protocols::mpi_refinement Namespace Reference

Classes
class	Clusterer
struct	MethodParams
class	MPI_Refine_Emperor
class	MPI_Refine_Master
class	MPI_Refinement
class	MultiObjective
class	Scheduler
class	Serial_Refine
class	StructAvrgMover
class	WorkUnit_bbGauss
class	WorkUnit_CombinePose
class	WorkUnit_FragInsert
class	WorkUnit_KicCloser
class	WorkUnit_LoopHash
class	WorkUnit_MD
class	WorkUnit_NormalMode
class	WorkUnit_PartialAbinitio
class	WorkUnit_RamaPerturber
class	WorkUnit_Relax
class	WorkUnit_Sampler

Typedefs
typedef utility::pointer::shared_ptr < MultiObjective >	MultiObjectiveOP
typedef utility::pointer::shared_ptr < MultiObjective const >	MultiObjectiveCOP
typedef utility::pointer::shared_ptr < WorkUnit_Sampler >	WorkUnit_SamplerOP
typedef utility::pointer::shared_ptr < WorkUnit_Sampler const >	WorkUnit_SamplerCOP

Functions
static basic::Tracer	TR ("MPI.LHR.C")
static basic::Tracer	TR ("MPI.LHR.E")
static basic::Tracer	TR ("MPI.LHR.M")
static basic::Tracer	TR ("MPI.LHR.A")
static basic::Tracer	TR ("MPI.LHR.O")
static basic::Tracer	TR ("MPI.LHR.S")
static basic::Tracer	TR ("protocols.mpi_refinement.SerialRefine")
static basic::Tracer	TR ("MPI.LHR.StructAvrger")
utility::vector1< std::pair < core::Size, core::Size > >	get_loop_info_full (core::io::silent::SilentStructOP ss, utility::vector1< bool > &is_terminus, std::string const &mode)
void	get_loop_info (core::io::silent::SilentStructOP ss, core::Size &res1, core::Size &res2, bool &is_terminus)
void	constrain_residue (core::pose::Pose &pose, core::Size const resno, utility::vector1< core::Size > exclres, std::string const &cst_type, core::Real const stdev)
utility::vector1< core::Size >	get_touched_res (core::pose::Pose const pose, utility::vector1< core::Size > const loopres, core::Real dist_cut)
protocols::minimization_packing::PackRotamersMoverOP	setup_packer (core::pose::Pose const &pose, core::kinematics::MoveMap const mm, core::scoring::ScoreFunctionCOP sfxn)
void	add_movemap_from_loopres (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const loopres, bool const nonideal)
void	ramp_minpack_loop (core::pose::Pose &pose, utility::vector1< core::Size > const loopres, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal, bool const ramp, bool const efficient, bool const envmin)
void	ramp_minpack_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal, bool const ramp)
void	add_poseinfo_to_ss (core::io::silent::SilentStruct &ss, core::pose::Pose const &ref_pose, std::string const &suffix)
core::Real	Zscore_to_library (core::Real const score, core::Real const mean, core::Real const stdev, core::Real const maxval, core::Real const minval)
utility::vector1< core::Size >	loopstring_to_loopvector (std::string const &loopstr, core::Size const ext)
utility::vector1 < utility::vector1< core::Size > >	loopstring_to_loopregions (std::string const &loopstr)
void	copy_pose_crd (core::pose::Pose const pose_frame, core::pose::Pose &pose_work, utility::vector1< utility::vector1< core::Size > > const loopregions)
void	mean_and_stdev (utility::vector1< core::Real > values, core::Real const frac, core::Real &shave_cut, core::Real &mean, core::Real &stdev)
void	superimpose_all (core::io::silent::SilentStructCOP ss_ref, protocols::wum::SilentStructStore &structs, utility::vector1< std::string > const columns_copy)
core::Real	CA_Sscore (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, core::Real &rmsd, utility::vector1< core::Size > const &loopres, bool const superimpose, core::Real const dbase)
core::Real	CA_Sscore (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, core::Real &rmsd, bool const superimpose, core::Real const dbase)
core::Real	distance (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, std::string const &similarity_measure, bool const superimpose)
void	add_init_dev_penalty (core::io::silent::SilentStructOP ss, ObjexxFCL::FArray2D< core::Real > const init_xyz, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
void	add_init_dev_penalty (core::io::silent::SilentStructOP ss, core::pose::Pose pose0, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
void	add_init_dev_penalty (protocols::wum::SilentStructStore &structs, core::pose::Pose const pose0, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
std::map< core::Size, utility::vector1< core::Real > >	read_ss2 (std::string ssfile)
static basic::Tracer	TR ("WorkUnit_Sampler.AggressiveType")
static basic::Tracer	TR ("WorkUnit_Sampler.LoopType")
static basic::Tracer	TR ("WorkUnit_Sampler.Relax")
static basic::Tracer	TR ("WorkUnit_Sampler")

