protocols::rna::movers Namespace Reference

Classes
class	ERRASER2Protocol
	Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job. More...
class	ERRASER2ProtocolCreator
class	ErraserMinimizerMover
class	ErraserMinimizerMoverCreator
class	RNA_Coarsify
	Make a fullatom RNA pose into a coarse representation. More...
class	RNA_CoarsifyCreator
class	RNA_Decoarsify
	Make a coarse RNA pose into a fullatom representation. More...
class	RNA_DecoarsifyCreator
class	RNA_DeNovoOptimizer
class	RNA_LoopCloser
	The RNA de novo structure modeling protocol. More...
class	RNAIdealizeMover
	Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization. More...
class	RNAIdealizeMoverCreator
class	RNAThreadAndMinimizeMover
	Thread a new sequence over a given RNA scaffold and do a little optimization. More...
class	RNAThreadAndMinimizeMoverCreator

Typedefs
using	ERRASER2ProtocolOP = utility::pointer::shared_ptr< ERRASER2Protocol >
using	ERRASER2ProtocolCOP = utility::pointer::shared_ptr< ERRASER2Protocol const >
using	ErraserMinimizerMoverOP = utility::pointer::shared_ptr< ErraserMinimizerMover >
using	ErraserMinimizerMoverCOP = utility::pointer::shared_ptr< const ErraserMinimizerMover >
using	RNA_CoarsifyOP = utility::pointer::shared_ptr< RNA_Coarsify >
using	RNA_CoarsifyCOP = utility::pointer::shared_ptr< RNA_Coarsify const >
using	RNA_DecoarsifyOP = utility::pointer::shared_ptr< RNA_Decoarsify >
using	RNA_DecoarsifyCOP = utility::pointer::shared_ptr< RNA_Decoarsify const >
typedef utility::pointer::shared_ptr< RNA_DeNovoOptimizer >	RNA_DeNovoOptimizerOP
typedef utility::pointer::shared_ptr< RNA_DeNovoOptimizer const >	RNA_DeNovoOptimizerCOP
typedef utility::pointer::shared_ptr< RNA_LoopCloser >	RNA_LoopCloserOP
typedef utility::pointer::shared_ptr< RNA_LoopCloser const >	RNA_LoopCloserCOP
typedef utility::pointer::shared_ptr< RNAIdealizeMover >	RNAIdealizeMoverOP
typedef utility::pointer::shared_ptr< RNAIdealizeMover const >	RNAIdealizeMoverCOP
typedef utility::pointer::shared_ptr< RNAThreadAndMinimizeMover >	RNAThreadAndMinimizeMoverOP
typedef utility::pointer::shared_ptr< RNAThreadAndMinimizeMover const >	RNAThreadAndMinimizeMoverCOP

Functions
static basic::Tracer	TR ("apps.public.rna.erraser.erraser2")
utility::vector1< core::Size >	all_pose_residues (core::pose::Pose const &pose)
void	show_accuracy_report (pose::Pose const &start_pose, std::string const &tag, core::Size const round)
bool	atoms_have_bond_to_bonded_atoms (pose::Pose const &pose, core::Size const ai, core::Size const ii, core::Size const aj, core::Size const jj)
bool	atoms_have_mutual_bond_to_atom (pose::Pose const &pose, core::Size const ai, core::Size const ii, core::Size const aj, core::Size const jj)
bool	bump_check (pose::Pose const &pose, core::Size const ii)
utility::vector1< core::Size >	determine_residues_to_rebuild (utility::vector1< core::Size > const &consider_rebuild_res, pose::Pose const &start_pose)
std::ostream &	operator<< (std::ostream &os, ERRASER2Protocol const &mover)
	private methods /// More...
utility::vector1< core::Size >	string_to_size_vector (std::string const &sv)
template<typename T >
void	remove_set1_elements_from_set2 (std::set< T > const &set1, std::set< T > &set2)
void	fill_gaps_and_remove_isolated_res (std::set< core::Size > &res_list, core::Size const total_res, std::set< core::Size > &res_remove)
std::set< core::Size >	find_nearby_res (Pose const &pose, std::set< core::Size > res_list_current, Real const dist_cutoff)
void	erase_if_in_any_slice (utility::vector1< std::set< core::Size > > const &res_list_sliced, core::Size const res, std::set< core::Size > &res_list_new)
void	clean_res_list (std::set< core::Size > &res_list_new, utility::vector1< std::set< core::Size > > const &res_list_sliced)
void	identify_chunks (Pose const &pose, utility::vector1< std::set< core::Size > > &sliced_list_final, core::Size const virtual_res_pos, core::Size const nproc)
core::Vector	com_of_true_residues (kinematics::MoveMap const &mm, Pose const &pose)
std::string	min_checkpoint_namer (core::Size const nstruct)
std::string	min_log_namer (core::Size const nstruct)
void	read_checkpoint_log (utility::vector1< core::Size > &chunk_indices, core::Size &start_idx, core::Size const nstruct)
void	write_checkpoint (utility::vector1< core::Size > const &chunk_indices, core::Size const cur_idx, core::Size const nstruct, Pose const &pose)
void	load_checkpoint (core::Size const nstruct, utility::vector1< core::Size > &chunk_indices, Pose &pose, core::Size &first_chunk)
std::ostream &	operator<< (std::ostream &os, RNA_Coarsify const &mover)
	private methods /// More...
std::ostream &	operator<< (std::ostream &os, RNA_Decoarsify const &mover)
	private methods /// More...
std::ostream &	operator<< (std::ostream &os, RNAIdealizeMover const &mover)
std::ostream &	operator<< (std::ostream &os, RNAThreadAndMinimizeMover const &mover)

