Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::stepwise::modeler::align Namespace Reference

Classes

class  StepWiseClusterer
 
class  StepWiseLegacyClusterer
 
class  StepWiseLegacyClustererSilentBased
 
class  StepWisePoseAligner
 

Typedefs

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

Functions

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 native_pose, utility::vector1< Size > const &moving_res_list, Real const rmsd_screen)
 
void superimpose_at_fixed_res (pose::Pose &pose, pose::Pose const &native_pose, Real &rmsd, Size &natoms_rmsd, bool skip_bulges)
 
Real superimpose_at_fixed_res_and_get_all_atom_rmsd (pose::Pose &pose, pose::Pose const &native_pose, bool skip_bulges)
 
void superimpose_recursively (pose::Pose &pose, pose::Pose const &native_pose, Real &rmsd, Size &natoms, bool skip_bulges=false)
 
Real superimpose_recursively (pose::Pose &pose, pose::Pose const &native_pose)
 
Real superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, std::map< Size, 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 (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 (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)
 

Variables

utility::vector1< std::string >
const 
extra_suite_atoms_upper = make_vector1( " P ", " OP1", " OP2", " O5'", "XO3'" )
 
utility::vector1< std::string >
const 
extra_suite_atoms_lower = make_vector1( " O ", "YP ","YOP2","YOP1","YO5'" )
 

Typedef Documentation

Function Documentation

void protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints ( pose::Pose pose,
pose::PoseCOP  native_pose,
utility::vector1< Size > const &  moving_res_list,
Real const  rmsd_screen 
)
core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::modeler::align::create_alignment_id_map ( 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 ( pose::Pose const &  mod_pose,
pose::Pose const &  ref_pose,
std::map< core::Size, core::Size res_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 
)
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 
)

References get_rmsd().

void protocols::stepwise::modeler::align::superimpose_at_fixed_res ( pose::Pose pose,
pose::Pose const &  native_pose,
Real rmsd,
Size natoms_rmsd,
bool  skip_bulges 
)
core::Real protocols::stepwise::modeler::align::superimpose_at_fixed_res_and_get_all_atom_rmsd ( pose::Pose pose,
pose::Pose const &  native_pose,
bool  skip_bulges 
)

References rmsd, and superimpose_at_fixed_res().

core::Real protocols::stepwise::modeler::align::superimpose_pose ( pose::Pose mod_pose,
pose::Pose const &  ref_pose,
std::map< Size, Size > const &  res_map 
)
void protocols::stepwise::modeler::align::superimpose_recursively ( pose::Pose pose,
pose::Pose const &  native_pose,
Real rmsd,
Size natoms,
bool  skip_bulges = false 
)
core::Real protocols::stepwise::modeler::align::superimpose_recursively ( pose::Pose pose,
pose::Pose const &  native_pose 
)

Variable Documentation

utility::vector1< std::string > const protocols::stepwise::modeler::align::extra_suite_atoms_lower = make_vector1( " O ", "YP ","YOP2","YOP1","YO5'" )
utility::vector1< std::string > const protocols::stepwise::modeler::align::extra_suite_atoms_upper = make_vector1( " P ", " OP1", " OP2", " O5'", "XO3'" )