test_bbmc.cc File Reference

run Monte Carlo for sampling protein conformation More...

#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/pose/PDBInfo.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 <core/types.hh>
#include <basic/Tracer.hh>
#include <basic/basic.hh>
#include <basic/options/option.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/pose/util.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.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 <core/optimization/Minimizer.hh>
#include <core/optimization/AtomTreeMinimizer.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
void *	my_main (void *)
void	get_resmap (pose::Pose const &pose, pose::Pose const &ref_pose, std::map< Size, Size > &resmap)
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)
std::string	get_tag (core::Size itrial, core::Real kT, int rank)
std::string	get_filename (std::string const suffix, core::Real t)
int	main (int argc, char *argv[])

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

Detailed Description

run Monte Carlo for sampling protein conformation

test centroid rot model

Author

Yuan Liu

Modified from Colin's backrub.cc, put all backbone algorithm(backrub, bbg, conrot) and all sidechain algorithm(sc, scmc), and MonteCarlo/ReplicaExchange together

Author

Yuan Liu

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()

std::string get_filename	(	std::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_resmap()

void get_resmap	(	pose::Pose const &	pose,
		pose::Pose const &	ref_pose,
		std::map< Size, Size > &	resmap
	)

References create_a3b_hbs::ii, beta_nonlocal::jj, beta_nonlocal::pose, and basic::options::TR.

Referenced by my_main().

get_tag()

std::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()

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, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, utility::file::file_exists(), basic::Tracer::flush(), get_ABGEO_string(), get_filename(), get_resmap(), 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::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(), basic::options::OptionKeys::in::file::residue_type_set, 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, test_mm_lj::step, 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().

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 get_ABGEO_string().

Variable Documentation

mc

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap mc

TR

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

static