Typedef Documentation

ERRASER2ProtocolCOP

using protocols::rna::movers::ERRASER2ProtocolCOP = typedef utility::pointer::shared_ptr< ERRASER2Protocol const >

ERRASER2ProtocolOP

using protocols::rna::movers::ERRASER2ProtocolOP = typedef utility::pointer::shared_ptr< ERRASER2Protocol >

ErraserMinimizerMoverCOP

typedef utility::pointer::shared_ptr< ErraserMinimizerMover const > protocols::rna::movers::ErraserMinimizerMoverCOP

ErraserMinimizerMoverOP

typedef utility::pointer::shared_ptr< ErraserMinimizerMover > protocols::rna::movers::ErraserMinimizerMoverOP

RNA_CoarsifyCOP

using protocols::rna::movers::RNA_CoarsifyCOP = typedef utility::pointer::shared_ptr< RNA_Coarsify const >

RNA_CoarsifyOP

using protocols::rna::movers::RNA_CoarsifyOP = typedef utility::pointer::shared_ptr< RNA_Coarsify >

RNA_DecoarsifyCOP

using protocols::rna::movers::RNA_DecoarsifyCOP = typedef utility::pointer::shared_ptr< RNA_Decoarsify const >

RNA_DecoarsifyOP

using protocols::rna::movers::RNA_DecoarsifyOP = typedef utility::pointer::shared_ptr< RNA_Decoarsify >

RNA_DeNovoOptimizerCOP

typedef utility::pointer::shared_ptr< RNA_DeNovoOptimizer const > protocols::rna::movers::RNA_DeNovoOptimizerCOP

RNA_DeNovoOptimizerOP

typedef utility::pointer::shared_ptr< RNA_DeNovoOptimizer > protocols::rna::movers::RNA_DeNovoOptimizerOP

RNA_LoopCloserCOP

typedef utility::pointer::shared_ptr< RNA_LoopCloser const > protocols::rna::movers::RNA_LoopCloserCOP

RNA_LoopCloserOP

typedef utility::pointer::shared_ptr< RNA_LoopCloser > protocols::rna::movers::RNA_LoopCloserOP

RNAIdealizeMoverCOP

typedef utility::pointer::shared_ptr< RNAIdealizeMover const > protocols::rna::movers::RNAIdealizeMoverCOP

RNAIdealizeMoverOP

typedef utility::pointer::shared_ptr< RNAIdealizeMover > protocols::rna::movers::RNAIdealizeMoverOP

RNAThreadAndMinimizeMoverCOP

typedef utility::pointer::shared_ptr< RNAThreadAndMinimizeMover const > protocols::rna::movers::RNAThreadAndMinimizeMoverCOP

RNAThreadAndMinimizeMoverOP

typedef utility::pointer::shared_ptr< RNAThreadAndMinimizeMover > protocols::rna::movers::RNAThreadAndMinimizeMoverOP

Function Documentation

all_pose_residues()

utility::vector1< core::Size > protocols::rna::movers::all_pose_residues

(

core::pose::Pose const &

pose

)

References core::pose::Pose::size().

atoms_have_bond_to_bonded_atoms()

bool protocols::rna::movers::atoms_have_bond_to_bonded_atoms	(	pose::Pose const &	pose,
		core::Size const	ai,
		core::Size const	ii,
		core::Size const	aj,
		core::Size const	jj
	)

References core::conformation::Conformation::atoms_are_bonded(), core::pose::Pose::conformation(), and core::pose::Pose::residue().

