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core::id::PartialAtomID Class Reference

Partial atom identifier class. Defined by an atom index and a residue number, or by an inter-residue-connection index, the number of bonds away from the inter-residue-connection atom, and a residue number. More...

#include <PartialAtomID.hh>

Public Member Functions

constexpr PartialAtomID ()
 Default constructor. More...
 
 PartialAtomID (PartialAtomID const &)=default
 Copy constructor. More...
 
 PartialAtomID (Size const atomno_in, Size const rsd_in)
 AtomID-like constructor; this ID is fully (not partially) resolved. More...
 
 PartialAtomID (Size const resconnid_in, Size const rsd_in, Size const bonds_from_resconn_in)
 Constructor to specify an inter-residue connection atom. More...
 
void set_complete (core::Size atomno_in, core::Size rsd_in)
 Set the value of atom and residue. More...
 
void set_partial (core::Size resconnid_in, core::Size bonds_from_resconn_in, core::Size rsd_in)
 Set the value of the inter-residue connection index and residue. More...
 
Size rsd () const
 Returns the residue number. More...
 
Size atomno () const
 Returns the atom index. More...
 
Size resconnid () const
 Returns the inter-residue connection index. More...
 
Size bonds_from_resconn () const
 Returns the number of chemical bonds away from the residue-connection atom the target atom is located. More...
 
bool valid () const
 Returns true if the PartialAtomID is valid. More...
 
bool complete () const
 
bool partial () const
 
utility::json_spirit::Value serialize () const
 serialize an AtomID to a json_spirit object More...
 
void deserialize (utility::json_spirit::mObject data)
 deserialize a json_spirit object to an AtomID More...
 

Static Public Member Functions

static constexpr PartialAtomID BOGUS_PARTIAL_ATOM_ID ()
 
static constexpr PartialAtomID CHAINBREAK_BOGUS_PARTIAL_ATOM_ID ()
 

Private Attributes

Size atomno_
 Atom number within the Residue. More...
 
Size resconnid_
 The index of the inter-residue connection for the atom of interest; the index of that atom may vary between different residue types and so when this information is used, it only partially specifies the identity of the atom on a residue. More...
 
Size bonds_from_resconn_
 The number of chemical bonds from the inter- residue connection atom and the atom of interest. 0 if the atom of interest is the inter-residue- connection atom. More...
 
Size rsd_
 Residue number within the complex. More...
 

Friends

std::ostream & operator<< (std::ostream &os, PartialAtomID const &a)
 stream << PartialAtomID More...
 
bool operator== (PartialAtomID const &a, PartialAtomID const &b)
 a and b are the same atom More...
 
bool operator!= (PartialAtomID const &a, PartialAtomID const &b)
 a and b are different atom More...
 
bool operator< (PartialAtomID const &a, PartialAtomID const &b)
 a is LOWER than b (e.g., first by smaller residue index number then by smaller atom index number) More...
 

Detailed Description

Partial atom identifier class. Defined by an atom index and a residue number, or by an inter-residue-connection index, the number of bonds away from the inter-residue-connection atom, and a residue number.

Constructor & Destructor Documentation

constexpr core::id::PartialAtomID::PartialAtomID ( )
inline

Default constructor.

Referenced by BOGUS_PARTIAL_ATOM_ID(), and CHAINBREAK_BOGUS_PARTIAL_ATOM_ID().

core::id::PartialAtomID::PartialAtomID ( PartialAtomID const &  )
inlinedefault

Copy constructor.

core::id::PartialAtomID::PartialAtomID ( Size const  atomno_in,
Size const  rsd_in 
)
inline

AtomID-like constructor; this ID is fully (not partially) resolved.

core::id::PartialAtomID::PartialAtomID ( Size const  resconnid_in,
Size const  rsd_in,
Size const  bonds_from_resconn_in 
)
inline

Constructor to specify an inter-residue connection atom.

