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protocols::ncbb Namespace Reference

Namespaces

 oop
 

Classes

class  NcbbDockDesignProtocol
 
class  NcbbDockDesignProtocolCreator
 
class  ResidueReplacementRebuildMover
 A simple method to mutate a pose fairly destructively, and barely recover. More...
 
class  ResidueReplacementRebuildMoverCreator
 
class  SecStructFinder
 
class  SecStructFinderCreator
 
class  SecStructMinimizeMover
 
class  SecStructMinimizeMoverCreator
 
class  SecStructMinimizeMultiFunc
 class for fitting a length of secondary structure keeping the same dihedrals More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< NcbbDockDesignProtocol
NcbbDockDesignProtocolOP
 
typedef
utility::pointer::shared_ptr
< NcbbDockDesignProtocol const > 
NcbbDockDesignProtocolCOP
 
typedef
utility::pointer::shared_ptr
< NcbbDockDesignProtocolCreator
NcbbDockDesignProtocolCreatorOP
 
typedef
utility::pointer::shared_ptr
< NcbbDockDesignProtocolCreator
const > 
NcbbDockDesignProtocolCreatorCOP
 
typedef
utility::pointer::shared_ptr
< ResidueReplacementRebuildMover
ResidueReplacementRebuildMoverOP
 
typedef
utility::pointer::shared_ptr
< ResidueReplacementRebuildMover
const > 
ResidueReplacementRebuildMoverCOP
 
typedef
utility::pointer::shared_ptr
< SecStructFinder
SecStructFinderOP
 
typedef
utility::pointer::shared_ptr
< SecStructFinder const > 
SecStructFinderCOP
 
typedef
utility::pointer::shared_ptr
< SecStructFinderCreator
SecStructFinderCreatorOP
 
typedef
utility::pointer::shared_ptr
< SecStructFinderCreator const > 
SecStructFinderCreatorCOP
 
typedef
utility::pointer::shared_ptr
< SecStructMinimizeMover
SecStructMinimizeMoverOP
 
typedef
utility::pointer::shared_ptr
< SecStructMinimizeMover const > 
SecStructMinimizeMoverCOP
 
typedef
utility::pointer::shared_ptr
< SecStructMinimizeMoverCreator
SecStructMinimizeMoverCreatorOP
 
typedef
utility::pointer::shared_ptr
< SecStructMinimizeMoverCreator
const > 
SecStructMinimizeMoverCreatorCOP
 

Functions

std::ostream & operator<< (std::ostream &os, ResidueReplacementRebuildMover const &mover)
 private methods /// More...
 
bool increment_dihedrals (utility::vector1< Real > &dihedrals, Real const dihedral_min_, Real const dihedral_max_, Real const bin_size_)
 
Size give_dihedral_index (core::Size n, utility::vector1< char > uniqs, std::string dihedral_pattern, std::string alpha_beta_pattern)
 
Size get_number_dihedrals (utility::vector1< char > uniqs, std::string const &dihedral_pattern, std::string const &alpha_beta_pattern)
 
void count_uniq_char (std::string pattern, core::Size &num, utility::vector1< char > &uniqs)
 
void ncbb_design_main_loop (core::Size loop_num, core::Size pert_num, core::pose::Pose pose, TrialMoverOP pert_trial, utility::vector1< core::Size > designable_positions, core::Size pep_start, core::Size pep_end, TaskAwareMinMoverOP desn_ta_min, core::scoring::ScoreFunctionOP score_fxn, MonteCarloOP mc)
 
void final_design_min (core::pose::Pose &pose, ScoreFunctionOP score_fxn_, core::pack::task::TaskFactoryOP desn_tf)
 
void calculate_statistics (core::pose::Pose const &pose, core::scoring::ScoreFunctionOP score_fxn)
 Calculate various statistics, and add them to the current JD2 job. More...
 
void setup_pert_foldtree (core::pose::Pose &pose)
 
void setup_filter_stats ()
 
void init_common_options (utility::tag::TagCOP tag, basic::datacache::DataMap &data, ScoreFunctionOP score_fxn_, Real &mc_temp_, Real &pert_mc_temp_, Real &pert_dock_rot_mag_, Real &pert_dock_trans_mag_, Real &pert_pep_small_temp_, Real &pert_pep_small_H_, Real &pert_pep_small_L_, Real &pert_pep_small_E_, Real &pert_pep_shear_temp_, Real &pert_pep_shear_H_, Real &pert_pep_shear_L_, Real &pert_pep_shear_E_, core::Size &pert_pep_num_rep_, core::Size &pert_num_, core::Size &dock_design_loop_num_, bool &no_design_, bool &final_design_min_, bool &use_soft_rep_, bool &mc_initial_pose_, bool &pymol_, bool &keep_history_)
 
void add_attributes_for_common_options (AttributeList &attlist)
 
void init_common_options (utility::tag::TagCOP tag, basic::datacache::DataMap &data, core::scoring::ScoreFunctionOP score_fxn_, core::Real &mc_temp_, core::Real &pert_mc_temp_, core::Real &pert_dock_rot_mag_, core::Real &pert_dock_trans_mag_, core::Real &pert_pep_small_temp_, core::Real &pert_pep_small_H_, core::Real &pert_pep_small_L_, core::Real &pert_pep_small_E_, core::Real &pert_pep_shear_temp_, core::Real &pert_pep_shear_H_, core::Real &pert_pep_shear_L_, core::Real &pert_pep_shear_E_, core::Size &pert_pep_num_rep_, core::Size &pert_num_, core::Size &dock_design_loop_num_, bool &no_design_, bool &final_design_min_, bool &use_soft_rep_, bool &mc_initial_pose_, bool &pymol_, bool &keep_history_)
 