Referenced by bump_check().

atoms_have_mutual_bond_to_atom()

bool protocols::rna::movers::atoms_have_mutual_bond_to_atom	(	pose::Pose const &	pose,
		core::Size const	ai,
		core::Size const	ii,
		core::Size const	aj,
		core::Size const	jj
	)

References core::conformation::Conformation::atoms_are_bonded(), core::pose::Pose::conformation(), and core::pose::Pose::residue().

Referenced by bump_check().

bump_check()

bool protocols::rna::movers::bump_check	(	pose::Pose const &	pose,
		core::Size const	ii
	)

References core::conformation::Residue::atom_name(), core::chemical::ResidueType::atom_type(), core::conformation::Conformation::atoms_are_bonded(), atoms_have_bond_to_bonded_atoms(), atoms_have_mutual_bond_to_atom(), core::pose::Pose::conformation(), core::chemical::AtomType::lj_radius(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), TR(), and core::conformation::Residue::xyz().

Referenced by determine_residues_to_rebuild().

clean_res_list()

void protocols::rna::movers::clean_res_list	(	std::set< core::Size > &	res_list_new,
		utility::vector1< std::set< core::Size > > const &	res_list_sliced
	)

References protocols::denovo_design::set_difference(), and TR().

Referenced by identify_chunks().

com_of_true_residues()

core::Vector protocols::rna::movers::com_of_true_residues	(	kinematics::MoveMap const &	mm,
		Pose const &	pose
	)

References core::kinematics::MoveMap::get_bb(), core::kinematics::MoveMap::get_chi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::rna::movers::ErraserMinimizerMover::process_entire_pose().

determine_residues_to_rebuild()

utility::vector1< core::Size > protocols::rna::movers::determine_residues_to_rebuild	(	utility::vector1< core::Size > const &	consider_rebuild_res,
		pose::Pose const &	start_pose
	)

References core::pose::rna::RNA_SuiteName::assign(), bump_check(), core::scoring::cart_bonded, core::pose::Pose::energies(), core::chemical::ResidueType::is_canonical_nucleic(), core::conformation::Residue::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::pose::Pose::residue_type(), core::scoring::rg, core::scoring::rna_torsion, core::pose::Pose::size(), and TR().

Referenced by protocols::rna::movers::ERRASER2Protocol::resample_full_model().

erase_if_in_any_slice()

void protocols::rna::movers::erase_if_in_any_slice	(	utility::vector1< std::set< core::Size > > const &	res_list_sliced,
		core::Size const	res,
		std::set< core::Size > &	res_list_new
	)

fill_gaps_and_remove_isolated_res()

void protocols::rna::movers::fill_gaps_and_remove_isolated_res	(	std::set< core::Size > &	res_list,
		core::Size const	total_res,
		std::set< core::Size > &	res_remove
	)

References remove_set1_elements_from_set2().

Referenced by identify_chunks().

find_nearby_res()

std::set< core::Size > protocols::rna::movers::find_nearby_res	(	Pose const &	pose,
		std::set< core::Size >	res_list_current,
		Real const	dist_cutoff
	)

References core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by identify_chunks().

identify_chunks()

void protocols::rna::movers::identify_chunks	(	Pose const &	pose,
		utility::vector1< std::set< core::Size > > &	sliced_list_final,
		core::Size const	virtual_res_pos,
		core::Size const	nproc
	)

References clean_res_list(), fill_gaps_and_remove_isolated_res(), find_nearby_res(), protocols::mean_field::max(), core::pose::Pose::size(), and TR().

Referenced by protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries().

load_checkpoint()

void protocols::rna::movers::load_checkpoint	(	core::Size const	nstruct,
		utility::vector1< core::Size > &	chunk_indices,
		Pose &	pose,
		core::Size &	first_chunk
	)

References min_checkpoint_namer(), and read_checkpoint_log().

