core::import_pose::pose_stream::SilentFilePoseInputStream Class Reference

#include <SilentFilePoseInputStream.hh>

Inheritance diagram for core::import_pose::pose_stream::SilentFilePoseInputStream:

Collaboration diagram for core::import_pose::pose_stream::SilentFilePoseInputStream:

Public Member Functions
	SilentFilePoseInputStream ()
	SilentFilePoseInputStream (utility::vector1< FileName > fns)
	SilentFilePoseInputStream (std::string const &fn)
	SilentFilePoseInputStream (utility::vector1< FileName > fns, bool order_by_energy)
	SilentFilePoseInputStream (utility::vector1< FileName > fns, core::Real energy_cut)
	SilentFilePoseInputStream (utility::vector1< FileName > fns, utility::vector1< string > input_tags)
	SilentFilePoseInputStream (utility::vector1< FileName > fns, utility::vector1< string > input_tags, core::Real energy_cut)
void	set_silent_file_data (core::io::silent::SilentFileDataOP &sfd)
void	set_record_source (bool const &setting)
	~SilentFilePoseInputStream ()
void	renumber_decoys (bool const setting)
void	tags (utility::vector1< string > tags)
void	filenames (utility::vector1< FileName > filenames)
core::Real	energy_cut () const
bool	renumber_decoys () const
utility::vector1< string >	tags () const
utility::vector1< FileName >	filenames () const
void	set_order_by_energy (bool const &setting)
virtual bool	has_another_pose ()
virtual void	reset ()
virtual void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set)
virtual void	fill_pose (core::pose::Pose &)
core::io::silent::SilentStructOP	next_struct ()
Public Member Functions inherited from core::import_pose::pose_stream::PoseInputStream
	PoseInputStream ()
virtual	~PoseInputStream ()
virtual utility::vector1 < core::pose::Pose >	get_all_poses (core::chemical::ResidueTypeSet const &residue_set)
void	preprocess_pose (core::pose::Pose &pose)
	Perform common operations on a Pose dependent on command-line options before finishing fill_pose. This includes optimizing hydrogens, adding constraints, and finding disulfides. This should be called in the fill_pose method of derived classes. More...

Private Types
typedef std::string	string
typedef utility::file::FileName	FileName

Private Member Functions
void	read_all_files_ ()

Private Attributes
utility::vector1< string >	tags_
utility::vector1< FileName >	filenames_
core::io::silent::SilentFileDataOP	sfd_
core::io::silent::SilentFileData::iterator	current_position_
bool	renumber_decoys_
core::Real	energy_cut_
bool	order_by_energy_
bool	record_source_

Detailed Description

Definition at line 38 of file SilentFilePoseInputStream.hh.

Member Typedef Documentation

typedef utility::file::FileName core::import_pose::pose_stream::SilentFilePoseInputStream::FileName

private

Definition at line 41 of file SilentFilePoseInputStream.hh.

typedef std::string core::import_pose::pose_stream::SilentFilePoseInputStream::string

private

Definition at line 40 of file SilentFilePoseInputStream.hh.

Constructor & Destructor Documentation

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( )

inline

Definition at line 45 of file SilentFilePoseInputStream.hh.

References sfd_.

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( utility::vector1< FileName >  fns)

inline

Definition at line 53 of file SilentFilePoseInputStream.hh.

References filenames(), and sfd_.

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( std::string const &  fn)

inline

Definition at line 60 of file SilentFilePoseInputStream.hh.

References filenames(), and sfd_.

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( utility::vector1< FileName >  fns, bool  order_by_energy  )

inline

Definition at line 69 of file SilentFilePoseInputStream.hh.

References filenames(), and sfd_.

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( utility::vector1< FileName >  fns, core::Real  energy_cut  )

inline

Definition at line 79 of file SilentFilePoseInputStream.hh.

References filenames(), and sfd_.

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( utility::vector1< FileName >  fns, utility::vector1< string >  input_tags  )

inline

Definition at line 89 of file SilentFilePoseInputStream.hh.

References filenames(), sfd_, and tags().

core::import_pose::pose_stream::SilentFilePoseInputStream::SilentFilePoseInputStream ( utility::vector1< FileName >  fns, utility::vector1< string >  input_tags, core::Real  energy_cut  )

inline

Definition at line 100 of file SilentFilePoseInputStream.hh.

References filenames(), sfd_, and tags().

core::import_pose::pose_stream::SilentFilePoseInputStream::~SilentFilePoseInputStream ( )

inline

Definition at line 118 of file SilentFilePoseInputStream.hh.

Member Function Documentation

core::Real core::import_pose::pose_stream::SilentFilePoseInputStream::energy_cut

(

)

const

Definition at line 111 of file SilentFilePoseInputStream.cc.

References energy_cut_.

Referenced by read_all_files_().

void core::import_pose::pose_stream::SilentFilePoseInputStream::filenames

(

utility::vector1< FileName >

filenames)

Definition at line 58 of file SilentFilePoseInputStream.cc.

References current_position_, filenames(), filenames_, read_all_files_(), and sfd_.

utility::vector1< FileName > core::import_pose::pose_stream::SilentFilePoseInputStream::filenames

(

)

const

Definition at line 99 of file SilentFilePoseInputStream.cc.

References filenames_.

Referenced by filenames(), and SilentFilePoseInputStream().

void core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose ( core::pose::Pose &  pose, core::chemical::ResidueTypeSet const &  residue_set  )

virtual

Implements core::import_pose::pose_stream::PoseInputStream.

Definition at line 123 of file SilentFilePoseInputStream.cc.