void add_attributes_for_common_options (utility::tag::AttributeList &attlist)
 
void final_design_min (core::pose::Pose &pose, core::scoring::ScoreFunctionOP score_fxn_, core::pack::task::TaskFactoryOP desn_tf)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< NcbbDockDesignProtocol const > protocols::ncbb::NcbbDockDesignProtocolCOP
typedef utility::pointer::shared_ptr< NcbbDockDesignProtocol > protocols::ncbb::NcbbDockDesignProtocolOP
typedef utility::pointer::shared_ptr< SecStructFinder const > protocols::ncbb::SecStructFinderCOP
typedef utility::pointer::shared_ptr< SecStructFinderCreator const > protocols::ncbb::SecStructFinderCreatorCOP
typedef utility::pointer::shared_ptr< SecStructFinderCreator > protocols::ncbb::SecStructFinderCreatorOP
typedef utility::pointer::shared_ptr< SecStructFinder > protocols::ncbb::SecStructFinderOP
typedef utility::pointer::shared_ptr< SecStructMinimizeMover const > protocols::ncbb::SecStructMinimizeMoverCOP
typedef utility::pointer::shared_ptr< SecStructMinimizeMover > protocols::ncbb::SecStructMinimizeMoverOP

Function Documentation

void protocols::ncbb::add_attributes_for_common_options ( utility::tag::AttributeList &  attlist)
void protocols::ncbb::add_attributes_for_common_options ( AttributeList &  attlist)
void protocols::ncbb::calculate_statistics ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionOP  score_fxn 
)
void protocols::ncbb::count_uniq_char ( std::string  pattern,
core::Size num,
utility::vector1< char > &  uniqs 
)
void protocols::ncbb::final_design_min ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  score_fxn_,
core::pack::task::TaskFactoryOP  desn_tf 
)
void protocols::ncbb::final_design_min ( core::pose::Pose pose,
ScoreFunctionOP  score_fxn_,
core::pack::task::TaskFactoryOP  desn_tf 
)
core::Size protocols::ncbb::get_number_dihedrals ( utility::vector1< char >  uniqs,
std::string const &  dihedral_pattern,
std::string const &  alpha_beta_pattern 
)
core::Size protocols::ncbb::give_dihedral_index ( core::Size  n,
utility::vector1< char >  uniqs,
std::string  dihedral_pattern,
std::string  alpha_beta_pattern 
)
bool protocols::ncbb::increment_dihedrals ( utility::vector1< Real > &  dihedrals,
Real const  dihedral_min_,
Real const  dihedral_max_,
Real const  bin_size_ 
)
void protocols::ncbb::init_common_options ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data,
core::scoring::ScoreFunctionOP  score_fxn_,
core::Real mc_temp_,
core::Real pert_mc_temp_,
core::Real pert_dock_rot_mag_,
core::Real pert_dock_trans_mag_,
core::Real pert_pep_small_temp_,
core::Real pert_pep_small_H_,
core::Real pert_pep_small_L_,
core::Real pert_pep_small_E_,
core::Real pert_pep_shear_temp_,
core::Real pert_pep_shear_H_,
core::Real pert_pep_shear_L_,
core::Real pert_pep_shear_E_,
core::Size pert_pep_num_rep_,
core::Size pert_num_,
core::Size dock_design_loop_num_,
bool no_design_,
bool final_design_min_,
bool use_soft_rep_,
bool mc_initial_pose_,
bool pymol_,
bool keep_history_ 
)
void protocols::ncbb::init_common_options ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data,
ScoreFunctionOP  score_fxn_,
Real mc_temp_,
Real pert_mc_temp_,
Real pert_dock_rot_mag_,
Real pert_dock_trans_mag_,
Real pert_pep_small_temp_,
Real pert_pep_small_H_,
Real pert_pep_small_L_,
Real pert_pep_small_E_,
Real pert_pep_shear_temp_,
Real pert_pep_shear_H_,
Real pert_pep_shear_L_,
Real pert_pep_shear_E_,
core::Size pert_pep_num_rep_,
core::Size pert_num_,
core::Size dock_design_loop_num_,
bool no_design_,
bool final_design_min_,
bool use_soft_rep_,
bool mc_initial_pose_,
bool pymol_,
bool keep_history_ 
)
void protocols::ncbb::ncbb_design_main_loop ( core::Size  loop_num,
core::Size  pert_num,
core::pose::Pose  pose,
TrialMoverOP  pert_trial,
utility::vector1< core::Size designable_positions,
core::Size  pep_start,
core::Size  pep_end,
TaskAwareMinMoverOP  desn_ta_min,
core::scoring::ScoreFunctionOP  score_fxn,
MonteCarloOP  mc 
)
std::ostream & protocols::ncbb::operator<< ( std::ostream &  os,
ResidueReplacementRebuildMover const &  mover 
)
void protocols::ncbb::setup_filter_stats ( )
void protocols::ncbb::setup_pert_foldtree ( core::pose::Pose pose)