#include <model.hpp>

Public Types
using	child_type = Model

Public Member Functions
const SpaceGroup *	find_spacegroup () const

const std::string &	get_info (const std::string &tag) const

Model &	first_model ()

const Model &	first_model () const

Model *	find_model (const std::string &model_name)

const Model *	find_model (const std::string &model_name) const

Model &	find_or_add_model (const std::string &model_name)

void	remove_model (const std::string &model_name)

void	renumber_models ()

Entity *	get_entity (const std::string &ent_id)

const Entity *	get_entity (const std::string &ent_id) const

Entity *	get_entity_of (const ConstResidueSpan &sub)

const Entity *	get_entity_of (const ConstResidueSpan &sub) const

Assembly *	find_assembly (const std::string &assembly_id)

Connection *	find_connection_by_name (const std::string &conn_name)

const Connection *	find_connection_by_name (const std::string &conn_name) const

Connection *	find_connection_by_cra (const const_CRA &cra1, const const_CRA &cra2, bool ignore_segment=false)

Connection *	find_connection (const AtomAddress &a1, const AtomAddress &a2)

size_t	ncs_given_count () const

double	get_ncs_multiplier () const

bool	ncs_not_expanded () const

void	add_conect_one_way (int serial1, int serial2, int order)

void	add_conect (int serial1, int serial2, int order)

void	merge_chain_parts (int min_sep=0)

void	remove_empty_chains ()

Structure	empty_copy () const

std::vector< Model > &	children ()

const std::vector< Model > &	children () const

void	setup_cell_images ()

Public Attributes
std::string	name

UnitCell	cell

std::string	spacegroup_hm

std::vector< Model >	models

std::vector< NcsOp >	ncs

std::vector< Entity >	entities

std::vector< Connection >	connections

std::vector< CisPep >	cispeps

std::vector< ModRes >	mod_residues

std::vector< Helix >	helices

std::vector< Sheet >	sheets

std::vector< Assembly >	assemblies

std::map< int, std::vector< int > >	conect_map

Metadata	meta

CoorFormat	input_format = CoorFormat::Unknown

bool	has_d_fraction = false

char	ter_status = '\0'
	in input PDB file: y = TER records were read, e = errors were detected

bool	has_origx = false
	Store ORIGXn / _database_PDB_matrix.origx*.

Transform	origx

std::map< std::string, std::string >	info
	Minimal metadata with keys being mmcif tags: _entry.id, _cell.Z_PDB, ...

std::vector< OldToNew >	shortened_ccd_codes
	Mapping of long (4+) CCD codes (residue names) to PDB-compatible ones.

std::vector< std::string >	raw_remarks
	original REMARK records stored if the file was read from the PDB format

double	resolution = 0
	simplistic resolution value from/for REMARK 2

Detailed Description

Definition at line 921 of file model.hpp.

Member Typedef Documentation

◆ child_type

using gemmi::Structure::child_type = Model

Definition at line 1089 of file model.hpp.

Member Function Documentation

◆ find_spacegroup()

const SpaceGroup * gemmi::Structure::find_spacegroup ( ) const

inline

Definition at line 955 of file model.hpp.

◆ get_info()

const std::string & gemmi::Structure::get_info ( const std::string & tag ) const

inline

Definition at line 959 of file model.hpp.

◆ first_model() [1/2]

Model & gemmi::Structure::first_model ( )

inline

Definition at line 965 of file model.hpp.

◆ first_model() [2/2]

const Model & gemmi::Structure::first_model ( ) const

inline

Definition at line 970 of file model.hpp.

◆ find_model() [1/2]

Model * gemmi::Structure::find_model ( const std::string & model_name )

inline

Definition at line 974 of file model.hpp.

◆ find_model() [2/2]

const Model * gemmi::Structure::find_model ( const std::string & model_name ) const

inline

Definition at line 977 of file model.hpp.

◆ find_or_add_model()

Model & gemmi::Structure::find_or_add_model ( const std::string & model_name )

inline

Definition at line 980 of file model.hpp.

