Gemmi C++ API
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Classes | Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
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 180 of file topo.hpp.

◆ find_resinfo()

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

Definition at line 204 of file topo.hpp.

◆ first_bond_in_link()

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

Definition at line 212 of file topo.hpp.

◆ take_bond()

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

Definition at line 219 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 230 of file topo.hpp.

◆ get_chirality()

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

Definition at line 243 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 
)

◆ 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 277 of file topo.hpp.

Member Data Documentation

◆ warnings

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

Definition at line 187 of file topo.hpp.

◆ only_bonds

bool gemmi::Topo::only_bonds = false

Definition at line 188 of file topo.hpp.

◆ chain_infos

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

Definition at line 189 of file topo.hpp.

◆ extras

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

Definition at line 190 of file topo.hpp.

◆ bonds

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

Definition at line 193 of file topo.hpp.

◆ angles

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

Definition at line 194 of file topo.hpp.

◆ torsions

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

Definition at line 195 of file topo.hpp.

◆ chirs

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

Definition at line 196 of file topo.hpp.

◆ planes

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

Definition at line 197 of file topo.hpp.

◆ bond_index

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

Definition at line 199 of file topo.hpp.

◆ angle_index

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

Definition at line 200 of file topo.hpp.

◆ torsion_index

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

Definition at line 201 of file topo.hpp.

◆ plane_index

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

Definition at line 202 of file topo.hpp.

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