gemmi::MonLib Struct Reference

#include <monlib.hpp>

Public Member Functions
const ChemLink *	get_link (const std::string &link_id) const
const ChemMod *	get_mod (const std::string &name) const
std::tuple< const ChemLink *, bool, const ChemComp::Aliasing *, const ChemComp::Aliasing * >	match_link (const Residue &res1, const std::string &atom1, char alt1, const Residue &res2, const std::string &atom2, char alt2, double min_bond_sq=0) const
void	add_monomer_if_present (const cif::Block &block)
bool	link_side_matches_residue (const ChemLink::Side &side, const std::string &res_name, ChemComp::Aliasing const **aliasing) const
std::string	path (const std::string &code) const
	Returns path to the monomer cif file (the file may not exist).
void	read_monomer_doc (const cif::Document &doc)
void	read_monomer_cif (const std::string &path_)
void	set_monomer_dir (const std::string &monomer_dir_)
bool	read_monomer_lib (const std::string &monomer_dir_, const std::vector< std::string > &resnames, const Logger &logger)
	Read mon_lib_list.cif, ener_lib.cif and required monomers.
double	find_ideal_distance (const const_CRA &cra1, const const_CRA &cra2) const
void	update_old_atom_names (Structure &st, const Logger &logger) const

Static Public Member Functions
static std::string	relative_monomer_path (const std::string &code)

Public Attributes
std::string	monomer_dir
std::map< std::string, ChemComp >	monomers
std::map< std::string, ChemLink >	links
std::map< std::string, ChemMod >	modifications
std::map< std::string, ChemComp::Group >	cc_groups
EnerLib	ener_lib

Detailed Description

Definition at line 106 of file monlib.hpp.

Member Function Documentation

get_link()

const ChemLink * gemmi::MonLib::get_link ( const std::string &  link_id ) const

inline

Definition at line 114 of file monlib.hpp.

get_mod()

const ChemMod * gemmi::MonLib::get_mod ( const std::string &  name ) const

inline

Definition at line 118 of file monlib.hpp.

match_link()

std::tuple< const ChemLink *, bool, const ChemComp::Aliasing *, const ChemComp::Aliasing * > gemmi::MonLib::match_link ( const Residue &  res1, const std::string &  atom1, char  alt1, const Residue &  res2, const std::string &  atom2, char  alt2, double  min_bond_sq = 0  ) const

inline

Definition at line 126 of file monlib.hpp.

add_monomer_if_present()

void gemmi::MonLib::add_monomer_if_present ( const cif::Block &  block )

inline

Definition at line 175 of file monlib.hpp.

link_side_matches_residue()

bool gemmi::MonLib::link_side_matches_residue ( const ChemLink::Side &  side, const std::string &  res_name, ChemComp::Aliasing const **  aliasing  ) const

inline

Definition at line 188 of file monlib.hpp.

path()

std::string gemmi::MonLib::path ( const std::string &  code ) const

inline

Returns path to the monomer cif file (the file may not exist).

Definition at line 209 of file monlib.hpp.

relative_monomer_path()

static std::string gemmi::MonLib::relative_monomer_path ( const std::string &  code )

static

read_monomer_doc()

void gemmi::MonLib::read_monomer_doc

(

const cif::Document &

doc

)

read_monomer_cif()

void gemmi::MonLib::read_monomer_cif

(

const std::string &

path_

)

set_monomer_dir()

void gemmi::MonLib::set_monomer_dir ( const std::string &  monomer_dir_ )

inline

Definition at line 219 of file monlib.hpp.

read_monomer_lib()

bool gemmi::MonLib::read_monomer_lib	(	const std::string &	monomer_dir_,
		const std::vector< std::string > &	resnames,
		const Logger &	logger
	)

Read mon_lib_list.cif, ener_lib.cif and required monomers.

Returns true if all requested monomers were added.

find_ideal_distance()

double gemmi::MonLib::find_ideal_distance	(	const const_CRA &	cra1,
		const const_CRA &	cra2
	)		const

update_old_atom_names()

void gemmi::MonLib::update_old_atom_names	(	Structure &	st,
		const Logger &	logger
	)		const

Member Data Documentation

monomer_dir

std::string gemmi::MonLib::monomer_dir

Definition at line 107 of file monlib.hpp.

monomers

std::map<std::string, ChemComp> gemmi::MonLib::monomers

Definition at line 108 of file monlib.hpp.

links

std::map<std::string, ChemLink> gemmi::MonLib::links

Definition at line 109 of file monlib.hpp.

modifications

std::map<std::string, ChemMod> gemmi::MonLib::modifications

Definition at line 110 of file monlib.hpp.

cc_groups

std::map<std::string, ChemComp::Group> gemmi::MonLib::cc_groups

Definition at line 111 of file monlib.hpp.

ener_lib

EnerLib gemmi::MonLib::ener_lib

Definition at line 112 of file monlib.hpp.

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The documentation for this struct was generated from the following file:

• include/gemmi/monlib.hpp