Referenced by protocols::rna::movers::ErraserMinimizerMover::process_entire_pose().

min_checkpoint_namer()

std::string protocols::rna::movers::min_checkpoint_namer

(

core::Size const

nstruct

)

Referenced by load_checkpoint(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), and write_checkpoint().

min_log_namer()

std::string protocols::rna::movers::min_log_namer

(

core::Size const

nstruct

)

Referenced by protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), read_checkpoint_log(), and write_checkpoint().

operator<<() [1/5]

std::ostream & protocols::rna::movers::operator<<	(	std::ostream &	os,
		ERRASER2Protocol const &	mover
	)

private methods ///

References protocols::rna::movers::ERRASER2Protocol::show().

operator<<() [2/5]

std::ostream & protocols::rna::movers::operator<<	(	std::ostream &	os,
		RNA_Coarsify const &	mover
	)

private methods ///

References protocols::rna::movers::RNA_Coarsify::show().

operator<<() [3/5]

std::ostream & protocols::rna::movers::operator<<	(	std::ostream &	os,
		RNA_Decoarsify const &	mover
	)

private methods ///

References protocols::rna::movers::RNA_Decoarsify::show().

operator<<() [4/5]

std::ostream & protocols::rna::movers::operator<<	(	std::ostream &	os,
		RNAIdealizeMover const &	mover
	)

References protocols::rna::movers::RNAIdealizeMover::show().

operator<<() [5/5]

std::ostream & protocols::rna::movers::operator<<	(	std::ostream &	os,
		RNAThreadAndMinimizeMover const &	mover
	)

References protocols::rna::movers::RNAThreadAndMinimizeMover::show().

read_checkpoint_log()

void protocols::rna::movers::read_checkpoint_log	(	utility::vector1< core::Size > &	chunk_indices,
		core::Size &	start_idx,
		core::Size const	nstruct
	)

References min_log_namer(), and string_to_size_vector().

Referenced by load_checkpoint().

remove_set1_elements_from_set2()

template<typename T >

void protocols::rna::movers::remove_set1_elements_from_set2	(	std::set< T > const &	set1,
		std::set< T > &	set2
	)

Referenced by fill_gaps_and_remove_isolated_res().

show_accuracy_report()

void protocols::rna::movers::show_accuracy_report	(	pose::Pose const &	start_pose,
		std::string const &	tag,
		core::Size const	round
	)

References core::pose::rna::RNA_SuiteName::assign(), protocols::noesy_assign::round(), core::pose::Pose::size(), and TR().

Referenced by protocols::rna::movers::ERRASER2Protocol::apply().

string_to_size_vector()

utility::vector1< core::Size > protocols::rna::movers::string_to_size_vector

(

std::string const &

sv

)

Referenced by protocols::rna::movers::ErraserMinimizerMover::parse_my_tag(), and read_checkpoint_log().

TR()

static basic::Tracer protocols::rna::movers::TR ( "apps.public.rna.erraser.erraser2"  )

static

Referenced by protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::rna::movers::ERRASER2Protocol::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::rna::movers::RNA_LoopCloser::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), bump_check(), clean_res_list(), determine_residues_to_rebuild(), identify_chunks(), protocols::rna::movers::ErraserMinimizerMover::initialize_from_options(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::rna::movers::ErraserMinimizerMover::parse_my_tag(), protocols::rna::movers::ERRASER2Protocol::parse_my_tag(), protocols::rna::movers::RNA_LoopCloser::passes_fast_scan(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), protocols::rna::movers::ErraserMinimizerMover::pyrimidine_flip_trial(), protocols::rna::movers::ERRASER2Protocol::resample_full_model(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), show_accuracy_report(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().

write_checkpoint()

void protocols::rna::movers::write_checkpoint	(	utility::vector1< core::Size > const &	chunk_indices,
		core::Size const	cur_idx,
		core::Size const	nstruct,
		Pose const &	pose
	)

References protocols::viewer::clear_conformation_viewers(), min_checkpoint_namer(), min_log_namer(), and protocols::stepwise::monte_carlo::output_to_silent_file().

Referenced by protocols::rna::movers::ErraserMinimizerMover::process_entire_pose().