protocols::stepwise::modeler::protein::InputStreamWithResidueInfo Class Reference

#include <InputStreamWithResidueInfo.hh>

Inheritance diagram for protocols::stepwise::modeler::protein::InputStreamWithResidueInfo:

Public Member Functions
	InputStreamWithResidueInfo (import_pose::pose_stream::PoseInputStreamOP pose_input_stream, utility::vector1< Size > const &input_res, utility::vector1< Size > const &slice_res)
	InputStreamWithResidueInfo (import_pose::pose_stream::PoseInputStreamOP pose_input_stream, utility::vector1< Size > const &input_res)
	~InputStreamWithResidueInfo ()
import_pose::pose_stream::PoseInputStreamOP &	pose_input_stream ()
utility::vector1< Size > const &	input_res ()
utility::vector1< Size > const &	slice_res ()
std::map< Size, Size > &	full_to_sub ()
void	set_slice_res (utility::vector1< Size > const &slice_res)
void	set_full_to_sub (std::map< Size, Size > const &full_to_sub)
void	set_rsd_set (chemical::ResidueTypeSetCAP &rsd_set)
void	reset ()
bool	has_another_pose () const
void	advance_to_next_pose_segment ()
void	copy_next_pose_segment (pose::Pose &pose)
void	copy_next_pose_segment (pose::Pose &pose, pose::Pose &import_pose, bool const check_sequence_matches, bool const align_pose_to_import_pose=false)
void	apply_current_pose_segment (pose::Pose &pose)
void	apply_current_pose_segment (pose::Pose &pose, pose::Pose &import_pose, bool const check_sequence_matches, bool const align_pose_to_import_pose=false)
void	set_backbone_only (bool const setting)
Size	compute_size ()

Private Member Functions
void	initialize_defaults ()
void	cleanup_pose (pose::Pose &import_pose) const
void	check_sequence (pose::Pose const &pose, pose::Pose const &import_pose)

Private Attributes
import_pose::pose_stream::PoseInputStreamOP	pose_input_stream_
utility::vector1< Size >	input_res_
utility::vector1< Size >	slice_res_
std::map< Size, Size >	full_to_sub_
chemical::ResidueTypeSetCAP	rsd_set_
bool	backbone_only_
pose::PoseOP	import_pose_

Constructor & Destructor Documentation

protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::InputStreamWithResidueInfo	(	import_pose::pose_stream::PoseInputStreamOP	pose_input_stream,
		utility::vector1< Size > const &	input_res,
		utility::vector1< Size > const &	slice_res
	)

References initialize_defaults().

Referenced by protocols::stepwise::modeler::protein::initialize_input_streams_with_residue_info().

protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::InputStreamWithResidueInfo	(	import_pose::pose_stream::PoseInputStreamOP	pose_input_stream,
		utility::vector1< Size > const &	input_res
	)

References initialize_defaults().

protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::~InputStreamWithResidueInfo

(

)

Member Function Documentation

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::advance_to_next_pose_segment

(

)

References import_pose_, pose_input_stream_, and rsd_set_.

Referenced by copy_next_pose_segment().

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::apply_current_pose_segment

(

pose::Pose &

pose

)

References import_pose_.

Referenced by copy_next_pose_segment().

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::apply_current_pose_segment	(	pose::Pose &	pose,
		pose::Pose &	import_pose,
		bool const	check_sequence_matches,
		bool const	align_pose_to_import_pose = false
	)

References backbone_only_, check_sequence(), core::pose::copydofs::copy_dofs_match_atom_names(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), full_to_sub_, input_res_, slice_res_, and core::scoring::superimpose_pose().

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::check_sequence ( pose::Pose const &  pose, pose::Pose const &  import_pose  )

private

References core::pose::Pose::annotated_sequence(), full_to_sub_, input_res_, core::pose::Pose::sequence(), slice_res_, and core::pose::Pose::total_residue().

Referenced by apply_current_pose_segment().

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::cleanup_pose ( pose::Pose &  import_pose ) const

private

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::ResidueType::has_variant_type(), protocols::farna::make_phosphate_nomenclature_matches_mini(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), core::chemical::VIRTUAL_O2PRIME_HYDROGEN, and core::chemical::VIRTUAL_PHOSPHATE.

Size protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::compute_size

(

)

References pose_input_stream_, and rsd_set_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::copy_next_pose_segment

(

pose::Pose &

pose

)

References advance_to_next_pose_segment(), apply_current_pose_segment(), and import_pose_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::copy_next_pose_segment	(	pose::Pose &	pose,
		pose::Pose &	import_pose,
		bool const	check_sequence_matches,
		bool const	align_pose_to_import_pose = false
	)

References advance_to_next_pose_segment(), apply_current_pose_segment(), and import_pose_.

std::map< Size, Size > & protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::full_to_sub

(

)

References full_to_sub_.

Referenced by set_full_to_sub().

bool protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::has_another_pose

(

)

const

References pose_input_stream_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::initialize_defaults ( )

private

References full_to_sub_, input_res_, and slice_res_.

Referenced by InputStreamWithResidueInfo().

utility::vector1< Size > const & protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::input_res

(

)

References input_res_.

import_pose::pose_stream::PoseInputStreamOP & protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::pose_input_stream

(

)

References pose_input_stream_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::reset

(

void

)

References pose_input_stream_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::set_backbone_only

(

bool const

setting

)

References backbone_only_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::set_full_to_sub

(

std::map< Size, Size > const &

full_to_sub

)

References full_to_sub(), and full_to_sub_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::set_rsd_set

(

chemical::ResidueTypeSetCAP &

rsd_set

)

References rsd_set_.

void protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::set_slice_res

(

utility::vector1< Size > const &

slice_res

)

References slice_res(), and slice_res_.

utility::vector1< Size > const & protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::slice_res

(

)

References slice_res_.

Referenced by set_slice_res().

Member Data Documentation

bool protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::backbone_only_

private

Referenced by apply_current_pose_segment(), and set_backbone_only().

std::map< Size, Size > protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::full_to_sub_

private

Referenced by apply_current_pose_segment(), check_sequence(), full_to_sub(), initialize_defaults(), and set_full_to_sub().

pose::PoseOP protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::import_pose_

private

Referenced by advance_to_next_pose_segment(), apply_current_pose_segment(), and copy_next_pose_segment().

utility::vector1< Size > protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::input_res_

private

Referenced by apply_current_pose_segment(), check_sequence(), initialize_defaults(), and input_res().

import_pose::pose_stream::PoseInputStreamOP protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::pose_input_stream_

private

Referenced by advance_to_next_pose_segment(), compute_size(), has_another_pose(), pose_input_stream(), and reset().

chemical::ResidueTypeSetCAP protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::rsd_set_

private

Referenced by advance_to_next_pose_segment(), compute_size(), and set_rsd_set().

utility::vector1< Size > protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::slice_res_

private

Referenced by apply_current_pose_segment(), check_sequence(), initialize_defaults(), set_slice_res(), and slice_res().

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

• src/protocols/stepwise/modeler/protein/InputStreamWithResidueInfo.hh
• src/protocols/stepwise/modeler/protein/InputStreamWithResidueInfo.cc