The third argument specifies the number of bonds away from the residue-connection atom that the indicated atom is. The three-argument constructor also disambiguates this partial ID from the two-argument constructor that is essentially a fully-resolved AtomID

Member Function Documentation

Size core::id::PartialAtomID::atomno ( ) const
inline
static constexpr PartialAtomID core::id::PartialAtomID::BOGUS_PARTIAL_ATOM_ID ( )
inlinestatic

References PartialAtomID().

Size core::id::PartialAtomID::bonds_from_resconn ( ) const
inline

Returns the number of chemical bonds away from the residue-connection atom the target atom is located.

References bonds_from_resconn_.

Referenced by core::id::operator<<(), core::conformation::Residue::resolve_partial_atom_id(), and serialize().

static constexpr PartialAtomID core::id::PartialAtomID::CHAINBREAK_BOGUS_PARTIAL_ATOM_ID ( )
inlinestatic

References PartialAtomID().

bool core::id::PartialAtomID::complete ( ) const
inline
void core::id::PartialAtomID::deserialize ( utility::json_spirit::mObject  data)
inline

deserialize a json_spirit object to an AtomID

References atomno_, bonds_from_resconn_, resconnid_, and rsd_.

bool core::id::PartialAtomID::partial ( ) const
inline

References resconnid_, and rsd_.

Size core::id::PartialAtomID::resconnid ( ) const
inline

Returns the inter-residue connection index.

References resconnid_.

Referenced by core::id::operator<<(), core::conformation::Residue::resolve_partial_atom_id(), and serialize().

Size core::id::PartialAtomID::rsd ( ) const
inline
utility::json_spirit::Value core::id::PartialAtomID::serialize ( ) const
inline

serialize an AtomID to a json_spirit object

References atomno(), atomno_, bonds_from_resconn(), bonds_from_resconn_, resconnid(), resconnid_, rsd(), and rsd_.

void core::id::PartialAtomID::set_complete ( core::Size  atomno_in,
core::Size  rsd_in 
)

Set the value of atom and residue.

References atomno_, bonds_from_resconn_, resconnid_, and rsd_.

void core::id::PartialAtomID::set_partial ( core::Size  resconnid_in,
core::Size  bonds_from_resconn_in,
core::Size  rsd_in 
)

Set the value of the inter-residue connection index and residue.

References atomno_, bonds_from_resconn_, resconnid_, and rsd_.

bool core::id::PartialAtomID::valid ( ) const
inline

Returns true if the PartialAtomID is valid.

Note
must return false for BOGUS_ATOM_ID

References atomno_, resconnid_, and rsd_.

Referenced by core::conformation::Residue::resolve_partial_atom_id().

Friends And Related Function Documentation

bool operator!= ( PartialAtomID const &  a,
PartialAtomID const &  b 
)
friend

a and b are different atom

bool operator< ( PartialAtomID const &  a,
PartialAtomID const &  b 
)
friend

a is LOWER than b (e.g., first by smaller residue index number then by smaller atom index number)

std::ostream& operator<< ( std::ostream &  os,
PartialAtomID const &  a 
)
friend

stream << PartialAtomID

bool operator== ( PartialAtomID const &  a,
PartialAtomID const &  b 
)
friend

a and b are the same atom

Member Data Documentation

Size core::id::PartialAtomID::atomno_
private

Atom number within the Residue.

Referenced by atomno(), complete(), deserialize(), serialize(), set_complete(), set_partial(), and valid().

Size core::id::PartialAtomID::bonds_from_resconn_
private

The number of chemical bonds from the inter- residue connection atom and the atom of interest. 0 if the atom of interest is the inter-residue- connection atom.

Referenced by bonds_from_resconn(), deserialize(), serialize(), set_complete(), and set_partial().

Size core::id::PartialAtomID::resconnid_
private

The index of the inter-residue connection for the atom of interest; the index of that atom may vary between different residue types and so when this information is used, it only partially specifies the identity of the atom on a residue.

Referenced by deserialize(), partial(), resconnid(), serialize(), set_complete(), set_partial(), and valid().

Size core::id::PartialAtomID::rsd_
private

Residue number within the complex.

Referenced by complete(), deserialize(), partial(), rsd(), serialize(), set_complete(), set_partial(), and valid().


The documentation for this class was generated from the following files: