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_, read_cif_func read_cif)
void	set_monomer_dir (const std::string &monomer_dir_)
bool	read_monomer_lib (const std::string &monomer_dir_, const std::vector< std::string > &resnames, read_cif_func read_cif, std::string *error=nullptr)
	Read mon_lib_list.cif, ener_lib.cif and required monomers.
double	find_ideal_distance (const const_CRA &cra1, const const_CRA &cra2) const
std::string	update_old_atom_names (Structure &st) const

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

Public Attributes
std::string	monomer_dir
EnerLib	ener_lib
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

Detailed Description

Definition at line 126 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 134 of file monlib.hpp.

get_mod()

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

inline

Definition at line 138 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 146 of file monlib.hpp.

add_monomer_if_present()

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

inline

Definition at line 195 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 208 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 229 of file monlib.hpp.

relative_monomer_path()

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

inlinestatic

Definition at line 233 of file monlib.hpp.

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_, read_cif_func  read_cif  )

inline

Definition at line 259 of file monlib.hpp.

set_monomer_dir()

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

inline

Definition at line 263 of file monlib.hpp.

read_monomer_lib()

bool gemmi::MonLib::read_monomer_lib ( const std::string &  monomer_dir_, const std::vector< std::string > &  resnames, read_cif_func  read_cif, std::string *  error = nullptr  )

inline

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

Returns true if all requested monomers were added.

Definition at line 271 of file monlib.hpp.

find_ideal_distance()

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

update_old_atom_names()

std::string gemmi::MonLib::update_old_atom_names

(

Structure &

st

)

const

Member Data Documentation

monomer_dir

std::string gemmi::MonLib::monomer_dir

Definition at line 127 of file monlib.hpp.

ener_lib

EnerLib gemmi::MonLib::ener_lib

Definition at line 128 of file monlib.hpp.

monomers

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

Definition at line 129 of file monlib.hpp.

links

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

Definition at line 130 of file monlib.hpp.

modifications

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

Definition at line 131 of file monlib.hpp.

cc_groups

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

Definition at line 132 of file monlib.hpp.

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

• /home/wojdyr/gemmi/gemmi/include/gemmi/monlib.hpp