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protocols::stepwise::monte_carlo::mover Namespace Reference

Namespaces

 options
 

Classes

class  AddMover
 
class  AddMoverCreator
 
class  AddOrDeleteMover
 
class  Attachment
 
class  DeleteMover
 
class  DeleteMoverCreator
 
class  FromScratchMover
 
class  FromScratchMoverCreator
 
class  ResampleMover
 
class  ResampleMoverCreator
 
class  StepWiseMasterMover
 Central mover of stepwise Monte Carlo protocols, handing work off to special move types. More...
 
class  StepWiseMove
 
class  StepWiseMoveSelector
 
class  TransientCutpointHandler
 
class  VaryLoopLengthMover
 In stepwise design, vary desired loop lengths by updating FullModelParameters. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< AddMover
AddMoverOP
 
typedef
utility::pointer::shared_ptr
< AddMoverCreator
AddMoverCreatorOP
 
typedef
utility::pointer::shared_ptr
< AddMoverCreator const > 
AddMoverCreatorCOP
 
typedef
utility::pointer::shared_ptr
< AddOrDeleteMover
AddOrDeleteMoverOP
 
typedef
utility::pointer::shared_ptr
< DeleteMover
DeleteMoverOP
 
typedef
utility::pointer::shared_ptr
< DeleteMoverCreator
DeleteMoverCreatorOP
 
typedef
utility::pointer::shared_ptr
< DeleteMoverCreator const > 
DeleteMoverCreatorCOP
 
typedef
utility::pointer::shared_ptr
< FromScratchMover
FromScratchMoverOP
 
typedef
utility::pointer::shared_ptr
< FromScratchMover const > 
FromScratchMoverCOP
 
typedef
utility::pointer::shared_ptr
< FromScratchMoverCreator
FromScratchMoverCreatorOP
 
typedef
utility::pointer::shared_ptr
< FromScratchMoverCreator
const > 
FromScratchMoverCreatorCOP
 
typedef
utility::pointer::shared_ptr
< ResampleMover
ResampleMoverOP
 
typedef
utility::pointer::shared_ptr
< ResampleMover const > 
ResampleMoverCOP
 
typedef
utility::pointer::shared_ptr
< ResampleMoverCreator
ResampleMoverCreatorOP
 
typedef
utility::pointer::shared_ptr
< ResampleMoverCreator const > 
ResampleMoverCreatorCOP
 
typedef
utility::pointer::shared_ptr
< StepWiseMasterMover
StepWiseMasterMoverOP
 
typedef
utility::pointer::shared_ptr
< StepWiseMasterMover const > 
StepWiseMasterMoverCOP
 
typedef
utility::pointer::shared_ptr
< StepWiseMove
StepWiseMoveOP
 
typedef
utility::pointer::shared_ptr
< StepWiseMove const > 
StepWiseMoveCOP
 
typedef
utility::pointer::shared_ptr
< Attachment
AttachmentOP
 
typedef
utility::pointer::shared_ptr
< Attachment const > 
AttachmentCOP
 
typedef utility::vector1
< core::Size
MoveElement
 
typedef utility::vector1
< Attachment
Attachments
 
typedef
utility::pointer::shared_ptr
< StepWiseMoveSelector
StepWiseMoveSelectorOP
 
typedef
utility::pointer::shared_ptr
< StepWiseMoveSelector const > 
StepWiseMoveSelectorCOP
 
typedef
utility::pointer::shared_ptr
< TransientCutpointHandler
TransientCutpointHandlerOP
 
typedef
utility::pointer::shared_ptr
< TransientCutpointHandler
const > 
TransientCutpointHandlerCOP
 
typedef
utility::pointer::shared_ptr
< VaryLoopLengthMover
VaryLoopLengthMoverOP
 
typedef
utility::pointer::shared_ptr
< VaryLoopLengthMover const > 
VaryLoopLengthMoverCOP
 

