core::pose::full_model_info Namespace Reference

Classes
class	FullModelInfo
	Keep track of all information related to how a subpose 'fits in' to global modeling scheme. More...
class	FullModelParameters

Typedefs
typedef utility::pointer::owning_ptr < FullModelInfo >	FullModelInfoOP
typedef utility::pointer::owning_ptr < FullModelParameters >	FullModelParametersOP
typedef utility::pointer::owning_ptr < FullModelParameters const >	FullModelParametersCOP

Enumerations
enum	FullModelParameterType {   NO_TYPE = 0, CALC_RMS, CHAIN, CUTPOINT_OPEN,   FIXED_DOMAIN, EXTRA_MINIMIZE, SAMPLE, RNA_SYN_CHI,   RNA_TERMINAL, LAST_TYPE }

Functions
FullModelInfo const &	const_full_model_info (pose::Pose const &pose)
FullModelInfo &	nonconst_full_model_info (pose::Pose &pose)
FullModelInfo const &	make_sure_full_model_info_is_setup (pose::Pose &pose)
void	set_full_model_info (pose::Pose &pose, FullModelInfoOP &full_model_info)
utility::vector1< Size >	reorder_moving_res_list_after_delete (utility::vector1< Size > const &moving_res_list, Size const &res_to_delete)
utility::vector1< Size >	reorder_res_list_after_delete (utility::vector1< Size > const &res_list, Size const &res_to_delete)
utility::vector1< Size >	reorder_moving_res_list_after_insert (utility::vector1< Size > const &moving_res_list, Size const &res_to_add)
utility::vector1< Size >	reorder_res_list_after_prepend (utility::vector1< Size > const &res_list, Size const &res_to_add, Size const offset=1)
utility::vector1< Size >	reorder_res_list_after_append (utility::vector1< Size > const &res_list, Size const &res_to_add, Size const offset=1)
void	update_res_list_in_full_model_info_and_pdb_info (pose::Pose &pose, utility::vector1< Size > const &res_list_new)
void	reorder_full_model_info_after_delete (core::pose::Pose &pose, core::Size const res_to_delete)
	Keep track of RNA centroid information inside the pose. More...
void	reorder_full_model_info_after_append (pose::Pose &pose, Size const res_to_add, Size const offset)
void	reorder_full_model_info_after_prepend (pose::Pose &pose, Size const res_to_add, Size const offset)
void	update_pdb_info_from_full_model_info (pose::Pose &pose)
utility::vector1< Size >	figure_out_chains_from_full_model_info (pose::Pose &pose)
utility::vector1< Size >	get_chains_full (pose::Pose const &pose)
utility::vector1< Size >	figure_out_chains_from_full_model_info_const (pose::Pose const &pose)
bool	check_full_model_info_OK (pose::Pose const &pose)
utility::vector1< Size > const &	get_res_list_from_full_model_info (pose::Pose &pose)
utility::vector1< Size > const &	get_res_list_from_full_model_info_const (pose::Pose const &pose)
utility::vector1 < utility::vector1< Size > >	get_move_elements_from_full_model_info (pose::Pose &pose)
utility::vector1 < utility::vector1< Size > >	get_move_elements_from_full_model_info_const (pose::Pose const &pose)
utility::vector1< Size >	get_moving_res_from_full_model_info (pose::Pose &pose)
utility::vector1< Size >	get_fixed_domain_from_full_model_info_const (pose::Pose const &pose)
core::Size	sub_to_full (core::Size const i, core::pose::Pose const &pose)
utility::vector1< Size >	sub_to_full (utility::vector1< Size > const &res_list, core::pose::Pose const &pose)
core::Size	full_to_sub (core::Size const i, core::pose::Pose const &pose)
Size	full_model_size (pose::Pose &pose)
void	update_pose_domain_map (Pose &pose, Size &pose_domain_number, utility::vector1< Size > &pose_domain_map)
utility::vector1< Size >	figure_out_pose_domain_map (pose::Pose &pose)
core::conformation::Residue const &	get_residue (Size const seqpos_in_full_model, pose::Pose const &pose, bool &found_residue)
core::conformation::Residue const &	get_residue (Size const seqpos_in_full_model, pose::Pose const &pose)
utility::vector1< Size >	get_res_num_from_pdb_info (pose::Pose const &pose)
Size	get_chain_for_full_model_resnum (Size const &resnum, pose::Pose const &pose)
Size	get_chain_for_resnum (Size const &resnum, pose::Pose const &pose)
void	initialize_parameters (FullModelParameters &full_model_parameters)

