protocols::mpi_refinement::Serial_Refine Class Reference

#include <Serial_Refine.hh>

Public Member Functions
	Serial_Refine ()
	~Serial_Refine ()
void	set_defaults ()
core::Real	apply (core::pose::Pose &pose, utility::vector1< core::Size > fixres)
void	init ()

Private Member Functions
void	load_structures_from_cmdline_into_library (core::pose::Pose const &pose, protocols::wum::SilentStructStore &library)
protocols::wum::SilentStructStore	perturb (MethodParams const &params, const core::io::silent::SilentStructOP &start_struct)
void	dump_structures (protocols::wum::SilentStructStore const &new_structs, bool score_only, std::string prefix) const
core::pose::Pose	get_average_structure (protocols::wum::SilentStructStore &decoys, utility::vector1< core::Size > const touse, std::string const columnname, bool const minimize) const

Private Attributes
protocols::wum::SilentStructStore	library_central_
protocols::wum::SilentStructStore	library_ref_
bool	native_given_
core::pose::Pose	native_pose_
Scheduler	scheduler_
MultiObjectiveOP	fobj_
std::map< std::string, core::Size >	ssids_by_name_

Constructor & Destructor Documentation

protocols::mpi_refinement::Serial_Refine::Serial_Refine

(

)

References core::init::init().

protocols::mpi_refinement::Serial_Refine::~Serial_Refine ( )

default

Member Function Documentation

core::Real protocols::mpi_refinement::Serial_Refine::apply	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	fixres
	)

References protocols::wum::SilentStructStore::add(), protocols::wum::SilentStructStore::all_add_energy(), protocols::wum::SilentStructStore::begin(), core::id::D, protocols::wum::SilentStructStore::end(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), protocols::wum::SilentStructStore::size(), core::pose::Pose::size(), protocols::wum::SilentStructStore::sort_by(), protocols::wum::SilentStructStore::store(), core::id::THETA, and protocols::mpi_refinement::TR().

void protocols::mpi_refinement::Serial_Refine::dump_structures ( protocols::wum::SilentStructStore const &  new_structs, bool  score_only, std::string  prefix  ) const

private

References protocols::abinitio::filename(), and core::io::silent::SilentFileData::write_silent_struct().

core::pose::Pose protocols::mpi_refinement::Serial_Refine::get_average_structure ( protocols::wum::SilentStructStore &  decoys, utility::vector1< core::Size > const  touse, std::string const  columnname, bool const  minimize  ) const

private

References protocols::wum::SilentStructStore::add(), protocols::mpi_refinement::StructAvrgMover::apply(), protocols::wum::SilentStructStore::begin(), protocols::wum::SilentStructStore::end(), protocols::wum::SilentStructStore::get_struct(), protocols::wum::SilentStructStore::size(), and protocols::mpi_refinement::TR().

void protocols::mpi_refinement::Serial_Refine::init

(

void

)

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::mpi_refinement::TR().

void protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library ( core::pose::Pose const &  pose, protocols::wum::SilentStructStore &  library  )

private

References protocols::wum::SilentStructStore::add(), protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::relax::AtomCoordinateCstMover::apply(), core::scoring::coordinate_constraint, protocols::relax::AtomCoordinateCstMover::cst_sd(), protocols::mpi_refinement::ramp_minpack_pose(), core::pose::set_ss_from_phipsi(), protocols::wum::SilentStructStore::size(), and protocols::mpi_refinement::TR().

SilentStructStore protocols::mpi_refinement::Serial_Refine::perturb ( MethodParams const &  params, const core::io::silent::SilentStructOP &  start_struct  )

private

References protocols::mpi_refinement::MethodParams::cstw, protocols::mpi_refinement::get_loop_info(), protocols::mpi_refinement::MethodParams::movertype, protocols::mpi_refinement::MethodParams::nperrun, protocols::mpi_refinement::MethodParams::relax_type, protocols::mpi_refinement::MethodParams::score_type, and protocols::mpi_refinement::TR().

void protocols::mpi_refinement::Serial_Refine::set_defaults

(

)

Member Data Documentation

MultiObjectiveOP protocols::mpi_refinement::Serial_Refine::fobj_

private

protocols::wum::SilentStructStore protocols::mpi_refinement::Serial_Refine::library_central_

private

protocols::wum::SilentStructStore protocols::mpi_refinement::Serial_Refine::library_ref_

private

bool protocols::mpi_refinement::Serial_Refine::native_given_

private

core::pose::Pose protocols::mpi_refinement::Serial_Refine::native_pose_

private

Scheduler protocols::mpi_refinement::Serial_Refine::scheduler_

private

std::map< std::string, core::Size > protocols::mpi_refinement::Serial_Refine::ssids_by_name_

private

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The documentation for this class was generated from the following files:

• src/protocols/mpi_refinement/Serial_Refine.hh
• src/protocols/mpi_refinement/Serial_Refine.cc