test_bbmc.org.cc File Reference

#include <protocols/branch_angle/BranchAngleOptimizer.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/backrub/BackrubMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/ReplicaExchangeMC.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMCMover.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <protocols/canonical_sampling/TrajectoryRecorder.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/PyMOLMover.hh>
#include <protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/MoveMap.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/scoring/mm/MMBondAngleResidueTypeParamSet.hh>
#include <basic/options/option.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <basic/options/option_macros.hh>
#include <core/scoring/rms_util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/methods/RG_Energy_Fast.hh>
#include <protocols/simple_moves/BBGaussianMover.hh>
#include <protocols/simple_moves/BBConRotMover.hh>
#include <utility/io/ozstream.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/FileName.hh>
#include <utility/exit.hh>
#include <numeric/random/random.hh>
#include <numeric/MultiDimensionalHistogram.hh>
#include <platform/types.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/backrub.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/mc.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <protocols/moves/MoverStatistics.hh>
#include <utility/io/mpistream.hh>
#include <fstream>
#include <string>
#include <ObjexxFCL/Fmath.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/prof.hh>

Functions
	OPT_1GRP_KEY (Integer, mc, ntrials) OPT_1GRP_KEY(Real
sm_prob	OPT_1GRP_KEY (Real, mc, backrub_prob) OPT_1GRP_KEY(Real
sm_prob conrot_prob	OPT_1GRP_KEY (Real, mc, kt) OPT_1GRP_KEY(Real
sm_prob conrot_prob mm_bend_weight	OPT_1GRP_KEY (Boolean, mc, detailed_balance) OPT_1GRP_KEY(Boolean
sm_prob conrot_prob mm_bend_weight initial_pack	OPT_1GRP_KEY (File, mc, movemap) OPT_1GRP_KEY(Integer
sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start	OPT_1GRP_KEY (Integer, mc, rmsd_region_stop) OPT_1GRP_KEY(File
sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap	OPT_1GRP_KEY (Integer, mc, score_stride) OPT_1GRP_KEY(Real
sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap fast_sc_prob void *	my_main (void *)
core::Real	periodic_range (core::Real a, core::Real x)
std::string	get_ABGEO_string (core::pose::Pose &p, core::Size start, core::Size stop)
string	get_tag (core::Size itrial, core::Real kT, int rank)
string	get_filename (string const suffix, core::Real t)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("pilot.wendao.bbmc")
	mc

Function Documentation

get_ABGEO_string()

std::string get_ABGEO_string	(	core::pose::Pose &	p,
		core::Size	start,
		core::Size	stop
	)

References ObjexxFCL::abs(), create_a3b_hbs::ii, basic::options::OptionKeys::AnchoredDesign::filters::omega, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, periodic_range(), oop_conformations::phi, oop_conformations::psi, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by my_main().

get_filename()

string get_filename	(	string const	suffix,
		core::Real	t
	)

References utility::file::FileName::base(), end, create_a3b_hbs::i, ObjexxFCL::index(), basic::options::option, runtime_assert, basic::options::OptionKeys::in::file::s, subloop_histogram::size, basic::options::OptionKeys::out::suffix, predPRE::t, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

get_tag()

string get_tag	(	core::Size	itrial,
		core::Real	kT,
		int	rank
	)

References basic::options::OptionKeys::relax::range::kT, ObjexxFCL::lead_zero_string_of(), and basic::options::OptionKeys::legacy_sewing::rank.

Referenced by my_main().

main()

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

References argv, basic::options::OptionKeys::in::file::centroid, test.T009_Exceptions::e, basic::init(), basic::options::OptionKeys::backrub::initial_pack, basic::options::OptionKeys::backrub::minimize_movemap, basic::options::OptionKeys::backrub::mm_bend_weight, basic::options::OptionKeys::in::file::movemap, my_main(), NEW_OPT, basic::options::OptionKeys::backrub::ntrials, basic::options::OptionKeys::backrub::sc_prob, basic::options::OptionKeys::backrub::sc_prob_uniform, basic::options::OptionKeys::backrub::sc_prob_withinrot, basic::options::OptionKeys::backrub::sm_prob, basic::options::OptionKeys::backrub::trajectory_stride, and viewer_main().

my_main()

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap fast_sc_prob void* my_main

(

void *

)

References utility::file::FileName::base(), basic::options::OptionKeys::in::file::centroid, in::file::centroid_input(), utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_file, basic::Tracer::Debug, utility::options::OptionKeys::options::exit, basic::Tracer::flush(), get_ABGEO_string(), get_filename(), get_tag(), create_a3b_hbs::i, create_a3b_hbs::ii, basic::options::OptionKeys::in::in, create_a3b_hbs::j, basic::options::OptionKeys::relax::range::kT, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::backrub::max_atoms, mc, basic::options::OptionKeys::backrub::min_atoms, basic::options::OptionKeys::backrub::minimize_movemap, test.T400_Refinement::minmover, basic::options::OptionKeys::backrub::mm_bend_weight, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::in::file::movemap, in::file::native(), docking::native_pose, ndx, lactamize::nr, create_a3b_hbs::nres, basic::options::OptionKeys::backrub::ntrials, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, kic_runner::pdb, backrub::pivot_atoms(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::legacy_sewing::rank, packing::resfile(), numeric::random::rg(), average_rmsds::rmsd, runtime_assert, in::file::s(), basic::options::OptionKeys::backrub::sc_prob, basic::options::OptionKeys::backrub::sc_prob_uniform, basic::options::OptionKeys::backrub::sc_prob_withinrot, beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::in::file::silent, in::file::silent_struct_type(), out::file::silent_struct_type(), subloop_histogram::size, basic::options::OptionKeys::backrub::sm_prob, test.T400_Refinement::smallmover, challenge::ss, extract_by_sidechain_sasa_score::tags, vancomycin::task, erraser_analysis::temp, docking::to_centroid, docking::to_fullatom, basic::options::TR, basic::options::OptionKeys::backrub::trajectory_stride, numeric::random::RandomGenerator::uniform(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and score::weights().

Referenced by main().

OPT_1GRP_KEY() [1/7]

sm_prob conrot_prob mm_bend_weight OPT_1GRP_KEY	(	Boolean	,
		mc	,
		detailed_balance
	)

OPT_1GRP_KEY() [2/7]

sm_prob conrot_prob mm_bend_weight initial_pack OPT_1GRP_KEY	(	File	,
		mc	,
		movemap
	)

OPT_1GRP_KEY() [3/7]

OPT_1GRP_KEY	(	Integer	,
		mc	,
		ntrials
	)

OPT_1GRP_KEY() [4/7]

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start OPT_1GRP_KEY	(	Integer	,
		mc	,
		rmsd_region_stop
	)

OPT_1GRP_KEY() [5/7]

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap OPT_1GRP_KEY	(	Integer	,
		mc	,
		score_stride
	)

OPT_1GRP_KEY() [6/7]

sm_prob OPT_1GRP_KEY	(	Real	,
		mc	,
		backrub_prob
	)

OPT_1GRP_KEY() [7/7]

sm_prob conrot_prob OPT_1GRP_KEY	(	Real	,
		mc	,
		kt
	)

periodic_range()

core::Real periodic_range	(	core::Real	a,
		core::Real	x
	)

References a, ObjexxFCL::mod(), and x.

Referenced by JDmover::ABGEO(), and get_ABGEO_string().

Variable Documentation

mc

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap mc

Referenced by my_main().

TR

basic::Tracer TR("pilot.wendao.bbmc") ( "pilot.wendao.bbmc"  )

static