Typedef Documentation

typedef utility::pointer::shared_ptr< MultiObjective const > protocols::mpi_refinement::MultiObjectiveCOP

typedef utility::pointer::shared_ptr< MultiObjective > protocols::mpi_refinement::MultiObjectiveOP

typedef utility::pointer::shared_ptr< WorkUnit_Sampler const > protocols::mpi_refinement::WorkUnit_SamplerCOP

typedef utility::pointer::shared_ptr< WorkUnit_Sampler > protocols::mpi_refinement::WorkUnit_SamplerOP

Function Documentation

void protocols::mpi_refinement::add_init_dev_penalty	(	core::io::silent::SilentStructOP	ss,
		ObjexxFCL::FArray2D< core::Real > const	init_xyz,
		std::string const &	mode,
		core::Real const	iha_cut,
		core::Real const	iha_penalty_slope
	)

References protocols::mean_field::min(), protocols::hybridization::score, and core::scoring::xyz_gdttm().

Referenced by add_init_dev_penalty(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

void protocols::mpi_refinement::add_init_dev_penalty	(	core::io::silent::SilentStructOP	ss,
		core::pose::Pose	pose0,
		std::string const &	mode,
		core::Real const	iha_cut,
		core::Real const	iha_penalty_slope
	)

References add_init_dev_penalty(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

void protocols::mpi_refinement::add_init_dev_penalty	(	protocols::wum::SilentStructStore &	structs,
		core::pose::Pose const	pose0,
		std::string const &	mode,
		core::Real const	iha_cut,
		core::Real const	iha_penalty_slope
	)

References protocols::comparative_modeling::features::A, add_init_dev_penalty(), core::chemical::element::F, protocols::wum::SilentStructStore::get_struct(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::residue(), protocols::wum::SilentStructStore::size(), core::pose::Pose::total_residue(), TR(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

void protocols::mpi_refinement::add_movemap_from_loopres	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const	loopres,
		bool const	nonideal
	)

References core::id::D, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::id::THETA.

Referenced by protocols::mpi_refinement::WorkUnit_Sampler::get_movemap(), and ramp_minpack_loop().

void protocols::mpi_refinement::add_poseinfo_to_ss	(	core::io::silent::SilentStruct &	ss,
		core::pose::Pose const &	ref_pose,
		std::string const &	suffix
	)

References core::io::silent::SilentStruct::add_energy(), core::scoring::CA_gdttm(), core::io::silent::SilentStruct::fill_pose(), core::scoring::gdtha(), core::conformation::Residue::is_protein(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), and protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library().

core::Real protocols::mpi_refinement::CA_Sscore	(	core::io::silent::SilentStructOP	ss1,
		core::io::silent::SilentStructOP	ss2,
		core::Real &	rmsd,
		utility::vector1< core::Size > const &	loopres,
		bool const	superimpose,
		core::Real const	dbase
	)

References core::scoring::calpha_superimpose_pose(), core::conformation::Residue::has(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), CA_Sscore(), protocols::mpi_refinement::MultiObjective::calculate_structure_diversity(), protocols::mpi_refinement::MPI_Refine_Master::create_WUs(), distance(), and protocols::mpi_refinement::Clusterer::get_distance().

core::Real protocols::mpi_refinement::CA_Sscore	(	core::io::silent::SilentStructOP	ss1,
		core::io::silent::SilentStructOP	ss2,
		core::Real &	rmsd,
		bool const	superimpose,
		core::Real const	dbase
	)

References CA_Sscore().

void protocols::mpi_refinement::constrain_residue	(	core::pose::Pose &	pose,
		core::Size const	resno,
		utility::vector1< core::Size >	exclres,
		std::string const &	cst_type,
		core::Real const	stdev
	)

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().

