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

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

Detailed Description

run Monte Carlo for sampling protein conformation

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

Function Documentation

main()

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

References 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, and basic::options::OptionKeys::backrub::trajectory_stride.

my_main()

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap fast_sc_prob void* my_main

(

void *

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::cst_file, create_a3b_hbs::i, basic::options::OptionKeys::relax::range::kT, mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::in::file::movemap, docking::native_pose, basic::options::OptionKeys::backrub::ntrials, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, kic_runner::pdb, beta_nonlocal::pose, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, packing::resfile(), numeric::random::rg(), basic::options::OptionKeys::backrub::sc_prob_uniform, basic::options::OptionKeys::backrub::sc_prob_withinrot, beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, vancomycin::task, docking::to_centroid, docking::to_fullatom, TR, numeric::random::RandomGenerator::uniform(), and basic::options::OptionKeys::inout::dbms::user.

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
	)

Variable Documentation

mc

sm_prob conrot_prob mm_bend_weight initial_pack rmsd_region_start minimize_movemap mc

Referenced by PoseWrap::add_floating_sc_csts(), HemeBindingMover::apply(), HECTMover::apply(), UBQ_E2Mover::apply(), A3BHbsDockDesignMinimizeMover::apply(), A3BPeptideBuilder::apply(), MikeLinkerMover::apply(), TrizaolamerDockDesignMinimizeMover::apply(), HbsDesignMover::apply(), OopDesignMover::apply(), PeptoidDesignMover::apply(), UBQ_GTPase_disulfide_Mover::apply(), MPFindInterfaceTestMover::apply(), TestQuickRelaxMover::apply(), MPDomainAssembly::apply(), aramid_main(), backrub_protocol(), capri15_relax(), HubDenovo::cen_fold(), zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), dna_stats(), do_backrub(), do_KIC(), A3BHbsCreatorMover::do_mc(), main(), mutate_random_residue(), my_main(), repack_cluster(), run(), run_mc(), sample_rna_dofs_new(), scmove_residue(), simple_loop_modeling_test(), small_min_test(), use_backrub(), viewer_main(), and zf_relax_test().

TR

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

static

Referenced by my_main().