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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::AtomIDcreate_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::AtomIDcreate_alignment_id_map_legacy (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)
 

Typedef Documentation

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 
)
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 
)
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 
)
std::unordered_set< std::string > const protocols::stepwise::modeler::align::extra_suite_atoms_lower ( {" O ","YP ","YOP2","YOP1","YO5'"}  )
std::unordered_set< std::string > const protocols::stepwise::modeler::align::extra_suite_atoms_upper ( {" P "," OP1"," OP2"," O5'","XO3'"}  )
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 
)
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 
)
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 
)