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protocols::swa::monte_carlo Namespace Reference

Classes

class  RNA_AddMover
 
class  RNA_AddOrDeleteMover
 
class  RNA_DeleteMover
 
class  RNA_O2StarMover
 
class  RNA_SWA_MonteCarloMover
 
class  RNA_TorsionMover
 
class  SubToFullInfo
 Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...
 

Typedefs

typedef
utility::pointer::owning_ptr
< RNA_AddMover
RNA_AddMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_AddOrDeleteMover
RNA_AddOrDeleteMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_DeleteMover
RNA_DeleteMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_O2StarMover
RNA_O2StarMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_SWA_MonteCarloMover
RNA_SWA_MonteCarloMoverOP
 
typedef
utility::pointer::owning_ptr
< RNA_TorsionMover
RNA_TorsionMoverOP
 
typedef
utility::pointer::owning_ptr
< SubToFullInfo
SubToFullInfoOP
 

Enumerations

enum  MovingResidueCase {
  NO_CASE =0, CHAIN_TERMINUS_5PRIME, CHAIN_TERMINUS_3PRIME, INTERNAL,
  FLOATING_BASE
}
 
enum  AddOrDeleteChoice { NO_ADD_OR_DELETE =0, ADD, DELETE }
 

Functions

MovingResidueCase get_moving_residue_case (pose::Pose const &pose, Size const i)
 
void get_potential_delete_residues (pose::Pose &pose, utility::vector1< Size > &possible_res, utility::vector1< MovingResidueCase > &moving_residue_cases, utility::vector1< AddOrDeleteChoice > &add_or_delete_choices)
 
void get_potential_add_residues (pose::Pose &pose, utility::vector1< Size > &possible_res, utility::vector1< MovingResidueCase > &moving_residue_cases, utility::vector1< AddOrDeleteChoice > &add_or_delete_choices)
 
void get_random_residue_at_chain_terminus (pose::Pose &pose, Size &residue_at_chain_terminus, MovingResidueCase &moving_residue_case, AddOrDeleteChoice &add_or_delete_choice, bool const disallow_delete)
 
SubToFullInfo const & const_sub_to_full_info_from_pose (pose::Pose &pose)
 
SubToFullInfononconst_sub_to_full_info_from_pose (pose::Pose &pose)
 
utility::vector1< Sizereorder_after_delete (utility::vector1< Size > moving_res_list, Size const &res_to_delete)
 
std::map< Size, Sizereorder_after_delete (std::map< Size, Size > sub_to_full, Size const &res_to_delete)
 
utility::vector1< Sizereorder_after_insert (utility::vector1< Size > moving_res_list, Size const &res_to_add)
 
std::map< Size, Sizereorder_after_prepend (std::map< Size, Size > sub_to_full, Size const &res_to_add)
 
std::map< Size, Sizereorder_after_append (std::map< Size, Size > sub_to_full, Size const &res_to_add)
 
void reorder_sub_to_full_info_after_delete (pose::Pose &pose, Size const res_to_delete)
 
void reorder_sub_to_full_info_after_append (pose::Pose &pose, Size const res_to_add)
 
void reorder_sub_to_full_info_after_prepend (pose::Pose &pose, Size const res_to_add)
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
NO_ADD_OR_DELETE 
ADD 
DELETE 
Enumerator
NO_CASE 
CHAIN_TERMINUS_5PRIME 
CHAIN_TERMINUS_3PRIME 
INTERNAL 
FLOATING_BASE 

Function Documentation

SubToFullInfo const& protocols::swa::monte_carlo::const_sub_to_full_info_from_pose ( pose::Pose pose)

Pose must already contain a sub_to_full_info object or this method will fail.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SUB_TO_FULL_INFO.

MovingResidueCase protocols::swa::monte_carlo::get_moving_residue_case ( pose::Pose const &  pose,
Size const  i 
)
void protocols::swa::monte_carlo::get_potential_add_residues ( pose::Pose pose,
utility::vector1< Size > &  possible_res,
utility::vector1< MovingResidueCase > &  moving_residue_cases,
utility::vector1< AddOrDeleteChoice > &  add_or_delete_choices 
)
void protocols::swa::monte_carlo::get_potential_delete_residues ( pose::Pose pose,
utility::vector1< Size > &  possible_res,
utility::vector1< MovingResidueCase > &  moving_residue_cases,
utility::vector1< AddOrDeleteChoice > &  add_or_delete_choices 
)
void protocols::swa::monte_carlo::get_random_residue_at_chain_terminus ( pose::Pose pose,
Size residue_at_chain_terminus,
MovingResidueCase &  moving_residue_case,
AddOrDeleteChoice &  add_or_delete_choice,
bool const  disallow_delete 
)
SubToFullInfo & protocols::swa::monte_carlo::nonconst_sub_to_full_info_from_pose ( pose::Pose pose)
std::map<Size,Size> protocols::swa::monte_carlo::reorder_after_append ( std::map< Size, Size sub_to_full,
Size const &  res_to_add 
)
utility::vector1<Size> protocols::swa::monte_carlo::reorder_after_delete ( utility::vector1< Size moving_res_list,
Size const &  res_to_delete 
)
std::map<Size,Size> protocols::swa::monte_carlo::reorder_after_delete ( std::map< Size, Size sub_to_full,
Size const &  res_to_delete 
)
utility::vector1<Size> protocols::swa::monte_carlo::reorder_after_insert ( utility::vector1< Size moving_res_list,
Size const &  res_to_add 
)
std::map<Size,Size> protocols::swa::monte_carlo::reorder_after_prepend ( std::map< Size, Size sub_to_full,
Size const &  res_to_add 
)
void protocols::swa::monte_carlo::reorder_sub_to_full_info_after_append ( pose::Pose pose,
Size const  res_to_add 
)
void protocols::swa::monte_carlo::reorder_sub_to_full_info_after_delete ( pose::Pose pose,
Size const  res_to_delete 
)
void protocols::swa::monte_carlo::reorder_sub_to_full_info_after_prepend ( pose::Pose pose,
Size const  res_to_add 
)