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protocols::splice::SampleRotamersFromPDB_RotamerSetOperation Class Reference

#include <SampleRotamersFromPDB.hh>

Inheritance diagram for protocols::splice::SampleRotamersFromPDB_RotamerSetOperation:
Inheritance graph
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Public Types

typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef
core::pack::task::PackerTask 		PackerTask
 
typedef
core::pack::task::PackerTaskCOP 		PackerTaskCOP
 
typedef
core::pack::rotamer_set::RotamerSet 		RotamerSet
 
typedef
core::pack::rotamer_set::Rotamers 		Rotamers
 
typedef
core::scoring::ScoreFunction 		ScoreFunction
 
typedef utility::graph::GraphCOP GraphCOP
 
typedef
core::pack::rotamer_set::RotamerSetOperationOP 		RotamerSetOperationOP
 

Public Member Functions

 SampleRotamersFromPDB_RotamerSetOperation ()
 
 SampleRotamersFromPDB_RotamerSetOperation (bool add_rot, utility::vector1< core::Size > SampleAtAlignedpositions, bool d, bool ccd, std::string file_name)
 
 ~SampleRotamersFromPDB_RotamerSetOperation () override
 
RotamerSetOperationOP clone () const override
 
void alter_rotamer_set (core::pose::Pose const &pose, core::scoring::ScoreFunction const &, core::pack::task::PackerTask const &, utility::graph::GraphCOP, core::pack::rotamer_set::RotamerSet &rotamer_set) override
 
void alter_rotamer_set_from_pdb (core::pose::Pose const &pose, core::pack::task::PackerTask const &ptask, core::pack::rotamer_set::RotamerSet &rotamer_set)
 
void alter_rotamer_set_from_db (core::pose::Pose const &pose, core::pack::task::PackerTask const &ptask, core::pack::rotamer_set::RotamerSet &rotamer_set)
 
void add_rotamer_to_rotamer_set (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSet &rotamer_set, core::conformation::ResidueOP cur_rot)
 
void add_rotamer_constraints (core::pose::Pose &pose, core::Size seqnum, core::conformation::ResidueOP cur_rot)
 
bool is_residue_allowed (core::chemical::ResidueType const &restype, core::pack::task::ResidueLevelTask const &rtask)
 
core::conformation::ResidueOP ROT2res (ROT rot, core::pose::Pose const &pose)
 
void add_pose (core::pose::PoseCOP pose)
 
void initialize_from_command_line ()
 
void fill_rotamer_matrix_from_db_file ()
 
void copy_rotamer_matrix (rot_matrix const &rm)
 
- Public Member Functions inherited from core::pack::rotamer_set::RotamerSetOperation
 RotamerSetOperation ()
 
 ~RotamerSetOperation () override
 
virtual Real increase_packer_residue_radius (pose::Pose const &pose, task::PackerTaskCOP the_task, core::Size residue_in) const
 

Private Attributes

utility::vector1
< core::pose::PoseCOP > 		poses_
 
bool add_rotamer_
 
utility::vector1< core::Size > SampleAtAlignedpositions_
 
bool debug_
 
bool ccd_
 
std::string db_file_
 
rot_matrix resi_vec_
 

Member Typedef Documentation

typedef utility::graph::GraphCOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::GraphCOP
typedef core::pack::task::PackerTask protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::PackerTask
typedef core::pack::task::PackerTaskCOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::PackerTaskCOP
typedef core::pose::Pose protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::Pose
typedef core::Real protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::Real
typedef core::pack::rotamer_set::Rotamers protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::Rotamers
typedef core::pack::rotamer_set::RotamerSet protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::RotamerSet
typedef core::pack::rotamer_set::RotamerSetOperationOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::RotamerSetOperationOP
typedef core::scoring::ScoreFunction protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ScoreFunction

Constructor & Destructor Documentation

protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::SampleRotamersFromPDB_RotamerSetOperation ( )
protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::SampleRotamersFromPDB_RotamerSetOperation ( bool  add_rot,
utility::vector1< core::Size >  SampleAtAlignedpositions,
bool  d,
bool  ccd,
std::string  file_name 
)
protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::~SampleRotamersFromPDB_RotamerSetOperation ( )
override

Member Function Documentation

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_pose ( core::pose::PoseCOP  pose)

References poses_.

Referenced by initialize_from_command_line().

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_constraints ( core::pose::Pose &  pose,
core::Size  seqnum,
core::conformation::ResidueOP  cur_rot 
)

References core::pose::Pose::add_constraint().

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set ( core::pose::Pose const &  pose,
core::pack::rotamer_set::RotamerSet &  rotamer_set,
core::conformation::ResidueOP  cur_rot 
)

References core::pack::rotamer_set::RotamerSet::add_rotamer_into_existing_group(), core::conformation::Residue::chain(), core::pose::Pose::conformation(), core::pack::rotamer_set::RotamerSet::num_rotamers(), core::conformation::Residue::place(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), and protocols::splice::TR().

