gemmi::Residue Struct Reference

#include <model.hpp>

Inheritance diagram for gemmi::Residue:

Public Types
using	OptionalNum = SeqId::OptionalNum
using	child_type = Atom

Public Member Functions
	Residue ()=default
	Residue (const ResidueId &rid) noexcept
Residue	empty_copy () const
std::vector< Atom > &	children ()
const std::vector< Atom > &	children () const
const Atom *	find_by_element (El el) const
Atom *	find_atom (const std::string &atom_name, char altloc, El el=El::X, bool strict_altloc=true)
	El::X means anything; in strict_altloc mode, '*' = any altloc, otherwise it's \0.
const Atom *	find_atom (const std::string &atom_name, char altloc, El el=El::X, bool strict_altloc=true) const
std::vector< Atom >::iterator	find_atom_iter (const std::string &atom_name, char altloc, El el=El::X)
AtomGroup	get (const std::string &atom_name)
Atom &	sole_atom (const std::string &atom_name)
const Atom *	get_ca () const
const Atom *	get_c () const
const Atom *	get_n () const
const Atom *	get_p () const
const Atom *	get_o3prim () const
bool	same_conformer (const Residue &other) const
bool	is_water () const
	Convenience function that duplicates functionality from resinfo.hpp.
UniqProxy< Atom >	first_conformer ()
ConstUniqProxy< Atom >	first_conformer () const
Public Member Functions inherited from gemmi::ResidueId
SeqId	group_key () const
bool	matches (const ResidueId &o) const
bool	matches_noseg (const ResidueId &o) const
bool	operator== (const ResidueId &o) const
std::string	str () const

Static Public Member Functions
static const char *	what ()

Public Attributes
std::string	subchain
std::string	entity_id
OptionalNum	label_seq
EntityType	entity_type = EntityType::Unknown
char	het_flag = '\0'
char	flag = '\0'
SiftsUnpResidue	sifts_unp
short	group_idx = 0
std::vector< Atom >	atoms
Public Attributes inherited from gemmi::ResidueId
SeqId	seqid
std::string	segment
std::string	name

Detailed Description

Definition at line 174 of file model.hpp.

Member Typedef Documentation

OptionalNum

using gemmi::Residue::OptionalNum = SeqId::OptionalNum

Definition at line 175 of file model.hpp.

child_type

using gemmi::Residue::child_type = Atom

Definition at line 203 of file model.hpp.

Constructor & Destructor Documentation

Residue() [1/2]

gemmi::Residue::Residue ( )

default

Residue() [2/2]

gemmi::Residue::Residue ( const ResidueId &  rid )

inlineexplicitnoexcept

Definition at line 189 of file model.hpp.

Member Function Documentation

what()

static const char * gemmi::Residue::what ( )

inlinestatic

Definition at line 176 of file model.hpp.

empty_copy()

Residue gemmi::Residue::empty_copy ( ) const

inline

Definition at line 192 of file model.hpp.

children() [1/2]

std::vector< Atom > & gemmi::Residue::children ( )

inline

Definition at line 204 of file model.hpp.

children() [2/2]

const std::vector< Atom > & gemmi::Residue::children ( ) const

inline

Definition at line 205 of file model.hpp.

find_by_element()

const Atom * gemmi::Residue::find_by_element ( El  el ) const

inline

Definition at line 207 of file model.hpp.

find_atom() [1/2]

Atom * gemmi::Residue::find_atom ( const std::string &  atom_name, char  altloc, El  el = El::X, bool  strict_altloc = true  )

inline

El::X means anything; in strict_altloc mode, '*' = any altloc, otherwise it's \0.

Definition at line 216 of file model.hpp.

find_atom() [2/2]

const Atom * gemmi::Residue::find_atom ( const std::string &  atom_name, char  altloc, El  el = El::X, bool  strict_altloc = true  ) const

inline

Definition at line 225 of file model.hpp.

find_atom_iter()

std::vector< Atom >::iterator gemmi::Residue::find_atom_iter ( const std::string &  atom_name, char  altloc, El  el = El::X  )

inline

Definition at line 230 of file model.hpp.

get()

AtomGroup gemmi::Residue::get ( const std::string &  atom_name )

inline

Definition at line 237 of file model.hpp.

sole_atom()

Atom & gemmi::Residue::sole_atom ( const std::string &  atom_name )

inline

Definition at line 244 of file model.hpp.

get_ca()

const Atom * gemmi::Residue::get_ca ( ) const

inline

Definition at line 252 of file model.hpp.

get_c()

const Atom * gemmi::Residue::get_c ( ) const

inline

Definition at line 253 of file model.hpp.

get_n()

const Atom * gemmi::Residue::get_n ( ) const

inline

Definition at line 254 of file model.hpp.

get_p()

const Atom * gemmi::Residue::get_p ( ) const

inline

Definition at line 256 of file model.hpp.

get_o3prim()

const Atom * gemmi::Residue::get_o3prim ( ) const

inline

Definition at line 257 of file model.hpp.

same_conformer()

bool gemmi::Residue::same_conformer ( const Residue &  other ) const

inline

Definition at line 259 of file model.hpp.

is_water()

bool gemmi::Residue::is_water ( ) const

inline

Convenience function that duplicates functionality from resinfo.hpp.

Returns true for HOH and DOD (and old alternative names of HOH), but not for OH and H3O/D3O.

Definition at line 268 of file model.hpp.

first_conformer() [1/2]

UniqProxy< Atom > gemmi::Residue::first_conformer ( )

inline

Definition at line 278 of file model.hpp.

first_conformer() [2/2]

ConstUniqProxy< Atom > gemmi::Residue::first_conformer ( ) const

inline

Definition at line 279 of file model.hpp.

Member Data Documentation

subchain

std::string gemmi::Residue::subchain

Definition at line 178 of file model.hpp.

entity_id

std::string gemmi::Residue::entity_id

Definition at line 179 of file model.hpp.

label_seq

OptionalNum gemmi::Residue::label_seq

Definition at line 180 of file model.hpp.

entity_type

EntityType gemmi::Residue::entity_type = EntityType::Unknown

Definition at line 181 of file model.hpp.

het_flag

char gemmi::Residue::het_flag = '\0'

Definition at line 182 of file model.hpp.

flag

char gemmi::Residue::flag = '\0'

Definition at line 183 of file model.hpp.

sifts_unp

SiftsUnpResidue gemmi::Residue::sifts_unp

Definition at line 184 of file model.hpp.

group_idx

short gemmi::Residue::group_idx = 0

Definition at line 185 of file model.hpp.

atoms

std::vector<Atom> gemmi::Residue::atoms

Definition at line 186 of file model.hpp.

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

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