Referenced by protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

void protocols::mpi_refinement::copy_pose_crd	(	core::pose::Pose const	pose_frame,
		core::pose::Pose &	pose_work,
		utility::vector1< utility::vector1< core::Size > > const	loopregions
	)

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

core::Real protocols::mpi_refinement::distance	(	core::io::silent::SilentStructOP	ss1,
		core::io::silent::SilentStructOP	ss2,
		std::string const &	similarity_measure,
		bool const	superimpose
	)

References CA_Sscore(), loopstring_to_loopvector(), and TR().

Referenced by core::scoring::methods::atoms_interact(), protocols::nonlocal::chunks_by_CA_CA_distance(), protocols::medal::cutpoint_probabilities(), core::io::determine_glycan_links(), protocols::mpi_refinement::Clusterer::energy_sort_cluster(), protocols::protein_interface_design::find_nearest_residue(), core::pose::carbohydrates::find_neighbor(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::magnesium::get_mg_ligands(), protocols::sic_dock::neighbor_count(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::prestore_sc_oversat(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::select::residue_selector::selection_positions(), protocols::loop_grower::transform_to_closest_symmunit(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().

void protocols::mpi_refinement::get_loop_info	(	core::io::silent::SilentStructOP	ss,
		core::Size &	res1,
		core::Size &	res2,
		bool &	is_terminus
	)

References core::sequence::end, get_loop_info_full(), core::scoring::rg, protocols::loops::start, and TR().

Referenced by protocols::mpi_refinement::MPI_Refine_Master::create_WUs(), and protocols::mpi_refinement::Serial_Refine::perturb().

utility::vector1< std::pair< core::Size, core::Size > > protocols::mpi_refinement::get_loop_info_full	(	core::io::silent::SilentStructOP	ss,
		utility::vector1< bool > &	is_terminus,
		std::string const &	mode
	)

References core::sequence::end, core::pose::parse_resnum(), protocols::loops::start, protocols::kinmatch::str(), and TR().

Referenced by get_loop_info(), and protocols::mpi_refinement::MPI_Refine_Master::init().

utility::vector1< core::Size > protocols::mpi_refinement::get_touched_res	(	core::pose::Pose const	pose,
		utility::vector1< core::Size > const	loopres,
		core::Real	dist_cut
	)

References core::conformation::Residue::n_mainchain_atoms(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by ramp_minpack_loop(), and protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2().

utility::vector1< utility::vector1< core::Size > > protocols::mpi_refinement::loopstring_to_loopregions

(

std::string const &

loopstr

)

References core::sequence::end, and protocols::loops::start.

Referenced by protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

utility::vector1< core::Size > protocols::mpi_refinement::loopstring_to_loopvector	(	std::string const &	loopstr,
		core::Size const	ext
	)

References core::sequence::end, and protocols::loops::start.

Referenced by protocols::mpi_refinement::MultiObjective::calculate_structure_diversity(), distance(), protocols::mpi_refinement::Clusterer::get_distance(), protocols::mpi_refinement::WorkUnit_Sampler::get_movemap(), and protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

void protocols::mpi_refinement::mean_and_stdev	(	utility::vector1< core::Real >	values,
		core::Real const	frac,
		core::Real &	shave_cut,
		core::Real &	mean,
		core::Real &	stdev
	)

References core::sequence::end, core::simple_metrics::metrics::mean, and protocols::loops::start.

