roc_optimizer.cc File Reference

#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <core/optimization/ParticleSwarmMinimizer.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/qsar/scoring_grid/AtrGrid.hh>
#include <protocols/qsar/scoring_grid/RepGrid.hh>
#include <protocols/qsar/scoring_grid/VdwGrid.hh>
#include <protocols/qsar/scoring_grid/HbaGrid.hh>
#include <protocols/qsar/scoring_grid/HbdGrid.hh>
#include <protocols/qsar/qsarOptFunc.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <devel/init.hh>
#include <numeric/roc_curve.hh>
#include <protocols/ligand_docking/Transform.hh>
#include <protocols/ligand_docking/SlideTogether.hh>
#include <protocols/ligand_docking/InterfaceScoreCalculator.hh>
#include <protocols/features/ProteinSilentReport.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <protocols/ligand_docking/StartFrom.hh>
#include <protocols/qsar/scoring_grid/GridSet.hh>
#include <basic/database/sql_utils.hh>
#include <basic/options/option_macros.hh>
#include <utility/io/izstream.hh>
#include <cppdb/frontend.h>

Classes
class	GridWeights

Functions
protocols::qsar::scoring_grid::GridSetCOP	setup_grids (GridWeights const &)
protocols::moves::MoverOP	setup_start_coords ()
protocols::moves::MoverOP	setup_transform_mover (protocols::qsar::scoring_grid::GridSetCOP grid_set)
protocols::moves::MoverOP	setup_slide_mover ()
protocols::moves::MoverOP	setup_score_mover (protocols::qsar::scoring_grid::GridSetCOP grid_set)
protocols::moves::MoverOP	setup_lowres_protocol (GridWeights const &weights)
void	setup_activity_table (utility::sql_database::sessionOP &db_session, std::string const &active_list_filename, std::string const &inactive_list_filename)
numeric::RocCurve	setup_roc_curve (utility::sql_database::sessionOP &db_session, core::Real cutoff)
void	dump_curve_to_db (utility::sql_database::sessionOP &db_session, core::Size const &curve_id, utility::vector1< std::pair< platform::Real, platform::Real > > const &curve)
GridWeights	optimize_weights (core::optimization::Multivec min, core::optimization::Multivec max, core::optimization::Multifunc &fitness, core::optimization::Multivec initial_values)
void	clean_up_database (utility::sql_database::sessionOP &db_session)
void	write_weights_to_db (utility::sql_database::sessionOP &db_session, GridWeights const &weights, core::Size const &cycle)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	roc_tracer ("ROC_optimizer")

Detailed Description

Author

Sam DeLuca

Function Documentation

clean_up_database()

void clean_up_database

(

utility::sql_database::sessionOP &

db_session

)

References globals::reporter, res, basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

Referenced by main().

dump_curve_to_db()

void dump_curve_to_db	(	utility::sql_database::sessionOP &	db_session,
		core::Size const &	curve_id,
		utility::vector1< std::pair< platform::Real, platform::Real > > const &	curve
	)

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

Referenced by main().

main()

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

References argv, GridWeights::atr(), numeric::RocCurve::calculate_auc(), clean_up_database(), cycle(), dump_curve_to_db(), test.T009_Exceptions::e, numeric::RocCurve::generate_roc_curve(), basic::database::get_db_session(), GridWeights::get_indices(), GridWeights::get_multivec(), GridWeights::hba(), GridWeights::hbd(), basic::init(), utility::mpi_rank(), NEW_OPT, optimize_weights(), basic::options::option, GridWeights::rep(), numeric::RocCurve::roc_curve(), roc_tracer, setup_activity_table(), setup_lowres_protocol(), setup_roc_curve(), GridWeights::vdw(), and write_weights_to_db().

optimize_weights()

GridWeights optimize_weights	(	core::optimization::Multivec	min,
		core::optimization::Multivec	max,
		core::optimization::Multifunc &	fitness,
		core::optimization::Multivec	initial_values
	)

References max(), and min().

Referenced by get_opte_data(), main(), and simple_opte_test().

setup_activity_table()

void setup_activity_table	(	utility::sql_database::sessionOP &	db_session,
		std::string const &	active_list_filename,
		std::string const &	inactive_list_filename
	)

References utility::io::izstream::close(), utility::io::izstream::eof(), getline(), basic::options::OptionKeys::in::in, line, utility::io::izstream::open(), basic::database::safely_prepare_statement(), and basic::database::safely_write_to_database().

Referenced by main().

setup_grids()

protocols::qsar::scoring_grid::GridSetCOP setup_grids

(

GridWeights const &

)

References test.T220_AtomAtomPairEnergies::atr, test.T220_AtomAtomPairEnergies::rep, roc_tracer, and basic::options::OptionKeys::remodel::vdw.

Referenced by setup_lowres_protocol().

setup_lowres_protocol()

protocols::moves::MoverOP setup_lowres_protocol

(

GridWeights const &

weights

)

References setup_grids(), setup_score_mover(), setup_slide_mover(), setup_start_coords(), setup_transform_mover(), and weights().

Referenced by main().

setup_roc_curve()

numeric::RocCurve setup_roc_curve	(	utility::sql_database::sessionOP &	db_session,
		core::Real	cutoff
	)

References extract_by_sidechain_sasa_score::cutoff, numeric::RocCurve::insert_point(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), select_string(), tag, and value.

Referenced by main().

setup_score_mover()

protocols::moves::MoverOP setup_score_mover

(

protocols::qsar::scoring_grid::GridSetCOP

grid_set

)

References chains, and beta_nonlocal::score_fxn.

Referenced by setup_lowres_protocol().

setup_slide_mover()

protocols::moves::MoverOP setup_slide_mover

(

)

References predPRE::chain.

Referenced by setup_lowres_protocol().

setup_start_coords()

protocols::moves::MoverOP setup_start_coords

(

)

References basic::options::option, and basic::options::OptionKeys::docking::ligand::start_from.

Referenced by setup_lowres_protocol().

setup_transform_mover()

protocols::moves::MoverOP setup_transform_mover

(

protocols::qsar::scoring_grid::GridSetCOP

grid_set

)

References basic::options::OptionKeys::hotspot::angle, predPRE::chain, basic::options::OptionKeys::cycles, erraser_analysis::temp, and basic::options::OptionKeys::mp::transform::transform.

Referenced by setup_lowres_protocol().

write_weights_to_db()

void write_weights_to_db	(	utility::sql_database::sessionOP &	db_session,
		GridWeights const &	weights,
		core::Size const &	cycle
	)

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

Referenced by main().

Variable Documentation

roc_tracer

basic::Tracer roc_tracer("ROC_optimizer") ( "ROC_optimizer"  )

static

Referenced by main(), and setup_grids().