◆ remove_model()

void gemmi::Structure::remove_model ( const std::string & model_name )

inline

Definition at line 984 of file model.hpp.

◆ renumber_models()

void gemmi::Structure::renumber_models ( )

inline

Definition at line 988 of file model.hpp.

◆ get_entity() [1/2]

Entity * gemmi::Structure::get_entity ( const std::string & ent_id )

inline

Definition at line 993 of file model.hpp.

◆ get_entity() [2/2]

const Entity * gemmi::Structure::get_entity ( const std::string & ent_id ) const

inline

Definition at line 996 of file model.hpp.

◆ get_entity_of() [1/2]

Entity * gemmi::Structure::get_entity_of ( const ConstResidueSpan & sub )

inline

Definition at line 1000 of file model.hpp.

◆ get_entity_of() [2/2]

const Entity * gemmi::Structure::get_entity_of ( const ConstResidueSpan & sub ) const

inline

Definition at line 1003 of file model.hpp.

◆ find_assembly()

Assembly * gemmi::Structure::find_assembly ( const std::string & assembly_id )

inline

Definition at line 1007 of file model.hpp.

◆ find_connection_by_name() [1/2]

Connection * gemmi::Structure::find_connection_by_name ( const std::string & conn_name )

inline

Definition at line 1011 of file model.hpp.

◆ find_connection_by_name() [2/2]

const Connection * gemmi::Structure::find_connection_by_name ( const std::string & conn_name ) const

inline

Definition at line 1014 of file model.hpp.

◆ find_connection_by_cra()

Connection * gemmi::Structure::find_connection_by_cra	(	const const_CRA &	cra1,
		const const_CRA &	cra2,
		bool	ignore_segment = `false`
	)

inline

Definition at line 1018 of file model.hpp.

◆ find_connection()

Connection * gemmi::Structure::find_connection	(	const AtomAddress &	a1,
		const AtomAddress &	a2
	)

inline

Definition at line 1030 of file model.hpp.

◆ ncs_given_count()

size_t gemmi::Structure::ncs_given_count ( ) const

inline

Definition at line 1038 of file model.hpp.

◆ get_ncs_multiplier()

double gemmi::Structure::get_ncs_multiplier ( ) const

inline

Definition at line 1041 of file model.hpp.

◆ ncs_not_expanded()

bool gemmi::Structure::ncs_not_expanded ( ) const

inline

Definition at line 1044 of file model.hpp.

◆ add_conect_one_way()

void gemmi::Structure::add_conect_one_way	(	int	serial1,
		int	serial2,
		int	order
	)

inline

Definition at line 1048 of file model.hpp.

◆ add_conect()

void gemmi::Structure::add_conect	(	int	serial1,
		int	serial2,
		int	order
	)

inline

Definition at line 1053 of file model.hpp.

◆ merge_chain_parts()

void gemmi::Structure::merge_chain_parts ( int min_sep = 0 )

inline

Definition at line 1058 of file model.hpp.

◆ remove_empty_chains()

void gemmi::Structure::remove_empty_chains ( )

inline

Definition at line 1063 of file model.hpp.

◆ empty_copy()

Structure gemmi::Structure::empty_copy ( ) const

inline

Definition at line 1069 of file model.hpp.

◆ children() [1/2]

std::vector< Model > & gemmi::Structure::children ( )

inline

Definition at line 1090 of file model.hpp.

◆ children() [2/2]

const std::vector< Model > & gemmi::Structure::children ( ) const

inline

Definition at line 1091 of file model.hpp.

◆ setup_cell_images()

void gemmi::Structure::setup_cell_images ( )

inline

Definition at line 1129 of file model.hpp.

Member Data Documentation

◆ name

std::string gemmi::Structure::name

Definition at line 922 of file model.hpp.

◆ cell

UnitCell gemmi::Structure::cell

Definition at line 923 of file model.hpp.

◆ spacegroup_hm

std::string gemmi::Structure::spacegroup_hm

Definition at line 924 of file model.hpp.

◆ models

std::vector<Model> gemmi::Structure::models

Definition at line 925 of file model.hpp.

