gemmi::Topo Struct Reference

#include <topo.hpp>

Classes
struct	Angle
struct	Bond
struct	ChainInfo
struct	Chirality
struct	FinalChemComp
struct	Link
struct	Mod
struct	Plane
struct	ResInfo
struct	Rule
struct	Torsion

Public Types
enum class	RKind {   Bond , Angle , Torsion , Chirality ,   Plane }

Public Member Functions
	Topo ()=default
	Topo (Topo const &)=delete
Topo &	operator= (Topo const &)=delete
ResInfo *	find_resinfo (const Residue *res)
Bond *	first_bond_in_link (const Link &link)
const Restraints::Bond *	take_bond (const Atom *a, const Atom *b) const
const Restraints::Angle *	take_angle (const Atom *a, const Atom *b, const Atom *c) const
const Chirality *	get_chirality (const Atom *ctr) const
double	ideal_chiral_abs_volume (const Chirality &ch) const
std::vector< Rule >	apply_restraints (const Restraints &rt, Residue &res, Residue *res2, Asu asu, char altloc1, char altloc2, bool require_alt)
void	apply_restraints_from_link (Link &link, const MonLib &monlib)
void	initialize_refmac_topology (Structure &st, Model &model0, MonLib &monlib, bool ignore_unknown_links=false)
void	apply_all_restraints (const MonLib &monlib)
void	create_indices ()
Link *	find_polymer_link (const AtomAddress &a1, const AtomAddress &a2)
void	set_cispeps_in_structure (Structure &st)
GEMMI_COLD void	err (const std::string &msg) const

Static Public Member Functions
template<typename T >
static int	has_atom (const Atom *a, const T &t)

Public Attributes
std::ostream *	warnings = nullptr
bool	only_bonds = false
std::vector< ChainInfo >	chain_infos
std::vector< Link >	extras
std::vector< Bond >	bonds
std::vector< Angle >	angles
std::vector< Torsion >	torsions
std::vector< Chirality >	chirs
std::vector< Plane >	planes
std::multimap< const Atom *, Bond * >	bond_index
std::multimap< const Atom *, Angle * >	angle_index
std::multimap< const Atom *, Torsion * >	torsion_index
std::multimap< const Atom *, Plane * >	plane_index

Detailed Description

Definition at line 23 of file topo.hpp.

Member Enumeration Documentation

RKind

enum class gemmi::Topo::RKind

strong

Enumerator
Bond
Angle
Torsion
Chirality
Plane

Definition at line 84 of file topo.hpp.

Constructor & Destructor Documentation

Topo() [1/2]

gemmi::Topo::Topo ( )

default

Topo() [2/2]

gemmi::Topo::Topo ( Topo const &  )

delete

Member Function Documentation

operator=()

Topo & gemmi::Topo::operator= ( Topo const &  )

delete

has_atom()

template<typename T >

static int gemmi::Topo::has_atom ( const Atom *  a, const T &  t  )

inlinestatic

Definition at line 176 of file topo.hpp.

find_resinfo()

ResInfo * gemmi::Topo::find_resinfo ( const Residue *  res )

inline

Definition at line 200 of file topo.hpp.

first_bond_in_link()

Bond * gemmi::Topo::first_bond_in_link ( const Link &  link )

inline

Definition at line 208 of file topo.hpp.

take_bond()

const Restraints::Bond * gemmi::Topo::take_bond ( const Atom *  a, const Atom *  b  ) const

inline

Definition at line 215 of file topo.hpp.

take_angle()

const Restraints::Angle * gemmi::Topo::take_angle ( const Atom *  a, const Atom *  b, const Atom *  c  ) const

inline

Definition at line 226 of file topo.hpp.

get_chirality()

const Chirality * gemmi::Topo::get_chirality ( const Atom *  ctr ) const

inline

Definition at line 239 of file topo.hpp.

ideal_chiral_abs_volume()

double gemmi::Topo::ideal_chiral_abs_volume

(

const Chirality &

ch

)

const

apply_restraints()

std::vector< Rule > gemmi::Topo::apply_restraints	(	const Restraints &	rt,
		Residue &	res,
		Residue *	res2,
		Asu	asu,
		char	altloc1,
		char	altloc2,
		bool	require_alt
	)

apply_restraints_from_link()

void gemmi::Topo::apply_restraints_from_link	(	Link &	link,
		const MonLib &	monlib
	)

initialize_refmac_topology()

void gemmi::Topo::initialize_refmac_topology	(	Structure &	st,
		Model &	model0,
		MonLib &	monlib,
		bool	ignore_unknown_links = false
	)

apply_all_restraints()

void gemmi::Topo::apply_all_restraints

(

const MonLib &

monlib

)

create_indices()

void gemmi::Topo::create_indices

(

)

find_polymer_link()

Link * gemmi::Topo::find_polymer_link ( const AtomAddress &  a1, const AtomAddress &  a2  )

inline

Definition at line 268 of file topo.hpp.

set_cispeps_in_structure()

void gemmi::Topo::set_cispeps_in_structure

(

Structure &

st

)

err()

GEMMI_COLD void gemmi::Topo::err ( const std::string &  msg ) const

inline

Definition at line 288 of file topo.hpp.

Member Data Documentation

warnings

std::ostream* gemmi::Topo::warnings = nullptr

Definition at line 183 of file topo.hpp.

only_bonds

bool gemmi::Topo::only_bonds = false

Definition at line 184 of file topo.hpp.

chain_infos

std::vector<ChainInfo> gemmi::Topo::chain_infos

Definition at line 185 of file topo.hpp.

extras

std::vector<Link> gemmi::Topo::extras

Definition at line 186 of file topo.hpp.

bonds

std::vector<Bond> gemmi::Topo::bonds

Definition at line 189 of file topo.hpp.

angles

std::vector<Angle> gemmi::Topo::angles

Definition at line 190 of file topo.hpp.

torsions

std::vector<Torsion> gemmi::Topo::torsions

Definition at line 191 of file topo.hpp.

chirs

std::vector<Chirality> gemmi::Topo::chirs

Definition at line 192 of file topo.hpp.

planes

std::vector<Plane> gemmi::Topo::planes

Definition at line 193 of file topo.hpp.

bond_index

std::multimap<const Atom*, Bond*> gemmi::Topo::bond_index

Definition at line 195 of file topo.hpp.

angle_index

std::multimap<const Atom*, Angle*> gemmi::Topo::angle_index

Definition at line 196 of file topo.hpp.

torsion_index

std::multimap<const Atom*, Torsion*> gemmi::Topo::torsion_index

Definition at line 197 of file topo.hpp.

plane_index

std::multimap<const Atom*, Plane*> gemmi::Topo::plane_index

Definition at line 198 of file topo.hpp.

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

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