class used to create/manipulate a database of sheets using a list of pdb files More...

#include <SheetDB.hh>

Inheritance diagram for protocols::denovo_design::components::SheetDB:

Public Member Functions
	SheetDB ()
	default constructor More...

SheetList	sheet_list (architects::Lengths const &lengths, StrandOrientations const &orientations, RegisterShifts const &shifts)
	query the database for a sheet and retrieve the list – if not found, tries to read from disk More...

SheetList	sheet_list_const (architects::Lengths const &lengths, StrandOrientations const &orientations, RegisterShifts const &shifts) const
	query the database for a sheet and retrieve the list – if not found, tries to read from disk More...

bool	has_data (architects::Lengths const &lengths, StrandOrientations const &orientations, RegisterShifts const &shifts) const
	query the database, returns whether data exists More...

void	set_db_path (std::string const &db_path)
	set location of sheet database files More...

void	set_sheetlist (SheetList const &list, core::Size const nstrands, std::string const &in_orientations, std::string const &in_lengths)
	add a sheet to the database More...

void	set_sheetlist_as_is (SheetList const &list, core::Size const nstrands, std::string const &orientations, std::string const &lengths)
	adds a sheet list as it is presented More...

void	add_sheet (core::pose::PoseOP pose, core::Size const nstrands, std::string const &orientations, std::string const &lengths_shifts, bool const check_descriptor_against_pose)
	add a sheet to the database More...

int	add_sheets_from_pose (core::pose::Pose &pose)
	adds sheet(s) based on a pose – returns # of sheets added More...

int	add_sheets_from_spairs (core::pose::Pose const &pose, protocols::fldsgn::topology::StrandPairingSet &spairs, protocols::fldsgn::topology::SS_Info2 const &ss_info)
	adds sheet(s) based on a strand pairing set and pose – returns # of sheets added More...

utility::vector1< core::Size >	nstrand_values () const
	queries the database for all strand lengths More...

utility::vector1< std::string >	orientations (core::Size const nstrands) const
	queries the database for all orientations with nstrands strands More...

utility::vector1< std::string >	lengths_shifts (core::Size const nstrands, std::string const &orientations) const
	queries the database for all lengths/shifts with nstrands strands and given orientations More...

void	set_idealize (bool const idealize_val)

Static Public Attributes
static core::Size const	MIN_STRAND_LEN = 4

static core::Size const	SHEETINFO_REMARK = 994

static core::Size const	SHEETSCORE_REMARK = 995

Protected Member Functions
void	load_sheetlist_from_file (core::Size const nstrands, std::string const &orientations, std::string const &strandinfo)
	reads sheetlist from the file database, and saves it to this database More...

Private Member Functions
SheetList	sheet_list (core::Size const nstrands, std::string const &orientations, std::string const &strandinfo)
	query the database for a sheet and retrieve the list – if not found, tries to read from disk More...

bool	has_data (core::Size const nstrands, std::string const &orient, std::string const &strandinfo) const
	queries the database to see if the requested data exists More...

SheetList	sheet_list_const (core::Size const nstrands, std::string const &orientations, std::string const &strandinfo) const
	query the database for a sheet and retrieve the list More...

SheetList	sheet_list (core::Size const nstrands, std::string const &orientations) const
	query the database for a sheet and retrieve the list with all lengths and shifts included More...

Private Attributes
bool	idealize_
	idealize poses before adding to db? (Default = true); More...

std::string	db_path_
	the location of the database files More...

MapByStrands	sheet_db_
	the guts of the database More...

Detailed Description

class used to create/manipulate a database of sheets using a list of pdb files

Constructor & Destructor Documentation

◆ SheetDB()

protocols::denovo_design::components::SheetDB::SheetDB ( )

default constructor

SheetDB Implementations.

default constructor

References sheet_db_.

Member Function Documentation

◆ add_sheet()

void protocols::denovo_design::components::SheetDB::add_sheet	(	core::pose::PoseOP	pose,
		core::Size const	nstrands,
		std::string const &	orientations,
		std::string const &	lengths_shifts,
		bool const	check_descriptor_against_pose = `true`
	)

add a sheet to the database

add a sheet to the database based on descriptors

References protocols::denovo_design::components::canonicalize(), core::chemical::CENTROID_t, lengths_shifts(), orientations(), protocols::denovo_design::components::pose_matches_description(), protocols::denovo_design::components::reverse_chains(), protocols::denovo_design::components::reverse_lengths(), protocols::denovo_design::components::reverse_orientations(), sheet_db_, core::util::switch_to_residue_type_set(), and protocols::TR().

Referenced by add_sheets_from_spairs().

