Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes
protocols::enzdes::EnzdesFlexBBProtocol Class Reference

#include <EnzdesFlexBBProtocol.hh>

Inheritance diagram for protocols::enzdes::EnzdesFlexBBProtocol:
Inheritance graph
[legend]
Collaboration diagram for protocols::enzdes::EnzdesFlexBBProtocol:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 EnzdesFlexBBProtocol ()
 ~EnzdesFlexBBProtocol ()
void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
bool is_flexible (core::Size seqpos) const
bool is_remodelable (core::Size seqpos) const
void get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions)
core::pack::task::PackerTaskOP modified_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task)
void test_flexbb_rotamer_sets (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task)
void remap_resid (core::pose::Pose const &pose, core::id::SequenceMapping const &smap)
EnzdesFlexibleRegionCOP enz_flexible_region (core::Size region) const
toolbox::match_enzdes_util::EnzdesLoopsFileCOP enz_loops_file () const
void generate_ensemble_for_region (core::pose::Pose &pose, core::Size region)
bool minimize_flexible_region (core::pose::Pose &pose, core::Size region, core::scoring::ScoreFunctionCOP scorefxn, std::set< core::Size > const &chi_to_move, bool const including_CA_angles, core::Real min_tolerance)
void generate_alc_ensemble_for_region (core::pose::Pose &pose, core::Size region)
void generate_backrub_ensemble_for_region (core::pose::Pose &pose, core::Size region)
void determine_flexible_regions (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP task)

Static Public Member Functions

static void register_options ()
 overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.

Protected Member Functions

bool assemble_next_best_loop_combination (core::pose::Pose &pose)
bool hack_assemble_next_loop_combination (core::pose::Pose &pose)
bool recover_loops_from_file (core::pose::Pose const &pose)
void setup_catalytic_residue_minimization_for_region (core::pose::Pose const &pose, core::Size region)

Protected Attributes

utility::vector1
< EnzdesFlexibleRegionOP
flex_regions_

Constructor & Destructor Documentation

protocols::enzdes::EnzdesFlexBBProtocol::EnzdesFlexBBProtocol ( )
protocols::enzdes::EnzdesFlexBBProtocol::~EnzdesFlexBBProtocol ( )

Member Function Documentation

void protocols::enzdes::EnzdesFlexBBProtocol::apply ( core::pose::Pose pose) [virtual]
bool protocols::enzdes::EnzdesFlexBBProtocol::assemble_next_best_loop_combination ( core::pose::Pose pose) [protected]

figure out which combination of loop conformations is the next most promising one

References flex_regions_, and protocols::enzdes::tr().

void protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP  task 
)
EnzdesFlexibleRegionCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_flexible_region ( core::Size  region) const [inline]

References flex_regions_.

toolbox::match_enzdes_util::EnzdesLoopsFileCOP protocols::enzdes::EnzdesFlexBBProtocol::enz_loops_file ( ) const [inline]
void protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region ( core::pose::Pose pose,
core::Size  region 
)
void protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region ( core::pose::Pose pose,
core::Size  region 
)
void protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region ( core::pose::Pose pose,
core::Size  region 
)
std::string protocols::enzdes::EnzdesFlexBBProtocol::get_name ( ) const [virtual]

Each derived class must specify its name. The class name.

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

void protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues ( core::pose::Pose const &  pose,
utility::vector1< bool > &  residue_positions 
)

As output, residue_position[i] is true for all neighbor residues including orginal input residues. The function is used to find all neighboring residues of the loop residues in case they need to be repacked or minimized in fullatom refinement.

References core::pose::Pose::energies(), is_flexible(), is_remodelable(), core::chemical::ResidueType::name(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by modified_task().

bool protocols::enzdes::EnzdesFlexBBProtocol::hack_assemble_next_loop_combination ( core::pose::Pose pose) [protected]

returns false if the last combination is reached, true otherwise

References flex_regions_.

bool protocols::enzdes::EnzdesFlexBBProtocol::is_flexible ( core::Size  seqpos) const
bool protocols::enzdes::EnzdesFlexBBProtocol::is_remodelable ( core::Size  seqpos) const
bool protocols::enzdes::EnzdesFlexBBProtocol::minimize_flexible_region ( core::pose::Pose pose,
core::Size  region,
core::scoring::ScoreFunctionCOP  scorefxn,
std::set< core::Size > const &  chi_to_move,
bool const  including_CA_angles,
core::Real  min_tolerance 
)

References flex_regions_.

core::pack::task::PackerTaskOP protocols::enzdes::EnzdesFlexBBProtocol::modified_task ( core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  orig_task 
)
bool protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file ( core::pose::Pose const &  pose) [protected]
void protocols::enzdes::EnzdesFlexBBProtocol::register_options ( ) [static]

overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method.

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

void protocols::enzdes::EnzdesFlexBBProtocol::remap_resid ( core::pose::Pose const &  pose,
core::id::SequenceMapping const &  smap 
) [virtual]

Reimplemented from protocols::enzdes::EnzdesBaseProtocol.

References flex_regions_.

void protocols::enzdes::EnzdesFlexBBProtocol::setup_catalytic_residue_minimization_for_region ( core::pose::Pose const &  pose,
core::Size  region 
) [protected]
void protocols::enzdes::EnzdesFlexBBProtocol::test_flexbb_rotamer_sets ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP  task 
)

Member Data Documentation


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines