gen_apo_grids.cc File Reference

search pocket and generate grids More...

#include <iostream>
#include <map>
#include <string>
#include <sstream>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/io/pdb/build_pose_as_is.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoringManager.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <basic/options/keys/packstat.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <utility/exit.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <fstream>
#include <utility/excn/Exceptions.hh>

Macros
#define	MAXCAVN   6
#define	MAXRESD   5.0
#define	T_FACTOR   2.0
#define	THRESHOLD   10.0
#define	MINNRES   2

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.match.gen_apo_grids")
void	assure (std::ifstream &in, const char *filename="")
void	assure (std::ofstream &in, const char *filename="")
int	main (int argc, char *argv[])

Detailed Description

search pocket and generate grids

Author

Yuan Liu flags example -mute all -unmute apps.pilot.wendao.gen_apo_grids -chname off -constant_seed -ignore_unrecognized_res -packstat:surface_accessibility -packstat:cavity_burial_probe_radius 3.0 -packstat:cluster_min_volume 30 -packstat:min_cluster_overlap 1.0 -packstat:min_cav_ball_radius 1.0 -packstat:min_surface_accessibility 1.4

Macro Definition Documentation

#define MAXCAVN   6

Referenced by main().

#define MAXRESD   5.0

Referenced by main().

#define MINNRES   2

Referenced by main().

#define T_FACTOR   2.0

Referenced by main().

#define THRESHOLD   10.0

Referenced by main().

Function Documentation

void assure ( std::ifstream &  in, const char *  filename = ""  )

inline

References utility::options::OptionKeys::options::exit, test.G202_Module_PythonPDB::filename, and fmt::fprintf().

Referenced by main().

void assure ( std::ofstream &  in, const char *  filename = ""  )

inline

References utility::options::OptionKeys::options::exit, test.G202_Module_PythonPDB::filename, and fmt::fprintf().

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

References assure(), basic::options::OptionKeys::packstat::cavity_burial_probe_radius, basic::options::OptionKeys::packstat::cluster_min_volume, utility::io::oc::cout, basic::options::OptionKeys::cp::cutoff, test.G202_Module_PythonPDB::filename, devel::init(), basic::options::OptionKeys::frags::j, basic::options::OptionKeys::in::file::l, numeric::xyzVector< typename >::length_squared(), numeric::log(), MAXCAVN, MAXRESD, basic::options::OptionKeys::packstat::min_cav_ball_radius, basic::options::OptionKeys::packstat::min_cluster_overlap, MINNRES, utility::excn::EXCN_Base::msg(), option, demo.D010_Pose_structure::pose, ObjexxFCL::pow(), test.T500_Packing::pr, basic::options::OptionKeys::cluster::radius, res, in::file::s(), erraser_single_res_analysis::score, erraser_analysis::sigma, basic::options::OptionKeys::out::suffix, basic::options::OptionKeys::packstat::surface_accessibility, T_FACTOR, THRESHOLD, utility::to_string(), TR(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, numeric::crick_equations::x(), basic::options::OptionKeys::in::file::xyz, numeric::crick_equations::y(), and numeric::crick_equations::z().

static THREAD_LOCAL basic::Tracer TR ( "apps.public.match.gen_apo_grids"  )

static

Referenced by main().