#include <SampleRotamersFromPDB.hh>

Inheritance diagram for protocols::splice::SampleRotamersFromPDB_RotamerSetOperation:

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

◆ GraphCOP

typedef utility::graph::GraphCOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::GraphCOP

◆ PackerTask

typedef core::pack::task::PackerTask protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::PackerTask

◆ PackerTaskCOP

typedef core::pack::task::PackerTaskCOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::PackerTaskCOP

◆ Pose

typedef core::pose::Pose protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::Pose

◆ Real

typedef core::Real protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::Real

◆ Rotamers

typedef core::pack::rotamer_set::Rotamers protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::Rotamers

◆ RotamerSet

typedef core::pack::rotamer_set::RotamerSet protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::RotamerSet

◆ RotamerSetOperationOP

typedef core::pack::rotamer_set::RotamerSetOperationOP protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::RotamerSetOperationOP

◆ ScoreFunction

typedef core::scoring::ScoreFunction protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ScoreFunction

Constructor & Destructor Documentation

◆ SampleRotamersFromPDB_RotamerSetOperation() [1/2]

protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::SampleRotamersFromPDB_RotamerSetOperation ( )

◆ SampleRotamersFromPDB_RotamerSetOperation() [2/2]

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

◆ ~SampleRotamersFromPDB_RotamerSetOperation()

protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::~SampleRotamersFromPDB_RotamerSetOperation ( )

override

Member Function Documentation

◆ add_pose()

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

References poses_.

Referenced by initialize_from_command_line().

◆ add_rotamer_constraints()

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().

◆ add_rotamer_to_rotamer_set()

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().

◆ alter_rotamer_set()

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_.

◆ alter_rotamer_set_from_db()

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::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), 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().

◆ alter_rotamer_set_from_pdb()

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::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), 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().

◆ clone()

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

overridevirtual

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

◆ copy_rotamer_matrix()

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

References resi_vec_.

◆ fill_rotamer_matrix_from_db_file()

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().

◆ initialize_from_command_line()

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().

◆ is_residue_allowed()

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