Typedef Documentation

typedef utility::pointer::owning_ptr< FullModelInfo > core::pose::full_model_info::FullModelInfoOP

typedef utility::pointer::owning_ptr< FullModelParameters const > core::pose::full_model_info::FullModelParametersCOP

typedef utility::pointer::owning_ptr< FullModelParameters > core::pose::full_model_info::FullModelParametersOP

Enumeration Type Documentation

enum core::pose::full_model_info::FullModelParameterType

Enumerator
NO_TYPE
CALC_RMS
CHAIN
CUTPOINT_OPEN
FIXED_DOMAIN
EXTRA_MINIMIZE
SAMPLE
RNA_SYN_CHI
RNA_TERMINAL
LAST_TYPE

Function Documentation

bool core::pose::full_model_info::check_full_model_info_OK

(

pose::Pose const &

pose

)

References const_full_model_info(), get_res_list_from_full_model_info_const(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), runtime_assert, sequence, core::pose::Pose::total_residue(), and core::pose::TR.

Referenced by nonconst_full_model_info(), and update_res_list_in_full_model_info_and_pdb_info().

FullModelInfo const & core::pose::full_model_info::const_full_model_info

(

pose::Pose const &

pose

)

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, basic::datacache::BasicDataCache::get_const_ptr(), and basic::datacache::BasicDataCache::has().

Referenced by check_full_model_info_OK(), full_to_sub(), core::scoring::methods::IntermolEnergy::get_chains_connected(), get_chains_full(), get_fixed_domain_from_full_model_info_const(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), get_move_elements_from_full_model_info_const(), core::scoring::methods::IntermolEnergy::get_num_chains_frozen(), core::scoring::methods::MissingEnergy::get_number_missing_residue_connections(), get_res_list_from_full_model_info_const(), get_residue(), core::scoring::methods::FreeMoietyEnergy::residue_energy(), sub_to_full(), core::scoring::loop_graph::LoopGraph::update(), and update_res_list_in_full_model_info_and_pdb_info().

utility::vector1< Size > core::pose::full_model_info::figure_out_chains_from_full_model_info

(

pose::Pose &

pose

)

References figure_out_chains_from_full_model_info_const(), and make_sure_full_model_info_is_setup().

Referenced by update_pdb_info_from_full_model_info().

utility::vector1< Size > core::pose::full_model_info::figure_out_chains_from_full_model_info_const

(

pose::Pose const &

pose

)

References get_chains_full(), get_res_list_from_full_model_info_const(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by figure_out_chains_from_full_model_info(), get_chain_for_resnum(), and core::scoring::methods::IntermolEnergy::get_chains_connected().

utility::vector1< Size > core::pose::full_model_info::figure_out_pose_domain_map

(

pose::Pose &

pose

)

References full_model_size(), and update_pose_domain_map().

Referenced by core::scoring::methods::MissingEnergy::get_number_missing_residue_connections(), and core::scoring::loop_graph::LoopGraph::update().

Size core::pose::full_model_info::full_model_size

(

pose::Pose &

pose

)

References nonconst_full_model_info(), and core::pose::full_model_info::FullModelInfo::size().

Referenced by figure_out_pose_domain_map().

core::Size core::pose::full_model_info::full_to_sub	(	core::Size const	i,
		core::pose::Pose const &	pose
	)

References const_full_model_info(), utility::vector1< T, class >::index(), and core::pose::full_model_info::FullModelInfo::res_list().

Size core::pose::full_model_info::get_chain_for_full_model_resnum	(	Size const &	resnum,
		pose::Pose const &	pose
	)

References get_chains_full().

Size core::pose::full_model_info::get_chain_for_resnum	(	Size const &	resnum,
		pose::Pose const &	pose
	)

References figure_out_chains_from_full_model_info_const().

utility::vector1< Size > core::pose::full_model_info::get_chains_full

(

pose::Pose const &

pose

)

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::full_sequence(), runtime_assert, sequence, and core::pose::Pose::total_residue().