Referenced by alter_rotamer_set_from_db(), and alter_rotamer_set_from_pdb().

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  ,
core::pack::task::PackerTask const &  ptask,
utility::graph::GraphCOP  ,
core::pack::rotamer_set::RotamerSet &  rotamer_set 
)
overridevirtual

Implements core::pack::rotamer_set::RotamerSetOperation.

References alter_rotamer_set_from_db(), alter_rotamer_set_from_pdb(), and poses_.

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db ( core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  ptask,
core::pack::rotamer_set::RotamerSet &  rotamer_set 
)

References add_rotamer_, add_rotamer_to_rotamer_set(), core::pack::rotamer_set::RotamerSet::begin(), ccd_, core::conformation::Residue::chain(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, debug_, core::pack::rotamer_set::RotamerSet::drop_rotamers(), core::pack::rotamer_set::RotamerSet::end(), core::conformation::Residue::has_variant_type(), is_residue_allowed(), core::pack::rotamer_set::RotamerSet::num_rotamers(), protocols::splice::printChi(), resi_vec_, core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), rot(), ROT2res(), core::pose::Pose::split_by_chain(), and protocols::splice::TR().

Referenced by alter_rotamer_set().

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb ( core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  ptask,
core::pack::rotamer_set::RotamerSet &  rotamer_set 
)

References add_rotamer_, add_rotamer_to_rotamer_set(), core::pack::rotamer_set::RotamerSet::begin(), ccd_, core::conformation::Residue::chain(), core::conformation::Residue::clone(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, debug_, core::pack::rotamer_set::RotamerSet::drop_rotamers(), core::pack::rotamer_set::RotamerSet::end(), protocols::rosetta_scripts::find_nearest_res(), core::conformation::Residue::has_variant_type(), core::pack::rotamer_set::RotamerSet::id_for_current_rotamer(), is_residue_allowed(), core::pack::rotamer_set::RotamerSet::num_rotamers(), core::pose::Pose::pdb_info(), poses_, protocols::splice::printChi(), core::pack::rotamer_set::RotamerSet::resid(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), SampleAtAlignedpositions_, core::pose::Pose::total_residue(), and protocols::splice::TR().

Referenced by alter_rotamer_set().

core::pack::rotamer_set::RotamerSetOperationOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::clone ( ) const
overridevirtual

Implements core::pack::rotamer_set::RotamerSetOperation.

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::copy_rotamer_matrix ( rot_matrix const &  rm)

References resi_vec_.

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::fill_rotamer_matrix_from_db_file ( )

References protocols::splice::ROT::AA, protocols::splice::ROT::chi_vec, db_file_, core::conformation::membrane::in, protocols::splice::is_identical_rotamer(), resi_vec_, rot(), protocols::sparta::split(), and protocols::splice::TR().

void protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::initialize_from_command_line ( )

References add_pose(), protocols::abinitio::filename(), core::import_pose::pose_from_file(), and protocols::splice::TR().

bool protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::is_residue_allowed ( core::chemical::ResidueType const &  restype,
core::pack::task::ResidueLevelTask const &  rtask 
)

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), and core::chemical::ResidueTypeBase::name3().

Referenced by alter_rotamer_set_from_db(), and alter_rotamer_set_from_pdb().

core::conformation::ResidueOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res ( ROT  rot,
core::pose::Pose const &  pose 
)

References protocols::splice::ROT::AA, core::chemical::aa_from_oneletter_code(), protocols::splice::ROT::chi_vec, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::FULL_ATOM_t, core::conformation::Conformation::modifiable_residue_type_set_for_conf(), and core::chemical::name_from_aa().

Referenced by alter_rotamer_set_from_db().

Member Data Documentation

bool protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_
private

Referenced by alter_rotamer_set_from_db(), and alter_rotamer_set_from_pdb().

bool protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ccd_
private

Referenced by alter_rotamer_set_from_db(), and alter_rotamer_set_from_pdb().

std::string protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::db_file_
private

Referenced by fill_rotamer_matrix_from_db_file().

bool protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::debug_
private

Referenced by alter_rotamer_set_from_db(), and alter_rotamer_set_from_pdb().

utility::vector1< core::pose::PoseCOP > protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::poses_
private

Referenced by add_pose(), alter_rotamer_set(), and alter_rotamer_set_from_pdb().

rot_matrix protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::resi_vec_
private

Referenced by alter_rotamer_set_from_db(), copy_rotamer_matrix(), and fill_rotamer_matrix_from_db_file().

utility::vector1< core::Size > protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::SampleAtAlignedpositions_
private

Referenced by alter_rotamer_set_from_pdb().

The documentation for this class was generated from the following files:
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