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

Returns the atom index.

References atomno_.

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

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

References atomno_, and rsd_.

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

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

Returns the residue number.

References rsd_.

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

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:

src/core/id/PartialAtomID.hh
src/core/id/PartialAtomID.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation