gen_apo_grids.cc File Reference

search pocket and generate grids More...

#include <string>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.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 <basic/options/keys/packstat.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <utility/exit.hh>
#include <core/scoring/methods/EnergyMethodOptions.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
void	assure (std::ifstream &in, const char *filename="")
void	assure (std::ofstream &in, const char *filename="")
int	main (int argc, char *argv[])

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

Detailed Description

search pocket and generate grids

Author

Yuan Liu @detail 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

MAXCAVN

#define MAXCAVN   6

MAXRESD

#define MAXRESD   5.0

MINNRES

#define MINNRES   2

T_FACTOR

#define T_FACTOR   2.0

THRESHOLD

#define THRESHOLD   10.0

Function Documentation

assure() [1/2]

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

inline

References utility::options::OptionKeys::options::exit, lactamize::filename, and fprintf().

Referenced by main().

assure() [2/2]

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

inline

References utility::options::OptionKeys::options::exit, lactamize::filename, and fprintf().

main()

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

References argv, assure(), basic::options::OptionKeys::packstat::cavity_burial_probe_radius, basic::options::OptionKeys::packstat::cluster_min_volume, compute_sasa(), extract_by_sidechain_sasa_score::cutoff, kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, 3d_histogram::dx, 3d_histogram::dy, 3d_histogram::dz, test.T009_Exceptions::e, lactamize::filename, kmeans_adaptive_kernel_density_bb_dependent_rotlib::flag, create_a3b_hbs::i, basic::init(), enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, numeric::xyzVector< T >::length_squared(), numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, MAXCAVN, MAXRESD, basic::options::OptionKeys::packstat::min_cav_ball_radius, basic::options::OptionKeys::packstat::min_cluster_overlap, MINNRES, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, ObjexxFCL::pow(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::pr, basic::options::OptionKeys::cluster::radius, res, in::file::s(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::sigma, subloop_histogram::size, 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, x, xx, basic::options::OptionKeys::in::file::xyz, predPRE::y, yy, predPRE::z, and test.T110_numeric::zz.

Variable Documentation

TR

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

static

Referenced by main().