Referenced by figure_out_chains_from_full_model_info_const(), and get_chain_for_full_model_resnum().

utility::vector1< Size > core::pose::full_model_info::get_fixed_domain_from_full_model_info_const

(

pose::Pose const &

pose

)

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), and core::pose::full_model_info::FullModelInfo::res_list().

utility::vector1< utility::vector1< Size > > core::pose::full_model_info::get_move_elements_from_full_model_info

(

pose::Pose &

pose

)

References get_move_elements_from_full_model_info_const(), and make_sure_full_model_info_is_setup().

utility::vector1< utility::vector1< Size > > core::pose::full_model_info::get_move_elements_from_full_model_info_const

(

pose::Pose const &

pose

)

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), utility::tools::make_vector1(), and core::pose::full_model_info::FullModelInfo::res_list().

Referenced by get_move_elements_from_full_model_info().

utility::vector1< Size > core::pose::full_model_info::get_moving_res_from_full_model_info

(

pose::Pose &

pose

)

References core::pose::full_model_info::FullModelInfo::fixed_domain_map(), nonconst_full_model_info(), and core::pose::full_model_info::FullModelInfo::res_list().

utility::vector1< Size > const & core::pose::full_model_info::get_res_list_from_full_model_info

(

pose::Pose &

pose

)

References nonconst_full_model_info(), and core::pose::full_model_info::FullModelInfo::res_list().

Referenced by update_pdb_info_from_full_model_info().

utility::vector1< Size > const & core::pose::full_model_info::get_res_list_from_full_model_info_const

(

pose::Pose const &

pose

)

References const_full_model_info(), and core::pose::full_model_info::FullModelInfo::res_list().

Referenced by core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), check_full_model_info_OK(), figure_out_chains_from_full_model_info_const(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose(), reorder_full_model_info_after_append(), reorder_full_model_info_after_delete(), and reorder_full_model_info_after_prepend().

utility::vector1< Size > core::pose::full_model_info::get_res_num_from_pdb_info

(

pose::Pose const &

pose

)

References core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

core::conformation::Residue const& core::pose::full_model_info::get_residue	(	Size const	seqpos_in_full_model,
		pose::Pose const &	pose,
		bool &	found_residue
	)

References const_full_model_info(), get_residue(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::pose::full_model_info::FullModelInfo::other_pose_list(), core::pose::full_model_info::FullModelInfo::res_list(), and core::pose::Pose::residue().

Referenced by core::scoring::loop_graph::LoopGraph::get_loop_atom(), and core::scoring::loop_graph::LoopGraph::update().

core::conformation::Residue const & core::pose::full_model_info::get_residue	(	Size const	seqpos_in_full_model,
		pose::Pose const &	pose
	)

References runtime_assert.

Referenced by get_residue().

void core::pose::full_model_info::initialize_parameters

(

FullModelParameters &

full_model_parameters

)

References CALC_RMS, CUTPOINT_OPEN, EXTRA_MINIMIZE, FIXED_DOMAIN, RNA_SYN_CHI, RNA_TERMINAL, SAMPLE, and core::pose::full_model_info::FullModelParameters::set_parameter_as_res_list().

Referenced by core::scoring::FACTSRsdTypeInfo::create_info(), and core::pose::full_model_info::FullModelParameters::FullModelParameters().

FullModelInfo const & core::pose::full_model_info::make_sure_full_model_info_is_setup

(

pose::Pose &

pose

)

References nonconst_full_model_info().

Referenced by figure_out_chains_from_full_model_info(), core::scoring::methods::IntermolEnergy::finalize_total_energy(), and get_move_elements_from_full_model_info().

FullModelInfo & core::pose::full_model_info::nonconst_full_model_info

(

pose::Pose &

pose

)

Either returns a non-const reference to the FullModelInfo object already stored in the pose, or creates a new FullModelInfo object, places it in the pose, and returns a non-const reference to it.

References check_full_model_info_OK(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, and basic::datacache::BasicDataCache::set().

