protocols::swa::InputStreamWithResidueInfo Class Reference

#include <InputStreamWithResidueInfo.hh>

Inheritance diagram for protocols::swa::InputStreamWithResidueInfo:

Collaboration diagram for protocols::swa::InputStreamWithResidueInfo:

Public Member Functions
	InputStreamWithResidueInfo (core::import_pose::pose_stream::PoseInputStreamOP pose_input_stream, utility::vector1< Size > const &input_res, utility::vector1< Size > const &slice_res)
	InputStreamWithResidueInfo (core::import_pose::pose_stream::PoseInputStreamOP pose_input_stream, utility::vector1< Size > const &input_res)
virtual	~InputStreamWithResidueInfo ()
core::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 (core::chemical::ResidueTypeSetCAP &rsd_set)
void	reset ()
bool	has_another_pose () const
void	copy_next_pose_segment (core::pose::Pose &pose)
void	copy_next_pose_segment (core::pose::Pose &pose, core::pose::Pose &import_pose, bool const check_sequence_matches, bool const align_pose_to_import_pose=false)
void	set_backbone_only (bool const setting)

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

Private Attributes
core::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_
core::chemical::ResidueTypeSetCAP	rsd_set_
bool	backbone_only_

Detailed Description

Definition at line 54 of file InputStreamWithResidueInfo.hh.

Constructor & Destructor Documentation

protocols::swa::InputStreamWithResidueInfo::InputStreamWithResidueInfo	(	core::import_pose::pose_stream::PoseInputStreamOP	pose_input_stream,
		utility::vector1< Size > const &	input_res,
		utility::vector1< Size > const &	slice_res
	)

Definition at line 156 of file InputStreamWithResidueInfo.cc.

References initialize_defaults().

Referenced by protocols::swa::initialize_input_streams_with_residue_info().

protocols::swa::InputStreamWithResidueInfo::InputStreamWithResidueInfo	(	core::import_pose::pose_stream::PoseInputStreamOP	pose_input_stream,
		utility::vector1< Size > const &	input_res
	)

Definition at line 168 of file InputStreamWithResidueInfo.cc.

References initialize_defaults().

protocols::swa::InputStreamWithResidueInfo::~InputStreamWithResidueInfo ( )

virtual

Definition at line 189 of file InputStreamWithResidueInfo.cc.

Member Function Documentation

void protocols::swa::InputStreamWithResidueInfo::check_sequence ( core::pose::Pose const &  pose, core::pose::Pose const &  import_pose  )

private

Definition at line 322 of file InputStreamWithResidueInfo.cc.

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 copy_next_pose_segment().

void protocols::swa::InputStreamWithResidueInfo::cleanup_pose ( core::pose::Pose &  import_pose) const

private

Definition at line 296 of file InputStreamWithResidueInfo.cc.

References core::chemical::ResidueType::has_variant_type(), protocols::rna::make_phosphate_nomenclature_matches_mini(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void protocols::swa::InputStreamWithResidueInfo::copy_next_pose_segment

(

core::pose::Pose &

pose)

Definition at line 229 of file InputStreamWithResidueInfo.cc.

void protocols::swa::InputStreamWithResidueInfo::copy_next_pose_segment	(	core::pose::Pose &	pose,
		core::pose::Pose &	import_pose,
		bool const	check_sequence_matches,
		bool const	align_pose_to_import_pose = false
	)

Definition at line 236 of file InputStreamWithResidueInfo.cc.

References core::pose::Pose::annotated_sequence(), backbone_only_, check_sequence(), core::pose::copy_dofs_match_atom_names(), protocols::swa::create_alignment_id_map(), full_to_sub_, input_res_, pose_input_stream_, rsd_set_, slice_res_, and core::scoring::superimpose_pose().

std::map< Size, Size > & protocols::swa::InputStreamWithResidueInfo::full_to_sub

(

)

Definition at line 201 of file InputStreamWithResidueInfo.cc.

References full_to_sub_.

Referenced by set_full_to_sub().

bool protocols::swa::InputStreamWithResidueInfo::has_another_pose

(

)

const

Definition at line 222 of file InputStreamWithResidueInfo.cc.

References pose_input_stream_.

void protocols::swa::InputStreamWithResidueInfo::initialize_defaults ( )

private

Definition at line 180 of file InputStreamWithResidueInfo.cc.

References full_to_sub_, input_res_, and slice_res_.

Referenced by InputStreamWithResidueInfo().

utility::vector1< Size > const & protocols::swa::InputStreamWithResidueInfo::input_res

(

)

Definition at line 195 of file InputStreamWithResidueInfo.cc.

References input_res_.

core::import_pose::pose_stream::PoseInputStreamOP & protocols::swa::InputStreamWithResidueInfo::pose_input_stream

(

)

Definition at line 192 of file InputStreamWithResidueInfo.cc.

References pose_input_stream_.

void protocols::swa::InputStreamWithResidueInfo::reset

(

void

)

Definition at line 216 of file InputStreamWithResidueInfo.cc.

References pose_input_stream_.

void protocols::swa::InputStreamWithResidueInfo::set_backbone_only

(

bool const

setting)

Definition at line 393 of file InputStreamWithResidueInfo.cc.

References backbone_only_.

void protocols::swa::InputStreamWithResidueInfo::set_full_to_sub

(

std::map< Size, Size > const &

full_to_sub)

Definition at line 207 of file InputStreamWithResidueInfo.cc.

References full_to_sub(), and full_to_sub_.

void protocols::swa::InputStreamWithResidueInfo::set_rsd_set

(

core::chemical::ResidueTypeSetCAP &

rsd_set)

Definition at line 210 of file InputStreamWithResidueInfo.cc.

References rsd_set_.

void protocols::swa::InputStreamWithResidueInfo::set_slice_res

(

utility::vector1< Size > const &

slice_res)

Definition at line 204 of file InputStreamWithResidueInfo.cc.

References slice_res(), and slice_res_.

utility::vector1< Size > const & protocols::swa::InputStreamWithResidueInfo::slice_res

(

)

Definition at line 198 of file InputStreamWithResidueInfo.cc.

References slice_res_.

Referenced by set_slice_res().

Member Data Documentation

bool protocols::swa::InputStreamWithResidueInfo::backbone_only_

private

Definition at line 105 of file InputStreamWithResidueInfo.hh.

Referenced by copy_next_pose_segment(), and set_backbone_only().

std::map< Size, Size > protocols::swa::InputStreamWithResidueInfo::full_to_sub_

private

Definition at line 103 of file InputStreamWithResidueInfo.hh.

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

utility::vector1< Size > protocols::swa::InputStreamWithResidueInfo::input_res_

private

Definition at line 101 of file InputStreamWithResidueInfo.hh.

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

core::import_pose::pose_stream::PoseInputStreamOP protocols::swa::InputStreamWithResidueInfo::pose_input_stream_

private

Definition at line 100 of file InputStreamWithResidueInfo.hh.

Referenced by copy_next_pose_segment(), has_another_pose(), pose_input_stream(), and reset().

core::chemical::ResidueTypeSetCAP protocols::swa::InputStreamWithResidueInfo::rsd_set_

private

Definition at line 104 of file InputStreamWithResidueInfo.hh.

Referenced by copy_next_pose_segment(), and set_rsd_set().

utility::vector1< Size > protocols::swa::InputStreamWithResidueInfo::slice_res_

private

Definition at line 102 of file InputStreamWithResidueInfo.hh.

Referenced by check_sequence(), copy_next_pose_segment(), 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/swa/InputStreamWithResidueInfo.hh
• src/protocols/swa/InputStreamWithResidueInfo.cc