Enumerations

enum  AttachmentType {
  NO_ATTACHMENT = 0, BOND_TO_PREVIOUS, BOND_TO_NEXT, JUMP_TO_PREV_IN_CHAIN,
  JUMP_TO_NEXT_IN_CHAIN, JUMP_DOCK, SUBMOTIF, LAST_ATTACHMENT_TYPE
}
 
enum  MoveType {
  NO_MOVE = 0, ADD, DELETE, FROM_SCRATCH,
  RESAMPLE, RESAMPLE_INTERNAL_LOCAL, ADD_SUBMOTIF, ADD_LOOP_RES,
  DELETE_LOOP_RES, LAST_ADD_OR_DELETE_CHOICE
}
 

Functions

void filter_for_proximity (pose::Pose const &pose, utility::vector1< core::Size > &partition_res, core::Size const center_res)
 
std::string name_from_move (StepWiseMove const &stepwise_move, Pose const &start_pose)
 
std::string residue_rebuild_log_namer (core::Size const resample_round, core::Size const nstruct)
 
std::string residue_rebuild_checkpoint_namer (core::Size const resample_round, core::Size const nstruct)
 
void read_checkpoint_log (utility::vector1< StepWiseMove > &stepwise_moves, core::Size &start_idx, core::Size const resample_round, core::Size const nstruct, Pose const &start_pose)
 
void write_checkpoint (utility::vector1< StepWiseMove > const &stepwise_moves, core::Size const start_idx, core::Size const resample_round, core::Size const nstruct, Pose const &output_pose)
 
void ensure_appropriate_foldtree_for_move (StepWiseMove const &stepwise_move, Pose &output_pose, core::kinematics::FoldTree &ft_to_restore)
 
void set_up_params_for_move (pose::Pose &output_pose, StepWiseMove const &stepwise_move)
 
modeler::StepWiseModelerOP setup_unified_stepwise_modeler (protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP mc_options, core::scoring::ScoreFunctionCOP scorefxn)
 
void initialize_move_type_name ()
 
std::string to_string (MoveType const &move_type)
 
MoveType move_type_from_string (std::string const &name)
 
void initialize_attachment_type_name ()
 
std::string to_string (AttachmentType const &attachment_type)
 
AttachmentType attachment_type_from_string (std::string const &name)
 
std::ostream & operator<< (std::ostream &os, StepWiseMove const &swa_move)
 
std::ostream & operator<< (std::ostream &os, Attachment const &attachment)
 
bool operator== (Attachment const &a, Attachment const &b)
 
bool operator== (StepWiseMove const &a, StepWiseMove const &b)
 
bool check_for_connections_for_all_submotif_residues (MoveElement const &move_element, utility::vector1< StepWiseMove > const &add_moves)
 
utility::vector1< std::pair
< core::Size, core::Size > > 
get_design_loops (FullModelParametersCOP parent_full_model_parameters)
 

Variables

std::map< MoveType, std::string > move_type_name
 
std::map< AttachmentType,
std::string > 
attachment_type_name
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AddMover > protocols::stepwise::monte_carlo::mover::AddMoverOP
typedef utility::pointer::shared_ptr< Attachment const > protocols::stepwise::monte_carlo::mover::AttachmentCOP
typedef utility::pointer::shared_ptr< Attachment > protocols::stepwise::monte_carlo::mover::AttachmentOP
typedef utility::pointer::shared_ptr< ResampleMover const > protocols::stepwise::monte_carlo::mover::ResampleMoverCOP
typedef utility::pointer::shared_ptr< StepWiseMove const > protocols::stepwise::monte_carlo::mover::StepWiseMoveCOP

