gemmi::ChemComp Struct Reference

#include <chemcomp.hpp>

Classes
struct	Aliasing
struct	Atom

Public Types
enum class	Group {   Peptide , PPeptide , MPeptide , Dna ,   Rna , DnaRna , Pyranose , Ketopyranose ,   Furanose , NonPolymer , Null }

Public Member Functions
const Aliasing &	get_aliasing (Group g) const
void	set_group (const std::string &s)
std::vector< Atom >::iterator	find_atom (const std::string &atom_id)
std::vector< Atom >::const_iterator	find_atom (const std::string &atom_id) const
bool	has_atom (const std::string &atom_id) const
std::vector< Atom >::iterator	find_atom_by_old_name (const std::string &old_id)
std::vector< Atom >::const_iterator	find_atom_by_old_name (const std::string &old_id) const
bool	has_old_names () const
int	get_atom_index (const std::string &atom_id) const
const Atom &	get_atom (const std::string &atom_id) const
void	remove_nonmatching_restraints ()
ChemComp &	remove_hydrogens ()

Static Public Member Functions
static Group	read_group (const std::string &str)
static const char *	group_str (Group g)
static bool	is_peptide_group (Group g)
	Check if the group (M-|P-)peptide.
static bool	is_nucleotide_group (Group g)
	Check if the group is DNA/RNA.

Public Attributes
std::string	name
std::string	type_or_group
Group	group = Group::Null
bool	has_coordinates = false
std::vector< Atom >	atoms
std::vector< Aliasing >	aliases
Restraints	rt

Detailed Description

Definition at line 326 of file chemcomp.hpp.

Member Enumeration Documentation

Group

enum class gemmi::ChemComp::Group

strong

Enumerator
Peptide
PPeptide
MPeptide
Dna
Rna
DnaRna
Pyranose
Ketopyranose
Furanose
NonPolymer
Null

Definition at line 328 of file chemcomp.hpp.

Member Function Documentation

get_aliasing()

const Aliasing & gemmi::ChemComp::get_aliasing ( Group  g ) const

inline

Definition at line 377 of file chemcomp.hpp.

read_group()

static Group gemmi::ChemComp::read_group ( const std::string &  str )

inlinestatic

Definition at line 384 of file chemcomp.hpp.

group_str()

static const char * gemmi::ChemComp::group_str ( Group  g )

inlinestatic

Definition at line 406 of file chemcomp.hpp.

set_group()

void gemmi::ChemComp::set_group ( const std::string &  s )

inline

Definition at line 423 of file chemcomp.hpp.

find_atom() [1/2]

std::vector< Atom >::iterator gemmi::ChemComp::find_atom ( const std::string &  atom_id )

inline

Definition at line 428 of file chemcomp.hpp.

find_atom() [2/2]

std::vector< Atom >::const_iterator gemmi::ChemComp::find_atom ( const std::string &  atom_id ) const

inline

Definition at line 432 of file chemcomp.hpp.

has_atom()

bool gemmi::ChemComp::has_atom ( const std::string &  atom_id ) const

inline

Definition at line 435 of file chemcomp.hpp.

find_atom_by_old_name() [1/2]

std::vector< Atom >::iterator gemmi::ChemComp::find_atom_by_old_name ( const std::string &  old_id )

inline

Definition at line 439 of file chemcomp.hpp.

find_atom_by_old_name() [2/2]

std::vector< Atom >::const_iterator gemmi::ChemComp::find_atom_by_old_name ( const std::string &  old_id ) const

inline

Definition at line 443 of file chemcomp.hpp.

has_old_names()

bool gemmi::ChemComp::has_old_names ( ) const

inline

Definition at line 446 of file chemcomp.hpp.

get_atom_index()

int gemmi::ChemComp::get_atom_index ( const std::string &  atom_id ) const

inline

Definition at line 451 of file chemcomp.hpp.

get_atom()

const Atom & gemmi::ChemComp::get_atom ( const std::string &  atom_id ) const

inline

Definition at line 458 of file chemcomp.hpp.

is_peptide_group()

static bool gemmi::ChemComp::is_peptide_group ( Group  g )

inlinestatic

Check if the group (M-|P-)peptide.

Definition at line 463 of file chemcomp.hpp.

is_nucleotide_group()

static bool gemmi::ChemComp::is_nucleotide_group ( Group  g )

inlinestatic

Check if the group is DNA/RNA.

Definition at line 468 of file chemcomp.hpp.

remove_nonmatching_restraints()

void gemmi::ChemComp::remove_nonmatching_restraints ( )

inline

Definition at line 472 of file chemcomp.hpp.

remove_hydrogens()

ChemComp & gemmi::ChemComp::remove_hydrogens ( )

inline

Definition at line 500 of file chemcomp.hpp.

Member Data Documentation

name

std::string gemmi::ChemComp::name

Definition at line 369 of file chemcomp.hpp.

type_or_group

std::string gemmi::ChemComp::type_or_group

Definition at line 370 of file chemcomp.hpp.

group

Group gemmi::ChemComp::group = Group::Null

Definition at line 371 of file chemcomp.hpp.

has_coordinates

bool gemmi::ChemComp::has_coordinates = false

Definition at line 372 of file chemcomp.hpp.

atoms

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

Definition at line 373 of file chemcomp.hpp.

aliases

std::vector<Aliasing> gemmi::ChemComp::aliases

Definition at line 374 of file chemcomp.hpp.

rt

Restraints gemmi::ChemComp::rt

Definition at line 375 of file chemcomp.hpp.

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

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