References current_position_, core::pose::Pose::data(), core::pack::interaction_graph::debug, has_another_pose(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, core::import_pose::pose_stream::PoseInputStream::preprocess_pose(), core::pose::setPoseExtraScores(), and core::import_pose::pose_stream::tr().

void core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose ( core::pose::Pose &  pose)

virtual

Implements core::import_pose::pose_stream::PoseInputStream.

Definition at line 157 of file SilentFilePoseInputStream.cc.

References current_position_, core::pose::Pose::data(), core::pack::interaction_graph::debug, has_another_pose(), core::pose::datacache::CacheableDataType::JOBDIST_OUTPUT_TAG, core::import_pose::pose_stream::PoseInputStream::preprocess_pose(), core::pose::setPoseExtraScores(), and core::import_pose::pose_stream::tr().

bool core::import_pose::pose_stream::SilentFilePoseInputStream::has_another_pose ( )

virtual

Implements core::import_pose::pose_stream::PoseInputStream.

Definition at line 115 of file SilentFilePoseInputStream.cc.

References current_position_, and sfd_.

Referenced by fill_pose(), and next_struct().

core::io::silent::SilentStructOP core::import_pose::pose_stream::SilentFilePoseInputStream::next_struct

(

)

Definition at line 193 of file SilentFilePoseInputStream.cc.

References current_position_, and has_another_pose().

void core::import_pose::pose_stream::SilentFilePoseInputStream::read_all_files_ ( )

private

Definition at line 208 of file SilentFilePoseInputStream.cc.

References energy_cut(), protocols::swa::rna::file_exists(), filenames_, order_by_energy_, record_source_, renumber_decoys(), sfd_, tags_, and core::import_pose::pose_stream::tr().

Referenced by filenames().

void core::import_pose::pose_stream::SilentFilePoseInputStream::renumber_decoys

(

bool const

setting)

Definition at line 95 of file SilentFilePoseInputStream.cc.

References renumber_decoys_.

bool core::import_pose::pose_stream::SilentFilePoseInputStream::renumber_decoys

(

)

const

Definition at line 107 of file SilentFilePoseInputStream.cc.

References renumber_decoys_.

Referenced by read_all_files_(), and set_silent_file_data().

void core::import_pose::pose_stream::SilentFilePoseInputStream::reset ( )

virtual

Implements core::import_pose::pose_stream::PoseInputStream.

Definition at line 67 of file SilentFilePoseInputStream.cc.

References current_position_, and sfd_.

void core::import_pose::pose_stream::SilentFilePoseInputStream::set_order_by_energy

(

bool const &

setting)

Definition at line 248 of file SilentFilePoseInputStream.cc.

References order_by_energy_.

void core::import_pose::pose_stream::SilentFilePoseInputStream::set_record_source

(

bool const &

setting)

Definition at line 253 of file SilentFilePoseInputStream.cc.

References record_source_.

void core::import_pose::pose_stream::SilentFilePoseInputStream::set_silent_file_data

(

core::io::silent::SilentFileDataOP &

sfd)

Definition at line 74 of file SilentFilePoseInputStream.cc.

References current_position_, filenames_, order_by_energy_, renumber_decoys(), sfd_, tags_, and core::import_pose::pose_stream::tr().

Referenced by protocols::swa::protein::StepWiseProteinPoseMinimizer::apply().

void core::import_pose::pose_stream::SilentFilePoseInputStream::tags

(

utility::vector1< string >

tags)

Definition at line 54 of file SilentFilePoseInputStream.cc.

References tags(), and tags_.

utility::vector1< std::string > core::import_pose::pose_stream::SilentFilePoseInputStream::tags

(

)

const

Definition at line 103 of file SilentFilePoseInputStream.cc.

References tags_.

Referenced by SilentFilePoseInputStream(), and tags().

Member Data Documentation

core::io::silent::SilentFileData::iterator core::import_pose::pose_stream::SilentFilePoseInputStream::current_position_

private

Definition at line 149 of file SilentFilePoseInputStream.hh.

Referenced by filenames(), fill_pose(), has_another_pose(), next_struct(), reset(), and set_silent_file_data().

core::Real core::import_pose::pose_stream::SilentFilePoseInputStream::energy_cut_

private

Definition at line 151 of file SilentFilePoseInputStream.hh.

Referenced by energy_cut().

utility::vector1< FileName > core::import_pose::pose_stream::SilentFilePoseInputStream::filenames_

private

Definition at line 147 of file SilentFilePoseInputStream.hh.

Referenced by filenames(), read_all_files_(), and set_silent_file_data().

bool core::import_pose::pose_stream::SilentFilePoseInputStream::order_by_energy_

private

Definition at line 152 of file SilentFilePoseInputStream.hh.

Referenced by read_all_files_(), set_order_by_energy(), and set_silent_file_data().

bool core::import_pose::pose_stream::SilentFilePoseInputStream::record_source_

private

Definition at line 153 of file SilentFilePoseInputStream.hh.

Referenced by read_all_files_(), and set_record_source().

bool core::import_pose::pose_stream::SilentFilePoseInputStream::renumber_decoys_

private

Definition at line 150 of file SilentFilePoseInputStream.hh.

Referenced by renumber_decoys().

core::io::silent::SilentFileDataOP core::import_pose::pose_stream::SilentFilePoseInputStream::sfd_

private

Definition at line 148 of file SilentFilePoseInputStream.hh.

Referenced by filenames(), has_another_pose(), read_all_files_(), reset(), set_silent_file_data(), and SilentFilePoseInputStream().

utility::vector1< string > core::import_pose::pose_stream::SilentFilePoseInputStream::tags_

private

Definition at line 146 of file SilentFilePoseInputStream.hh.

Referenced by read_all_files_(), set_silent_file_data(), and tags().

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

• src/core/import_pose/pose_stream/SilentFilePoseInputStream.hh
• src/core/import_pose/pose_stream/SilentFilePoseInputStream.cc