protocols::stepwise::modeler::align Namespace Reference

Classes
class	StepWiseClusterer
class	StepWiseLegacyClusterer
class	StepWiseLegacyClustererSilentBased
class	StepWisePoseAligner

Typedefs
typedef utility::pointer::shared_ptr < StepWiseClusterer >	StepWiseClustererOP
typedef utility::pointer::shared_ptr < StepWiseClusterer const >	StepWiseClustererCOP
typedef utility::pointer::shared_ptr < StepWiseLegacyClusterer >	StepWiseLegacyClustererOP
typedef utility::pointer::shared_ptr < StepWiseLegacyClusterer const >	StepWiseLegacyClustererCOP
typedef utility::pointer::shared_ptr < StepWiseLegacyClustererSilentBased >	StepWiseLegacyClustererSilentBasedOP
typedef utility::pointer::shared_ptr < StepWiseLegacyClustererSilentBased const >	StepWiseLegacyClustererSilentBasedCOP
typedef utility::pointer::shared_ptr < StepWisePoseAligner >	StepWisePoseAlignerOP
typedef utility::pointer::shared_ptr < StepWisePoseAligner const >	StepWisePoseAlignerCOP

Functions
std::unordered_set < std::string > const	extra_suite_atoms_upper ({" P "," OP1"," OP2"," O5'","XO3'"})
std::unordered_set < std::string > const	extra_suite_atoms_lower ({" O ","YP ","YOP2","YOP1","YO5'"})
bool	match_up_to_rna_dna (char const nt1, char const nt2)
core::Real	get_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, utility::vector1< core::Size > const &calc_rms_res, bool const check_align_at_superimpose_res, bool const check_switch)
core::Real	get_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, bool const check_align_at_superimpose_res, bool const check_switch)
void	align_pose_and_add_rmsd_constraints (pose::Pose &pose, pose::PoseCOP align_pose, utility::vector1< core::Size > const &moving_res_list, Real const rmsd_screen)
Real	superimpose_with_stepwise_aligner (pose::Pose &pose, pose::Pose const &align_pose, bool const superimpose_over_all_instantiated)
Real	superimpose_pose_legacy (pose::Pose &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > const &res_map)
	Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map. Simple wrapper around superimpose_pose using IDs. More...
id::AtomID_Map< id::AtomID >	create_alignment_id_map_legacy (pose::Pose const &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &superimpose_res)
id::AtomID_Map< id::AtomID >	create_alignment_id_map_legacy (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)

Typedef Documentation

typedef utility::pointer::shared_ptr< StepWiseClusterer const > protocols::stepwise::modeler::align::StepWiseClustererCOP

typedef utility::pointer::shared_ptr< StepWiseClusterer > protocols::stepwise::modeler::align::StepWiseClustererOP

typedef utility::pointer::shared_ptr< StepWiseLegacyClusterer const > protocols::stepwise::modeler::align::StepWiseLegacyClustererCOP

typedef utility::pointer::shared_ptr< StepWiseLegacyClusterer > protocols::stepwise::modeler::align::StepWiseLegacyClustererOP

typedef utility::pointer::shared_ptr< StepWiseLegacyClustererSilentBased const > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBasedCOP

typedef utility::pointer::shared_ptr< StepWiseLegacyClustererSilentBased > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBasedOP

typedef utility::pointer::shared_ptr< StepWisePoseAligner const > protocols::stepwise::modeler::align::StepWisePoseAlignerCOP

typedef utility::pointer::shared_ptr< StepWisePoseAligner > protocols::stepwise::modeler::align::StepWisePoseAlignerOP

Function Documentation

void protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints	(	pose::Pose &	pose,
		pose::PoseCOP	align_pose,
		utility::vector1< core::Size > const &	moving_res_list,
		Real const	rmsd_screen
	)

References protocols::stepwise::modeler::align::StepWisePoseAligner::apply(), protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraints(), protocols::stepwise::modeler::figure_out_root_partition_res(), core::pose::Pose::fold_tree(), core::scoring::rms_at_corresponding_atoms_no_super(), core::kinematics::FoldTree::root(), protocols::stepwise::modeler::align::StepWisePoseAligner::set_root_partition_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_atom_id_map(), and core::pose::TR().

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), and protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root().

core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::modeler::align::create_alignment_id_map_legacy	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		utility::vector1< core::Size > const &	superimpose_res
	)

References protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), and core::pose::Pose::size().

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_poses(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), and protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::apply_current_pose_segment().

core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::modeler::align::create_alignment_id_map_legacy	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::Size, core::Size >	res_map
	)

References core::pose::initialize_atomid_map(), core::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), and core::pose::Pose::size().

std::unordered_set< std::string > const protocols::stepwise::modeler::align::extra_suite_atoms_lower

(

{" O ","YP ","YOP2","YOP1","YO5'"}

)

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map().

std::unordered_set< std::string > const protocols::stepwise::modeler::align::extra_suite_atoms_upper

(

{" P "," OP1"," OP2"," O5'","XO3'"}

)

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map().

core::Real protocols::stepwise::modeler::align::get_rmsd	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		utility::vector1< core::Size > const &	calc_rms_res,
		bool const	check_align_at_superimpose_res,
		bool const	check_switch
	)

References protocols::stepwise::modeler::figure_out_root_partition_res(), get_rmsd(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(), protocols::stepwise::modeler::align::StepWisePoseAligner::initialize(), protocols::stepwise::modeler::align::StepWisePoseAligner::set_root_partition_res(), and protocols::stepwise::modeler::align::StepWisePoseAligner::set_user_defined_calc_rms_res().

Referenced by protocols::rna::setup::RNA_CSA_JobDistributor::average_pairwise_distance(), and protocols::stepwise::modeler::align::StepWiseClusterer::check_for_closeness().

core::Real protocols::stepwise::modeler::align::get_rmsd	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		bool const	check_align_at_superimpose_res,
		bool const	check_switch
	)

Referenced by get_rmsd().

bool protocols::stepwise::modeler::align::match_up_to_rna_dna	(	char const	nt1,
		char const	nt2
	)

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local().

core::Real protocols::stepwise::modeler::align::superimpose_pose_legacy	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::Size, core::Size > const &	res_map
	)

Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map. Simple wrapper around superimpose_pose using IDs.

Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map.

References core::id::AtomID_Map< T >::all_default(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), and core::scoring::superimpose_pose().

Referenced by protocols::stepwise::modeler::merge_two_poses(), and protocols::stepwise::modeler::slice().

core::Real protocols::stepwise::modeler::align::superimpose_with_stepwise_aligner	(	pose::Pose &	pose,
		pose::Pose const &	align_pose,
		bool const	superimpose_over_all_instantiated
	)

References protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_over_all_poses(), and protocols::stepwise::modeler::align::StepWisePoseAligner::set_superimpose_over_all_instantiated().

Referenced by protocols::rna::setup::RNA_CSA_JobDistributor::check_for_closeness(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), and protocols::stepwise::monte_carlo::prepare_silent_struct().