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protocols::denovo_design::components::SheetDB Class Reference

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:
Inheritance graph
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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::Sizenstrand_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

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

default constructor

SheetDB Implementations.

default constructor

References sheet_db_.

Member Function Documentation

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 
)
int protocols::denovo_design::components::SheetDB::add_sheets_from_pose ( core::pose::Pose pose)
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 
)
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(), and protocols::denovo_design::components::orientations_str().

Referenced by sheet_list().

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_.

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 sheet_db_.

Referenced by add_sheet().

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::sequence::end, core::io::silent::SilentFileData::end(), protocols::abinitio::filename(), core::io::silent::SilentFileData::read_file(), set_sheetlist(), core::id::to_string(), and protocols::TR().

Referenced by sheet_list().

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

queries the database for all strand lengths

References sheet_db_.

utility::vector1< std::string > protocols::denovo_design::components::SheetDB::orientations ( core::Size const  nstrands) const
void protocols::denovo_design::components::SheetDB::set_db_path ( std::string const &  db_path)
inline

set location of sheet database files

References db_path_.

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

References idealize_.

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 
)
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().

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(), and protocols::denovo_design::components::orientations_str().

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().

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 sheet_db_.

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(), and protocols::denovo_design::components::orientations_str().

Referenced by sheet_list().

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

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().

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().

core::Size const protocols::denovo_design::components::SheetDB::MIN_STRAND_LEN = 4
static
MapByStrands protocols::denovo_design::components::SheetDB::sheet_db_
private
core::Size const protocols::denovo_design::components::SheetDB::SHEETINFO_REMARK = 994
static
core::Size const protocols::denovo_design::components::SheetDB::SHEETSCORE_REMARK = 995
static

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