◆ ncs

std::vector<NcsOp> gemmi::Structure::ncs

Definition at line 926 of file model.hpp.

◆ entities

std::vector<Entity> gemmi::Structure::entities

Definition at line 927 of file model.hpp.

◆ connections

std::vector<Connection> gemmi::Structure::connections

Definition at line 928 of file model.hpp.

◆ cispeps

std::vector<CisPep> gemmi::Structure::cispeps

Definition at line 929 of file model.hpp.

◆ mod_residues

std::vector<ModRes> gemmi::Structure::mod_residues

Definition at line 930 of file model.hpp.

◆ helices

std::vector<Helix> gemmi::Structure::helices

Definition at line 931 of file model.hpp.

◆ sheets

std::vector<Sheet> gemmi::Structure::sheets

Definition at line 932 of file model.hpp.

◆ assemblies

std::vector<Assembly> gemmi::Structure::assemblies

Definition at line 933 of file model.hpp.

◆ conect_map

std::map<int, std::vector<int> > gemmi::Structure::conect_map

Definition at line 934 of file model.hpp.

◆ meta

Metadata gemmi::Structure::meta

Definition at line 935 of file model.hpp.

◆ input_format

CoorFormat gemmi::Structure::input_format = CoorFormat::Unknown

Definition at line 937 of file model.hpp.

◆ has_d_fraction

bool gemmi::Structure::has_d_fraction = false

Definition at line 938 of file model.hpp.

◆ ter_status

char gemmi::Structure::ter_status = '\0'

in input PDB file: y = TER records were read, e = errors were detected

Definition at line 940 of file model.hpp.

◆ has_origx

bool gemmi::Structure::has_origx = false

Store ORIGXn / _database_PDB_matrix.origx*.

Definition at line 943 of file model.hpp.

◆ origx

Transform gemmi::Structure::origx

Definition at line 944 of file model.hpp.

◆ info

std::map<std::string, std::string> gemmi::Structure::info

Minimal metadata with keys being mmcif tags: _entry.id, _cell.Z_PDB, ...

Definition at line 947 of file model.hpp.

◆ shortened_ccd_codes

std::vector<OldToNew> gemmi::Structure::shortened_ccd_codes

Mapping of long (4+) CCD codes (residue names) to PDB-compatible ones.

Definition at line 949 of file model.hpp.

◆ raw_remarks

std::vector<std::string> gemmi::Structure::raw_remarks

original REMARK records stored if the file was read from the PDB format

Definition at line 951 of file model.hpp.

◆ resolution

double gemmi::Structure::resolution = 0

simplistic resolution value from/for REMARK 2

Definition at line 953 of file model.hpp.

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

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

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

◆ child_type

Member Function Documentation

◆ find_spacegroup()

◆ get_info()

◆ first_model() [1/2]

◆ first_model() [2/2]

◆ find_model() [1/2]

◆ find_model() [2/2]

◆ find_or_add_model()

◆ remove_model()

◆ renumber_models()

◆ get_entity() [1/2]

◆ get_entity() [2/2]

◆ get_entity_of() [1/2]

◆ get_entity_of() [2/2]

◆ find_assembly()

◆ find_connection_by_name() [1/2]

◆ find_connection_by_name() [2/2]

◆ find_connection_by_cra()

◆ find_connection()

◆ ncs_given_count()

◆ get_ncs_multiplier()

◆ ncs_not_expanded()

◆ add_conect_one_way()

◆ add_conect()

◆ merge_chain_parts()

◆ remove_empty_chains()

◆ empty_copy()

◆ children() [1/2]

◆ children() [2/2]

◆ setup_cell_images()

Member Data Documentation

◆ name

◆ cell

◆ spacegroup_hm

◆ models

◆ ncs

◆ entities

◆ connections

◆ cispeps

◆ mod_residues

◆ helices

◆ sheets

◆ assemblies

◆ conect_map

◆ meta

◆ input_format

◆ has_d_fraction

◆ ter_status

◆ has_origx

◆ origx

◆ info

◆ shortened_ccd_codes

◆ raw_remarks

◆ resolution