◆ add_sheets_from_pose()

int protocols::denovo_design::components::SheetDB::add_sheets_from_pose ( core::pose::Pose & pose )

adds sheet(s) based on a pose – returns # of sheets added

adds sheet(s) based on a strand pairing set and pose

References add_sheets_from_spairs(), protocols::fldsgn::topology::calc_strand_pairing_set(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::simple_filters::dssp(), core::pose::Pose::empty(), core::chemical::FULL_ATOM_t, core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), and protocols::TR().

◆ add_sheets_from_spairs()

int protocols::denovo_design::components::SheetDB::add_sheets_from_spairs	(	core::pose::Pose const &	pose,
		protocols::fldsgn::topology::StrandPairingSet &	spairs,
		protocols::fldsgn::topology::SS_Info2 const &	ss_info
	)

adds sheet(s) based on a strand pairing set and pose – returns # of sheets added

adds sheet(s) based on a strand pairing set and pose

References add_sheet(), protocols::denovo_design::components::extract_sheets_from_pose(), protocols::denovo_design::components::extract_sheets_from_strandlist(), idealize_, protocols::denovo_design::components::num_strands(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::fldsgn::topology::StrandPairingSet::strand_pairings(), and protocols::TR().

Referenced by add_sheets_from_pose().

◆ has_data() [1/2]

bool protocols::denovo_design::components::SheetDB::has_data	(	architects::Lengths const &	lengths,
		StrandOrientations const &	orientations,
		RegisterShifts const &	shifts
	)		const

query the database, returns whether data exists

query the database for a set of orientations and shifts

References protocols::denovo_design::components::make_strand_info_str(), orientations(), and protocols::denovo_design::components::orientations_str().

Referenced by sheet_list().

◆ has_data() [2/2]

bool protocols::denovo_design::components::SheetDB::has_data	(	core::Size const	nstrands,
		std::string const &	orient,
		std::string const &	strandinfo
	)		const

private

queries the database to see if the requested data exists

References sheet_db_.

◆ lengths_shifts()

utility::vector1< std::string > protocols::denovo_design::components::SheetDB::lengths_shifts	(	core::Size const	nstrands,
		std::string const &	orientations
	)		const

queries the database for all lengths/shifts with nstrands strands and given orientations

References orientations(), and sheet_db_.

Referenced by add_sheet().

◆ load_sheetlist_from_file()

void protocols::denovo_design::components::SheetDB::load_sheetlist_from_file	(	core::Size const	nstrands,
		std::string const &	orientations,
		std::string const &	strandinfo
	)

protected

reads sheetlist from the file database, and saves it to this database

reads sheetlist from the file database, and saves it to this database – should always be called with canonical descriptors

References core::io::silent::SilentFileData::begin(), protocols::denovo_design::components::canonicalize(), db_path_, core::io::silent::SilentFileData::end(), core::sequence::end, protocols::abinitio::filename(), orientations(), core::io::silent::SilentFileData::read_file(), set_sheetlist(), core::id::to_string(), and protocols::TR().

Referenced by sheet_list().

◆ nstrand_values()

utility::vector1< core::Size > protocols::denovo_design::components::SheetDB::nstrand_values ( ) const

queries the database for all strand lengths

References sheet_db_.

◆ orientations()

utility::vector1< std::string > protocols::denovo_design::components::SheetDB::orientations ( core::Size const nstrands ) const

queries the database for all orientations with nstrands strands

References sheet_db_.

Referenced by add_sheet(), protocols::denovo_design::components::canonicalize(), protocols::denovo_design::components::find_orientations_and_lengths(), has_data(), lengths_shifts(), load_sheetlist_from_file(), protocols::denovo_design::components::parse_orientations(), protocols::denovo_design::components::reverse_lengths(), set_sheetlist_as_is(), sheet_list(), and sheet_list_const().

◆ set_db_path()

void protocols::denovo_design::components::SheetDB::set_db_path ( std::string const & db_path )

inline

set location of sheet database files

References db_path_.

◆ set_idealize()

void protocols::denovo_design::components::SheetDB::set_idealize ( bool const idealize_val )

inline

References idealize_.

◆ set_sheetlist()

void protocols::denovo_design::components::SheetDB::set_sheetlist	(	SheetList const &	list,
		core::Size const	nstrands,
		std::string const &	in_orientations,
		std::string const &	in_lengths
	)

add a sheet to the database

adds a sheetlist to the database with given descriptors

References protocols::denovo_design::components::canonicalize(), protocols::denovo_design::components::reverse_chains(), protocols::denovo_design::components::reverse_lengths(), protocols::denovo_design::components::reverse_orientations(), and set_sheetlist_as_is().

Referenced by load_sheetlist_from_file().

