Gemmi C++ API
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Classes | Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
gemmi::Model Struct Reference

#include <model.hpp>

Public Types

using child_type = Chain
 

Public Member Functions

 Model (std::string mname) noexcept
 
Chain * find_chain (const std::string &chain_name)
 
const Chain * find_chain (const std::string &chain_name) const
 
Chain * find_last_chain (const std::string &chain_name)
 
void remove_chain (const std::string &chain_name)
 
void merge_chain_parts (int min_sep=0)
 
ResidueSpan get_subchain (const std::string &sub_name)
 
ConstResidueSpan get_subchain (const std::string &sub_name) const
 
std::vector< ResidueSpan > subchains ()
 
std::vector< ConstResidueSpan > subchains () const
 
std::map< std::string, std::string > subchain_to_chain () const
 
Residue * find_residue (const std::string &chain_name, const ResidueId &rid)
 
const Residue * find_residue (const std::string &chain_name, const ResidueId &rid) const
 
ResidueGroup find_residue_group (const std::string &chain_name, SeqId seqid)
 
Residue & sole_residue (const std::string &chain_name, SeqId seqid)
 
std::vector< std::string > get_all_residue_names () const
 
CRA find_cra (const AtomAddress &address, bool ignore_segment=false)
 
const_CRA find_cra (const AtomAddress &address, bool ignore_segment=false) const
 
CraProxy all ()
 
ConstCraProxy all () const
 
Atom * find_atom (const AtomAddress &address)
 
const Atom * find_atom (const AtomAddress &address) const
 
std::array< int, 3 > get_indices (const Chain *c, const Residue *r, const Atom *a) const
 
std::bitset<(size_t) El::END > present_elements () const
 
CRA get_cra (Atom *atom)
 
Chain * get_parent_of (Residue *res)
 
Model empty_copy () const
 
std::vector< Chain > & children ()
 
const std::vector< Chain > & children () const
 

Static Public Member Functions

static const char * what ()
 

Public Attributes

std::string name
 
std::vector< Chain > chains
 

Detailed Description

Definition at line 697 of file model.hpp.

Member Typedef Documentation

◆ child_type

using gemmi::Model::child_type = Chain

Definition at line 845 of file model.hpp.

Constructor & Destructor Documentation

◆ Model()

gemmi::Model::Model ( std::string  mname)
inlineexplicitnoexcept

Definition at line 701 of file model.hpp.

Member Function Documentation

◆ what()

static const char * gemmi::Model::what ( )
inlinestatic

Definition at line 698 of file model.hpp.

◆ find_chain() [1/2]

Chain * gemmi::Model::find_chain ( const std::string &  chain_name)
inline

Definition at line 704 of file model.hpp.

◆ find_chain() [2/2]

const Chain * gemmi::Model::find_chain ( const std::string &  chain_name) const
inline

Definition at line 707 of file model.hpp.

◆ find_last_chain()

Chain * gemmi::Model::find_last_chain ( const std::string &  chain_name)
inline

Definition at line 712 of file model.hpp.

◆ remove_chain()

void gemmi::Model::remove_chain ( const std::string &  chain_name)
inline

Definition at line 719 of file model.hpp.

◆ merge_chain_parts()

void gemmi::Model::merge_chain_parts ( int  min_sep = 0)
inline

Definition at line 724 of file model.hpp.

◆ get_subchain() [1/2]

ResidueSpan gemmi::Model::get_subchain ( const std::string &  sub_name)
inline

Definition at line 733 of file model.hpp.

◆ get_subchain() [2/2]

ConstResidueSpan gemmi::Model::get_subchain ( const std::string &  sub_name) const
inline

Definition at line 739 of file model.hpp.

◆ subchains() [1/2]

std::vector< ResidueSpan > gemmi::Model::subchains ( )
inline

Definition at line 743 of file model.hpp.

◆ subchains() [2/2]

std::vector< ConstResidueSpan > gemmi::Model::subchains ( ) const
inline

Definition at line 746 of file model.hpp.

◆ subchain_to_chain()

std::map< std::string, std::string > gemmi::Model::subchain_to_chain ( ) const
inline

Definition at line 750 of file model.hpp.

◆ find_residue() [1/2]

Residue * gemmi::Model::find_residue ( const std::string &  chain_name,
const ResidueId &  rid 
)
inline

Definition at line 763 of file model.hpp.

◆ find_residue() [2/2]

const Residue * gemmi::Model::find_residue ( const std::string &  chain_name,
const ResidueId &  rid 
) const
inline

Definition at line 770 of file model.hpp.

◆ find_residue_group()

ResidueGroup gemmi::Model::find_residue_group ( const std::string &  chain_name,
SeqId  seqid 
)
inline

Definition at line 775 of file model.hpp.

◆ sole_residue()

Residue & gemmi::Model::sole_residue ( const std::string &  chain_name,
SeqId  seqid 
)
inline

Definition at line 783 of file model.hpp.

◆ get_all_residue_names()

std::vector< std::string > gemmi::Model::get_all_residue_names ( ) const
inline

Definition at line 790 of file model.hpp.

◆ find_cra() [1/2]

CRA gemmi::Model::find_cra ( const AtomAddress &  address,
bool  ignore_segment = false 
)
inline

Definition at line 799 of file model.hpp.

◆ find_cra() [2/2]

const_CRA gemmi::Model::find_cra ( const AtomAddress &  address,
bool  ignore_segment = false 
) const
inline

Definition at line 814 of file model.hpp.

◆ all() [1/2]

CraProxy gemmi::Model::all ( )
inline

Definition at line 818 of file model.hpp.

◆ all() [2/2]

ConstCraProxy gemmi::Model::all ( ) const
inline

Definition at line 819 of file model.hpp.

◆ find_atom() [1/2]

Atom * gemmi::Model::find_atom ( const AtomAddress &  address)
inline

Definition at line 821 of file model.hpp.

◆ find_atom() [2/2]

const Atom * gemmi::Model::find_atom ( const AtomAddress &  address) const
inline

Definition at line 822 of file model.hpp.

◆ get_indices()

std::array< int, 3 > gemmi::Model::get_indices ( const Chain *  c,
const Residue *  r,
const Atom *  a 
) const
inline

Definition at line 824 of file model.hpp.

◆ present_elements()

std::bitset<(size_t) El::END > gemmi::Model::present_elements ( ) const
inline

Definition at line 831 of file model.hpp.

◆ get_cra()

CRA gemmi::Model::get_cra ( Atom *  atom)
inline

Definition at line 840 of file model.hpp.

◆ get_parent_of()

Chain * gemmi::Model::get_parent_of ( Residue *  res)
inline

Definition at line 841 of file model.hpp.

◆ empty_copy()

Model gemmi::Model::empty_copy ( ) const
inline

Definition at line 844 of file model.hpp.

◆ children() [1/2]

std::vector< Chain > & gemmi::Model::children ( )
inline

Definition at line 846 of file model.hpp.

◆ children() [2/2]

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

Definition at line 847 of file model.hpp.

Member Data Documentation

◆ name

std::string gemmi::Model::name

Definition at line 699 of file model.hpp.

◆ chains

std::vector<Chain> gemmi::Model::chains

Definition at line 700 of file model.hpp.

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