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Rosetta
2020.50
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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... | |
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.
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inline |
Default constructor.
Referenced by BOGUS_PARTIAL_ATOM_ID(), and CHAINBREAK_BOGUS_PARTIAL_ATOM_ID().
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inlinedefault |
Copy constructor.
AtomID-like constructor; this ID is fully (not partially) resolved.
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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
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inline |
Returns the atom index.
References atomno_.
Referenced by core::id::operator<<(), core::conformation::Residue::resolve_partial_atom_id(), and serialize().
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inlinestatic |
References PartialAtomID().
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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().
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inlinestatic |
References PartialAtomID().
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inline |
Referenced by core::conformation::Residue::resolve_partial_atom_id().
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inline |
deserialize a json_spirit object to an AtomID
References atomno_, bonds_from_resconn_, resconnid_, and rsd_.
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inline |
References resconnid_, and rsd_.
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inline |
Returns the inter-residue connection index.
References resconnid_.
Referenced by core::id::operator<<(), core::conformation::Residue::resolve_partial_atom_id(), and serialize().
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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().
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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 | ||
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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 | ||
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Set the value of the inter-residue connection index and residue.
References atomno_, bonds_from_resconn_, resconnid_, and rsd_.
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inline |
Returns true if the PartialAtomID is valid.
References atomno_, resconnid_, and rsd_.
Referenced by core::conformation::Residue::resolve_partial_atom_id().
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friend |
a and b are different atom
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friend |
a is LOWER than b (e.g., first by smaller residue index number then by smaller atom index number)
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friend |
stream << PartialAtomID
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friend |
a and b are the same atom
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private |
Atom number within the Residue.
Referenced by atomno(), complete(), deserialize(), serialize(), set_complete(), set_partial(), and valid().
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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().
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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().
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private |
Residue number within the complex.
Referenced by complete(), deserialize(), partial(), rsd(), serialize(), set_complete(), set_partial(), and valid().