protocols::chromophore::ReadResidueCoordinatesFromPDB Class Reference

re-reading residue's coordinates from a PDB file More...

#include <ReadResidueCoordinatesFromPDB.hh>

Inheritance diagram for protocols::chromophore::ReadResidueCoordinatesFromPDB:

Public Member Functions
	ReadResidueCoordinatesFromPDB ()
	Default constructor. More...
	~ReadResidueCoordinatesFromPDB () override
	Destructor. More...
ReadResidueCoordinatesFromPDBOP	clone () const
	Clone operation: make a copy of this object, and return an owning pointer to the copy. More...
utility::vector1< std::tuple< std::string, core::Vector > >	get_residue_coordinates (int const resnum, char const chain_name) const
void	read_coordinates_from_file (std::string const &filename, utility::vector1< std::tuple< int, char > > const &residues_to_read)
void	read_coordinates (std::istream &instream, utility::vector1< std::tuple< int, char > > const &residues_to_read)
bool	coordinates_exist (int const resnum, char const chain_name) const
core::Size	number_of_residues () const

Private Member Functions
void	parse_pdb (std::istream &instream, core::io::StructFileRep &sfr)
void	save_residue_coordinates (core::io::ResidueInformation const &residue, int const resnum, char const chain_name)

Private Attributes
std::map< std::tuple< int, char >, utility::vector1< std::tuple< std::string, core::Vector > > >	coordinates_

Detailed Description

re-reading residue's coordinates from a PDB file

Author

Nina Bozhanova (nbozh.nosp@m.anov.nosp@m.a@gma.nosp@m.il.c.nosp@m.om)

Constructor & Destructor Documentation

ReadResidueCoordinatesFromPDB()

protocols::chromophore::ReadResidueCoordinatesFromPDB::ReadResidueCoordinatesFromPDB ( )

default

Default constructor.

~ReadResidueCoordinatesFromPDB()

protocols::chromophore::ReadResidueCoordinatesFromPDB::~ReadResidueCoordinatesFromPDB ( )

overridedefault

Destructor.

Member Function Documentation

clone()

ReadResidueCoordinatesFromPDBOP protocols::chromophore::ReadResidueCoordinatesFromPDB::clone

(

)

const

Clone operation: make a copy of this object, and return an owning pointer to the copy.

coordinates_exist()

bool protocols::chromophore::ReadResidueCoordinatesFromPDB::coordinates_exist	(	int const	resnum,
		char const	chain_name
	)		const

References coordinates_.

Referenced by get_residue_coordinates(), and save_residue_coordinates().

get_residue_coordinates()

utility::vector1< std::tuple< std::string, core::Vector > > protocols::chromophore::ReadResidueCoordinatesFromPDB::get_residue_coordinates	(	int const	resnum,
		char const	chain_name
	)		const

References coordinates_, and coordinates_exist().

number_of_residues()

core::Size protocols::chromophore::ReadResidueCoordinatesFromPDB::number_of_residues

(

)

const

References coordinates_.

parse_pdb()

void protocols::chromophore::ReadResidueCoordinatesFromPDB::parse_pdb ( std::istream &  instream, core::io::StructFileRep &  sfr  )

private

References core::io::pdb::create_sfr_from_pdb_file_contents().

Referenced by read_coordinates().

read_coordinates()

void protocols::chromophore::ReadResidueCoordinatesFromPDB::read_coordinates	(	std::istream &	instream,
		utility::vector1< std::tuple< int, char > > const &	residues_to_read
	)

References core::io::AtomInformation::chainID, protocols::loops::chainID, core::io::StructFileRep::chains(), parse_pdb(), core::io::AtomInformation::resSeq, protocols::loops::resSeq, and save_residue_coordinates().

Referenced by read_coordinates_from_file().

read_coordinates_from_file()

void protocols::chromophore::ReadResidueCoordinatesFromPDB::read_coordinates_from_file	(	std::string const &	filename,
		utility::vector1< std::tuple< int, char > > const &	residues_to_read
	)

References protocols::abinitio::filename(), and read_coordinates().

save_residue_coordinates()

void protocols::chromophore::ReadResidueCoordinatesFromPDB::save_residue_coordinates ( core::io::ResidueInformation const &  residue, int const  resnum, char const  chain_name  )

private

References core::io::ResidueInformation::atoms(), coordinates_, coordinates_exist(), core::io::AtomInformation::name, core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by read_coordinates().

Member Data Documentation

coordinates_

std::map< std::tuple < int, char >, utility::vector1 <std::tuple <std::string, core::Vector> > > protocols::chromophore::ReadResidueCoordinatesFromPDB::coordinates_

private

Referenced by coordinates_exist(), get_residue_coordinates(), number_of_residues(), and save_residue_coordinates().

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

• src/protocols/chromophore/ReadResidueCoordinatesFromPDB.hh
• src/protocols/chromophore/ReadResidueCoordinatesFromPDB.cc