◆ set_sheetlist_as_is()

void protocols::denovo_design::components::SheetDB::set_sheetlist_as_is	(	SheetList const &	list,
		core::Size const	nstrands,
		std::string const &	orientations,
		std::string const &	lengths
	)

adds a sheet list as it is presented

References orientations(), and sheet_db_.

Referenced by set_sheetlist().

◆ sheet_list() [1/3]

SheetList protocols::denovo_design::components::SheetDB::sheet_list	(	architects::Lengths const &	lengths,
		StrandOrientations const &	orientations,
		RegisterShifts const &	shifts
	)

query the database for a sheet and retrieve the list – if not found, tries to read from disk

query the database for a set of orientations and shifts

References protocols::denovo_design::components::make_strand_info_str(), orientations(), and protocols::denovo_design::components::orientations_str().

◆ sheet_list() [2/3]

SheetList protocols::denovo_design::components::SheetDB::sheet_list	(	core::Size const	nstrands,
		std::string const &	orientations
	)		const

private

query the database for a sheet and retrieve the list with all lengths and shifts included

query the database for a sheet and retrieve the list

References orientations(), and sheet_db_.

◆ sheet_list() [3/3]

SheetList protocols::denovo_design::components::SheetDB::sheet_list	(	core::Size const	nstrands,
		std::string const &	orientations,
		std::string const &	strandinfo
	)

private

query the database for a sheet and retrieve the list – if not found, tries to read from disk

query the database for a sheet and retrieve the list

References has_data(), load_sheetlist_from_file(), sheet_db_, sheet_list_const(), and protocols::TR().

◆ sheet_list_const() [1/2]

SheetList protocols::denovo_design::components::SheetDB::sheet_list_const	(	architects::Lengths const &	lengths,
		StrandOrientations const &	orientations,
		RegisterShifts const &	shifts
	)		const

query the database for a sheet and retrieve the list – if not found, tries to read from disk

query the database for a set of orientations and shifts

References protocols::denovo_design::components::make_strand_info_str(), orientations(), and protocols::denovo_design::components::orientations_str().

Referenced by sheet_list().

◆ sheet_list_const() [2/2]

SheetList protocols::denovo_design::components::SheetDB::sheet_list_const	(	core::Size const	nstrands,
		std::string const &	orientations,
		std::string const &	strandinfo
	)		const

private

query the database for a sheet and retrieve the list

References sheet_db_.

Member Data Documentation

◆ db_path_

std::string protocols::denovo_design::components::SheetDB::db_path_

private

the location of the database files

Referenced by load_sheetlist_from_file(), and set_db_path().

◆ idealize_

bool protocols::denovo_design::components::SheetDB::idealize_

private

idealize poses before adding to db? (Default = true);

Referenced by add_sheets_from_spairs(), and set_idealize().

◆ MIN_STRAND_LEN

core::Size const protocols::denovo_design::components::SheetDB::MIN_STRAND_LEN = 4

static

Referenced by protocols::denovo_design::components::graph_from_strandpairings(), and protocols::denovo_design::components::prune_unpaired_residues().

◆ sheet_db_

MapByStrands protocols::denovo_design::components::SheetDB::sheet_db_

private

the guts of the database

Referenced by add_sheet(), has_data(), lengths_shifts(), nstrand_values(), orientations(), set_sheetlist_as_is(), sheet_list(), sheet_list_const(), and SheetDB().

◆ SHEETINFO_REMARK

core::Size const protocols::denovo_design::components::SheetDB::SHEETINFO_REMARK = 994

static

◆ SHEETSCORE_REMARK

core::Size const protocols::denovo_design::components::SheetDB::SHEETSCORE_REMARK = 995

static

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

src/protocols/denovo_design/components/SheetDB.hh
src/protocols/denovo_design/components/SheetDB.cc

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SheetDB()

Member Function Documentation

◆ add_sheet()

◆ add_sheets_from_pose()

◆ add_sheets_from_spairs()

◆ has_data() [1/2]

◆ has_data() [2/2]

◆ lengths_shifts()

◆ load_sheetlist_from_file()

◆ nstrand_values()

◆ orientations()

◆ set_db_path()

◆ set_idealize()

◆ set_sheetlist()

◆ set_sheetlist_as_is()

◆ sheet_list() [1/3]

◆ sheet_list() [2/3]

◆ sheet_list() [3/3]

◆ sheet_list_const() [1/2]

◆ sheet_list_const() [2/2]

Member Data Documentation

◆ db_path_

◆ idealize_

◆ MIN_STRAND_LEN

◆ sheet_db_

◆ SHEETINFO_REMARK

◆ SHEETSCORE_REMARK