Referenced by core::scoring::methods::OtherPoseEnergy::finalize_total_energy(), full_model_size(), get_moving_res_from_full_model_info(), get_res_list_from_full_model_info(), make_sure_full_model_info_is_setup(), core::scoring::methods::FreeMoietyEnergy::setup_for_scoring(), and update_pose_domain_map().

void core::pose::full_model_info::reorder_full_model_info_after_append	(	pose::Pose &	pose,
		Size const	res_to_add,
		Size const	offset
	)

References get_res_list_from_full_model_info_const(), reorder_res_list_after_append(), and update_res_list_in_full_model_info_and_pdb_info().

void core::pose::full_model_info::reorder_full_model_info_after_delete	(	pose::Pose &	pose,
		Size const	res_to_delete
	)

Keep track of RNA centroid information inside the pose.

References get_res_list_from_full_model_info_const(), reorder_res_list_after_delete(), and update_res_list_in_full_model_info_and_pdb_info().

void core::pose::full_model_info::reorder_full_model_info_after_prepend	(	pose::Pose &	pose,
		Size const	res_to_add,
		Size const	offset
	)

References get_res_list_from_full_model_info_const(), reorder_res_list_after_prepend(), and update_res_list_in_full_model_info_and_pdb_info().

utility::vector1<Size> core::pose::full_model_info::reorder_moving_res_list_after_delete	(	utility::vector1< Size > const &	moving_res_list,
		Size const &	res_to_delete
	)

utility::vector1<Size> core::pose::full_model_info::reorder_moving_res_list_after_insert	(	utility::vector1< Size > const &	moving_res_list,
		Size const &	res_to_add
	)

utility::vector1< Size > core::pose::full_model_info::reorder_res_list_after_append	(	utility::vector1< Size > const &	res_list,
		Size const &	res_to_add,
		Size const	offset = 1
	)

Referenced by reorder_full_model_info_after_append().

utility::vector1< Size > core::pose::full_model_info::reorder_res_list_after_delete	(	utility::vector1< Size > const &	res_list,
		Size const &	res_to_delete
	)

Referenced by reorder_full_model_info_after_delete().

utility::vector1< Size > core::pose::full_model_info::reorder_res_list_after_prepend	(	utility::vector1< Size > const &	res_list,
		Size const &	res_to_add,
		Size const	offset = 1
	)

Referenced by reorder_full_model_info_after_prepend().

void core::pose::full_model_info::set_full_model_info	(	pose::Pose &	pose,
		FullModelInfoOP &	full_model_info
	)

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, basic::datacache::BasicDataCache::set(), and update_pdb_info_from_full_model_info().

core::Size core::pose::full_model_info::sub_to_full	(	core::Size const	i,
		core::pose::Pose const &	pose
	)

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::res_list(), and runtime_assert.

utility::vector1< Size > core::pose::full_model_info::sub_to_full	(	utility::vector1< Size > const &	res_list,
		core::pose::Pose const &	pose
	)

References const_full_model_info(), and core::pose::full_model_info::FullModelInfo::sub_to_full().

void core::pose::full_model_info::update_pdb_info_from_full_model_info

(

pose::Pose &

pose

)

References core::chemical::chr_chains(), figure_out_chains_from_full_model_info(), get_res_list_from_full_model_info(), core::pose::Pose::pdb_info(), and core::pose::Pose::total_residue().

Referenced by set_full_model_info(), and update_res_list_in_full_model_info_and_pdb_info().

void core::pose::full_model_info::update_pose_domain_map	(	Pose &	pose,
		Size &	pose_domain_number,
		utility::vector1< Size > &	pose_domain_map
	)

References nonconst_full_model_info(), core::pose::full_model_info::FullModelInfo::other_pose_list(), and core::pose::full_model_info::FullModelInfo::res_list().

Referenced by figure_out_pose_domain_map().

void core::pose::full_model_info::update_res_list_in_full_model_info_and_pdb_info	(	pose::Pose &	pose,
		utility::vector1< Size > const &	res_list_new
	)

References check_full_model_info_OK(), core::pose::full_model_info::FullModelInfo::clone_info(), const_full_model_info(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, runtime_assert, basic::datacache::BasicDataCache::set(), and update_pdb_info_from_full_model_info().

Referenced by reorder_full_model_info_after_append(), reorder_full_model_info_after_delete(), and reorder_full_model_info_after_prepend().