Enumeration Type Documentation

Enumerator
NO_ATTACHMENT 
BOND_TO_PREVIOUS 
BOND_TO_NEXT 
JUMP_TO_PREV_IN_CHAIN 
JUMP_TO_NEXT_IN_CHAIN 
JUMP_DOCK 
SUBMOTIF 
LAST_ATTACHMENT_TYPE 
Enumerator
NO_MOVE 
ADD 
DELETE 
FROM_SCRATCH 
RESAMPLE 
RESAMPLE_INTERNAL_LOCAL 
ADD_SUBMOTIF 
ADD_LOOP_RES 
DELETE_LOOP_RES 
LAST_ADD_OR_DELETE_CHOICE 

Function Documentation

AttachmentType protocols::stepwise::monte_carlo::mover::attachment_type_from_string ( std::string const &  name)
bool protocols::stepwise::monte_carlo::mover::check_for_connections_for_all_submotif_residues ( MoveElement const &  move_element,
utility::vector1< StepWiseMove > const &  add_moves 
)
void protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move ( StepWiseMove const &  stepwise_move,
Pose output_pose,
core::kinematics::FoldTree ft_to_restore 
)
void protocols::stepwise::monte_carlo::mover::filter_for_proximity ( pose::Pose const &  pose,
utility::vector1< core::Size > &  partition_res,
core::Size const  center_res 
)
utility::vector1< std::pair< core::Size, core::Size > > protocols::stepwise::monte_carlo::mover::get_design_loops ( FullModelParametersCOP  parent_full_model_parameters)
void protocols::stepwise::monte_carlo::mover::initialize_attachment_type_name ( )
void protocols::stepwise::monte_carlo::mover::initialize_move_type_name ( )
MoveType protocols::stepwise::monte_carlo::mover::move_type_from_string ( std::string const &  name)
std::string protocols::stepwise::monte_carlo::mover::name_from_move ( StepWiseMove const &  stepwise_move,
Pose const &  start_pose 
)
inline
std::ostream & protocols::stepwise::monte_carlo::mover::operator<< ( std::ostream &  os,
StepWiseMove const &  swa_move 
)
std::ostream & protocols::stepwise::monte_carlo::mover::operator<< ( std::ostream &  os,
Attachment const &  attachment 
)
bool protocols::stepwise::monte_carlo::mover::operator== ( Attachment const &  a,
Attachment const &  b 
)
bool protocols::stepwise::monte_carlo::mover::operator== ( StepWiseMove const &  a,
StepWiseMove const &  b 
)
void protocols::stepwise::monte_carlo::mover::read_checkpoint_log ( utility::vector1< StepWiseMove > &  stepwise_moves,
core::Size start_idx,
core::Size const  resample_round,
core::Size const  nstruct,
Pose const &  start_pose 
)
std::string protocols::stepwise::monte_carlo::mover::residue_rebuild_checkpoint_namer ( core::Size const  resample_round,
core::Size const  nstruct 
)
std::string protocols::stepwise::monte_carlo::mover::residue_rebuild_log_namer ( core::Size const  resample_round,
core::Size const  nstruct 
)
void protocols::stepwise::monte_carlo::mover::set_up_params_for_move ( pose::Pose output_pose,
StepWiseMove const &  stepwise_move 
)
modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::setup_unified_stepwise_modeler ( protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptionsCOP  mc_options,
core::scoring::ScoreFunctionCOP  scorefxn 
)
std::string protocols::stepwise::monte_carlo::mover::to_string ( MoveType const &  move_type)
std::string protocols::stepwise::monte_carlo::mover::to_string ( AttachmentType const &  attachment_type)
void protocols::stepwise::monte_carlo::mover::write_checkpoint ( utility::vector1< StepWiseMove > const &  stepwise_moves,
core::Size const  start_idx,
core::Size const  resample_round,
core::Size const  nstruct,
Pose const &  output_pose 
)

Variable Documentation

std::map< AttachmentType, std::string> protocols::stepwise::monte_carlo::mover::attachment_type_name
std::map< MoveType, std::string> protocols::stepwise::monte_carlo::mover::move_type_name