An object wrapper for reading atom_tree_diff files, complete with embedded reference structures. More...

#include <atom_tree_diff.hh>

Inheritance diagram for core::import_pose::atom_tree_diffs::AtomTreeDiff:

Collaboration diagram for core::import_pose::atom_tree_diffs::AtomTreeDiff:

Public Member Functions
	AtomTreeDiff ()

	AtomTreeDiff (std::string filename)

virtual	~AtomTreeDiff ()

bool	has_ref_pose (std::string const &tag) const
	returns true if a reference struct with the given tag is present More...

bool	has_tag (std::string const &tag) const
	True if a (non-reference) structure with the given tag is present in the file. More...

bool	has_ref_tag (std::string const &tag) const

ScoresPairList const &	scores () const
	Return list of (pose tag, score sets) pairs for all poses, in file order. More...

void	read_pose (std::string const &tag, core::pose::Pose &pose_out)
	Reads the pose data from file and reconstructs the complete pose. More...

void	read_pose (std::string const &tag, core::pose::Pose &pose_out, core::pose::Pose const &ref_pose)
	Reads the pose data from file and reconstructs the complete pose, using the supplied reference pose. More...

void	read_file (std::string filename)

core::pose::PoseCOP	ref_pose_for (std::string const &tag)
	Returns the default reference pose for the given tag. Fails if none is available. More...

core::pose::PoseOPs const &	all_ref_poses () const
	Allows access to and mutation of (!) the references poses stored in this file. Use with caution. More...

RefTags const &	get_ref_tags () const

TagScoreMap const &	get_tag_score_map () const

int	count (std::string const &tag) const

Static Public Member Functions
static void	sort_by (std::string const &score_name, ScoresPairList &scores, bool descending=false)
	Utility function for selecting subsets of structures by score. More...

Private Member Functions
	AtomTreeDiff (AtomTreeDiff const &)

Private Attributes
ScoresPairList	scores_

RefTags	ref_tags_

TagScoreMap	tag_idx_
	Maps tags to indices in scores_. More...

std::map< std::string, long >	offsets_
	The map of (tag, file position) for getting random access to the structural data. More...

std::map< std::string, core::pose::PoseOP >	ref_poses_
	The map of (tag, reference pose) for decoding the diffs. Some could be null. More...

core::pose::PoseOPs	unique_ref_poses_
	All references poses from the file, one copy each for convenience. More...

std::ifstream	in_

bool	file_read_

Detailed Description

An object wrapper for reading atom_tree_diff files, complete with embedded reference structures.

Only works with uncompressed files, because we have to be able to to random access (seekg) to pull out single structures in random order.

Definition at line 67 of file atom_tree_diff.hh.

Constructor & Destructor Documentation

core::import_pose::atom_tree_diffs::AtomTreeDiff::AtomTreeDiff ( )

Definition at line 69 of file atom_tree_diff.cc.

core::import_pose::atom_tree_diffs::AtomTreeDiff::AtomTreeDiff ( std::string filename)

Definition at line 79 of file atom_tree_diff.cc.

References read_file().

core::import_pose::atom_tree_diffs::AtomTreeDiff::~AtomTreeDiff ( )

virtual

Definition at line 146 of file atom_tree_diff.cc.

References in_.

core::import_pose::atom_tree_diffs::AtomTreeDiff::AtomTreeDiff ( AtomTreeDiff const & )

private

Member Function Documentation

core::pose::PoseOPs const& core::import_pose::atom_tree_diffs::AtomTreeDiff::all_ref_poses ( ) const

inline

Allows access to and mutation of (!) the references poses stored in this file. Use with caution.

This exists to allow setup on stored reference poses for properties that don't get saved/restored in PDB format, like covalent constraints for enzyme design.

Definition at line 103 of file atom_tree_diff.hh.

References unique_ref_poses_.

int core::import_pose::atom_tree_diffs::AtomTreeDiff::count ( std::string const & tag) const

inline

Definition at line 110 of file atom_tree_diff.hh.

References ref_tags_.

RefTags const& core::import_pose::atom_tree_diffs::AtomTreeDiff::get_ref_tags ( ) const

inline

Definition at line 106 of file atom_tree_diff.hh.

References ref_tags_.

TagScoreMap const& core::import_pose::atom_tree_diffs::AtomTreeDiff::get_tag_score_map ( ) const

inline

Definition at line 108 of file atom_tree_diff.hh.

References tag_idx_.

bool core::import_pose::atom_tree_diffs::AtomTreeDiff::has_ref_pose ( std::string const & tag) const

returns true if a reference struct with the given tag is present

Definition at line 151 of file atom_tree_diff.cc.

References ref_poses_.

bool core::import_pose::atom_tree_diffs::AtomTreeDiff::has_ref_tag ( std::string const & tag) const

Definition at line 159 of file atom_tree_diff.cc.

References ref_poses_.

bool core::import_pose::atom_tree_diffs::AtomTreeDiff::has_tag ( std::string const & tag) const

True if a (non-reference) structure with the given tag is present in the file.

Definition at line 155 of file atom_tree_diff.cc.

References tag_idx_.

void core::import_pose::atom_tree_diffs::AtomTreeDiff::read_file ( std::string filename)

Definition at line 90 of file atom_tree_diff.cc.

References core::sequence::end, file_read_, core::import_pose::atom_tree_diffs::header_from_atom_tree_diff(), in_, offsets_, core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), ref_poses_, ref_tags_, scores(), scores_, protocols::loops::start, tag_idx_, and unique_ref_poses_.

Referenced by AtomTreeDiff().

void core::import_pose::atom_tree_diffs::AtomTreeDiff::read_pose	(	std::string const &	tag,
		core::pose::Pose &	pose_out
	)

Reads the pose data from file and reconstructs the complete pose.

Definition at line 174 of file atom_tree_diff.cc.

References ref_poses_.

void core::import_pose::atom_tree_diffs::AtomTreeDiff::read_pose	(	std::string const &	tag,
		core::pose::Pose &	pose_out,
		core::pose::Pose const &	ref_pose
	)

Reads the pose data from file and reconstructs the complete pose, using the supplied reference pose.

Definition at line 182 of file atom_tree_diff.cc.

References core::import_pose::atom_tree_diffs::header_from_atom_tree_diff(), in_, offsets_, and core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().

core::pose::PoseCOP core::import_pose::atom_tree_diffs::AtomTreeDiff::ref_pose_for ( std::string const & tag)

Returns the default reference pose for the given tag. Fails if none is available.

Definition at line 201 of file atom_tree_diff.cc.

References ref_poses_.

ScoresPairList const& core::import_pose::atom_tree_diffs::AtomTreeDiff::scores ( ) const

inline

Return list of (pose tag, score sets) pairs for all poses, in file order.

Definition at line 84 of file atom_tree_diff.hh.

References scores_.

Referenced by read_file(), and protocols::ligand_docking::select_best_poses().

void core::import_pose::atom_tree_diffs::AtomTreeDiff::sort_by	(	std::string const &	score_name,
		ScoresPairList &	scores,
		bool	descending = `false`
	)

static

Utility function for selecting subsets of structures by score.

Definition at line 164 of file atom_tree_diff.cc.

Referenced by protocols::ligand_docking::select_best_poses().

Member Data Documentation

bool core::import_pose::atom_tree_diffs::AtomTreeDiff::file_read_

mutableprivate

Definition at line 141 of file atom_tree_diff.hh.

Referenced by read_file().

std::ifstream core::import_pose::atom_tree_diffs::AtomTreeDiff::in_

private

Definition at line 139 of file atom_tree_diff.hh.

Referenced by read_file(), read_pose(), and ~AtomTreeDiff().

std::map< std::string, long > core::import_pose::atom_tree_diffs::AtomTreeDiff::offsets_

private

The map of (tag, file position) for getting random access to the structural data.

Definition at line 130 of file atom_tree_diff.hh.

Referenced by read_file(), and read_pose().

std::map< std::string, core::pose::PoseOP > core::import_pose::atom_tree_diffs::AtomTreeDiff::ref_poses_

private

The map of (tag, reference pose) for decoding the diffs. Some could be null.

Definition at line 133 of file atom_tree_diff.hh.

Referenced by has_ref_pose(), has_ref_tag(), read_file(), read_pose(), and ref_pose_for().

RefTags core::import_pose::atom_tree_diffs::AtomTreeDiff::ref_tags_

private

Maps reference tags to how many associated atom_tree_diff structs exist... int is needed here because there are 0 atom tree diffs to start with

Definition at line 124 of file atom_tree_diff.hh.

Referenced by count(), get_ref_tags(), and read_file().

ScoresPairList core::import_pose::atom_tree_diffs::AtomTreeDiff::scores_

private

The list of (tag,scores) pairs for the diffed structures, for efficient selection of subsets. (E.g. the top 5% by total score.) Memory cost is probably ~1 kb / structure.

Definition at line 120 of file atom_tree_diff.hh.

Referenced by read_file(), and scores().

TagScoreMap core::import_pose::atom_tree_diffs::AtomTreeDiff::tag_idx_

private

Maps tags to indices in scores_.

Definition at line 127 of file atom_tree_diff.hh.

Referenced by get_tag_score_map(), has_tag(), and read_file().

core::pose::PoseOPs core::import_pose::atom_tree_diffs::AtomTreeDiff::unique_ref_poses_

private

All references poses from the file, one copy each for convenience.

Definition at line 136 of file atom_tree_diff.hh.

Referenced by all_ref_poses(), and read_file().

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

src/core/import_pose/atom_tree_diffs/atom_tree_diff.hh
src/core/import_pose/atom_tree_diffs/atom_tree_diff.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation