johnk_parametrize_geometric_solvation.cc File Reference

#include <devel/init.hh>
#include <core/types.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Atom.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/etable/EtableOptions.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/hbonds/HBEvalTuple.hh>
#include <core/scoring/hbonds/types.hh>
#include <core/scoring/hbonds/constants.hh>
#include <basic/Tracer.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <numeric/constants.hh>
#include <numeric/conversions.hh>
#include <basic/options/option_macros.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>
#include <cmath>
#include <iostream>
#include <iomanip>
#include <map>
#include <core/pose/annotated_sequence.hh>

Classes
struct	GridInfo

Functions
std::string	setup_pdb_line (core::Vector const &atom_pos, core::Size const &atomnum, core::Real const &Bfac)
void	dump_grid_pdb (std::string const &pdb_fname, GridInfo const &grid_info, std::vector< std::vector< std::vector< core::Real > > > const &grid_values)
void	dump_water_grid_file (std::string const &fname, GridInfo const &grid_info, std::vector< std::vector< std::vector< core::Real > > > const &grid_values)
int	main (int argc, char *argv[])
	General testing code. More...

Variables
static basic::Tracer	TR ("apps.pilot.johnk_parametrize_geometric_solvation.main")

Function Documentation

dump_grid_pdb()

void dump_grid_pdb	(	std::string const &	pdb_fname,
		GridInfo const &	grid_info,
		std::vector< std::vector< std::vector< core::Real > > > const &	grid_values
	)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), utility::io::ozstream::open(), erraser_single_res_analysis::out, setup_pdb_line(), GridInfo::xnum_points, GridInfo::xorigin, GridInfo::ynum_points, GridInfo::yorigin, GridInfo::ystep, GridInfo::znum_points, GridInfo::zorigin, and GridInfo::zstep.

Referenced by main().

dump_water_grid_file()

void dump_water_grid_file	(	std::string const &	fname,
		GridInfo const &	grid_info,
		std::vector< std::vector< std::vector< core::Real > > > const &	grid_values
	)

References utility::io::ozstream::clear(), utility::io::ozstream::close(), PREcst::fname, utility::io::ozstream::open(), erraser_single_res_analysis::out, GridInfo::xnum_points, GridInfo::xorigin, GridInfo::xstep, GridInfo::ynum_points, GridInfo::yorigin, GridInfo::ystep, GridInfo::znum_points, GridInfo::zorigin, and GridInfo::zstep.

main()

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

General testing code.

References argv, utility::io::ozstream::clear(), utility::io::ozstream::close(), build_jacobian::distance, measure_params::dot(), dump_grid_pdb(), test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), basic::options::OptionKeys::relax::range::kT, numeric::log(), NEW_OPT, basic::options::OptionKeys::ProQ::normalize, utility::io::ozstream::open(), option, erraser_single_res_analysis::out, beta_nonlocal::pose, numeric::conversions::radians(), basic::options::OptionKeys::in::file::residue_type_set, setup_pdb_line(), td, TR, GridInfo::xnum_points, GridInfo::xorigin, GridInfo::xstep, GridInfo::ynum_points, GridInfo::yorigin, GridInfo::ystep, GridInfo::znum_points, GridInfo::zorigin, and GridInfo::zstep.

setup_pdb_line()

std::string setup_pdb_line	(	core::Vector const &	atom_pos,
		core::Size const &	atomnum,
		core::Real const &	Bfac
	)

References basic::options::OptionKeys::optE::fixed.

Referenced by dump_grid_pdb(), and main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.johnk_parametrize_geometric_solvation.main") ( "apps.pilot.johnk_parametrize_geometric_solvation.main"  )

static

Referenced by main().