Referenced by protocols::mpi_refinement::Scheduler::pick_enrich_methods().

void protocols::mpi_refinement::ramp_minpack_loop	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const	loopres,
		core::scoring::ScoreFunctionCOP	sfxn,
		bool const	nonideal,
		bool const	ramp,
		bool const	efficient,
		bool const	envmin
	)

References add_movemap_from_loopres(), core::scoring::cart_bonded, core::id::D, core::scoring::fa_rep, get_touched_res(), core::optimization::MinimizerOptions::max_iter(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::optimization::CartesianMinimizer::run(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), setup_packer(), and core::id::THETA.

Referenced by ramp_minpack_pose().

void protocols::mpi_refinement::ramp_minpack_pose	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionCOP	sfxn,
		bool const	nonideal,
		bool const	ramp
	)

References ramp_minpack_loop(), and core::pose::Pose::size().

Referenced by protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

std::map< core::Size, utility::vector1< core::Real > > protocols::mpi_refinement::read_ss2

(

std::string

ssfile

)

References protocols::sparta::split().

protocols::minimization_packing::PackRotamersMoverOP protocols::mpi_refinement::setup_packer	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMap const	mm,
		core::scoring::ScoreFunctionCOP	sfxn
	)

References core::kinematics::MoveMap::get_chi(), and core::pose::Pose::size().

Referenced by ramp_minpack_loop(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), and protocols::mpi_refinement::WorkUnit_Sampler::repack().

void protocols::mpi_refinement::superimpose_all	(	core::io::silent::SilentStructCOP	ss_ref,
		protocols::wum::SilentStructStore &	structs,
		utility::vector1< std::string > const	columns_copy
	)

References protocols::wum::SilentStructStore::add(), core::scoring::calpha_superimpose_pose(), protocols::wum::SilentStructStore::clear(), protocols::wum::SilentStructStore::get_struct(), protocols::wum::SilentStructStore::size(), and TR().

Referenced by protocols::mpi_refinement::MultiObjective::update_library_seeds().

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.S"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.C"  )

static

Referenced by add_init_dev_penalty(), distance(), get_loop_info(), get_loop_info_full(), protocols::mpi_refinement::WorkUnit_Sampler::get_movemap(), protocols::mpi_refinement::Scheduler::pick_enrich_methods(), protocols::mpi_refinement::Scheduler::prepare_enrich_stage(), protocols::mpi_refinement::Scheduler::prepare_search_stage(), protocols::mpi_refinement::Scheduler::proceed(), protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2(), protocols::mpi_refinement::Scheduler::read_cmd(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_Relax::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), and superimpose_all().

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.StructAvrger"  )

static

Referenced by protocols::mpi_refinement::StructAvrgMover::apply(), protocols::mpi_refinement::StructAvrgMover::predict_region(), protocols::mpi_refinement::StructAvrgMover::report_dev(), protocols::mpi_refinement::StructAvrgMover::shave_poses(), protocols::mpi_refinement::StructAvrgMover::StructAvrgMover(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.E"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.O"  )

static

Referenced by protocols::mpi_refinement::MultiObjective::filter_similar(), protocols::mpi_refinement::MultiObjective::set_defaults(), protocols::mpi_refinement::MultiObjective::update_library_NSGAII(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "protocols.mpi_refinement.SerialRefine"  )

static

Referenced by protocols::mpi_refinement::Serial_Refine::apply(), protocols::mpi_refinement::Serial_Refine::get_average_structure(), protocols::mpi_refinement::Serial_Refine::init(), protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), and protocols::mpi_refinement::Serial_Refine::perturb().

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.A"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler.AggressiveType"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "MPI.LHR.M"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler.LoopType"  )

static

static basic::Tracer protocols::mpi_refinement::TR ( "WorkUnit_Sampler.Relax"  )

static

core::Real protocols::mpi_refinement::Zscore_to_library	(	core::Real const	score,
		core::Real const	mean,
		core::Real const	stdev,
		core::Real const	maxval,
		core::Real const	minval
	)

References core::simple_metrics::metrics::mean.