residue const &	acc_res,
		core::conformation::Residue const &	don_res,
		core::Size	acc_base2,
		core::Size	acc_base,
		core::Size	acc_ind,
		core::Size	hdon_ind
	)

References numeric::dihedral_radians(), and write_hbgeom_to_db().

Referenced by write_hbgeoms_to_database().

write_hbgeom_to_db()

void write_hbgeom_to_db	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		std::string const &	geom_name,
		core::Real	geometry
	)

References basic::options::OptionKeys::mp::geometry, basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Referenced by write_AHD_to_db(), write_ahdist_to_db(), write_BAH_to_db(), and write_chi_to_db().

write_hbgeom_types_to_database()

void write_hbgeom_types_to_database

(

utility::sql_database::sessionOP

db_session

)

References basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Referenced by main().

write_hbgeoms_to_database()

void write_hbgeoms_to_database	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		core::pose::Pose const &	pose,
		hbgeoms_to_measure const &	geoms,
		core::Size	res1ind,
		core::Size	res2ind
	)

References create_a3b_hbs::ii, beta_nonlocal::jj, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, write_AHD_to_db(), write_ahdist_to_db(), write_BAH_to_db(), and write_chi_to_db().

Referenced by write_scores_and_hbond_geoms_to_database().

write_new_respair_to_database()

boost::uuids::uuid write_new_respair_to_database	(	utility::sql_database::sessionOP	db_session,
		protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo const &	mcfi
	)

return the new respair_id uuid created by this insertion

References numeric::random::rg(), basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Referenced by sweep_params_from_match_constraint_file().

write_respair_scores_to_database()

void write_respair_scores_to_database	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	conf_id,
		core::scoring::ScoreFunction const &	sfxn,
		core::pose::Pose &	pose,
		core::Size	res1ind,
		core::Size	res2ind
	)

References test.T200_Scoring::emap, create_a3b_hbs::ii, beta_nonlocal::pose, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), basic::options::OptionKeys::frags::scoring::scoring, and test.T120_core::sfxn.

Referenced by write_scores_and_hbond_geoms_to_database().

write_score_types_to_database()

void write_score_types_to_database

(

utility::sql_database::sessionOP

db_session

)

write to database all the score types possible; there may be overlap if this is called multiple times on a single database, (e.g. multiple invocations) so I'm using the "INSERT OR IGNORE" SQL statement. This code is basically a complete rip off of ScoreTypeFeatures::insert_score_type_rows

References enumerate_junctions::default, utility::sql_database::DatabaseMode::mysql, utility::sql_database::name_from_database_mode(), utility::sql_database::DatabaseMode::postgres, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), basic::options::OptionKeys::blivens::score_type, basic::options::OptionKeys::frags::scoring::scoring, utility::sql_database::DatabaseMode::sqlite3, and utility_exit_with_message.

Referenced by main().

write_scores_and_hbond_geoms_to_database()

void write_scores_and_hbond_geoms_to_database	(	utility::sql_database::sessionOP	db_session,
		boost::uuids::uuid const	respair_id,
		core::scoring::ScoreFunction const &	sfxn,
		core::pose::Pose &	pose,
		hbgeoms_to_measure const &	geoms,
		core::Size	res1ind,
		core::Size	res2ind
	)

References beta_nonlocal::pose, numeric::random::rg(), basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), test.T120_core::sfxn, write_hbgeoms_to_database(), and write_respair_scores_to_database().

Referenced by sweep_params_from_match_constraint_file().