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core::chemical::AddAtomAlias Class Reference

A patch operation for adding an atom alias to a ResidueType. More...

#include <PatchOperation.hh>

Inheritance diagram for core::chemical::AddAtomAlias:
Inheritance graph
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Public Member Functions

 AddAtomAlias (std::string const &rosetta_atom_name_in, utility::vector1< std::string > const &aliases_in, std::string const &preferred_alias_in)
 
bool apply (MutableResidueType &rsd) const override
 Apply this patch to the given ResidueType. More...
 
std::string name () const override
 Return the name of this PatchOperation ("AddAtomAlias"). More...
 
utility::vector1< std::string > adds_atoms () override
 Return a list of all atom names that this operation adds (as aliases). More...
 
- Public Member Functions inherited from core::chemical::PatchOperation
 ~PatchOperation () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
virtual std::string deletes_atom ()
 Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues. More...
 
virtual std::string adds_property () const
 Which property, if any, is added. More...
 
virtual ResidueProperty adds_property_enum () const
 Which property, if any, is added. More...
 
virtual std::string deletes_property () const
 Which property, if any, is deleted. More...
 
virtual ResidueProperty deletes_property_enum () const
 Which property, if any, is deleted. More...
 
virtual std::string deletes_variant () const
 Which variant, if any, is deleted. More...
 
virtual VariantType deletes_variant_enum () const
 Which variant, if any, is deleted, by enum. More...
 
virtual bool may_change_aa ()
 Generates a new aa. More...
 
virtual bool changes_connections_on (ResidueType const &, std::string const &) const
 Can this case change connections for the atom on the residue? More...
 
virtual std::string generates_name3 ()
 Generates name3. More...
 
virtual std::string generates_interchangeability_group ()
 Generates interchangeability_group. More...
 
virtual bool generates_base_residue ()
 Generates base residue – legacy for D_AA – do not use otherwise. More...
 
virtual bool applies_to_placeholder () const
 Special – does this apply to 'minimal', placeholder types? Generally true, unless updating aa or name3. More...
 

Private Attributes

std::string rosetta_atom_name_
 
utility::vector1< std::string > aliases_
 
std::string preferred_alias_
 

Detailed Description

A patch operation for adding an atom alias to a ResidueType.

Note
See residue_io.cc for a description of atom aliases.
Remarks
Atom aliases were graciously added to Rosetta by Rocco Moretti.
Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Constructor & Destructor Documentation

core::chemical::AddAtomAlias::AddAtomAlias ( std::string const &  rosetta_atom_name_in,
utility::vector1< std::string > const &  aliases_in,
std::string const &  preferred_alias_in 
)

Member Function Documentation

utility::vector1< std::string > core::chemical::AddAtomAlias::adds_atoms ( )
inlineoverridevirtual

Return a list of all atom names that this operation adds (as aliases).

All of the aliases for an atom must be offered as options to the ResidueTypeFinder.

Reimplemented from core::chemical::PatchOperation.

References aliases_.

bool core::chemical::AddAtomAlias::apply ( MutableResidueType rsd) const
overridevirtual

Apply this patch to the given ResidueType.

Returns
true on failure
Remarks
Because ResidueType is not throwing exceptions, this will never return true. Failure will lead to exits from ResidueType. ~Labonte

Implements core::chemical::PatchOperation.

References core::chemical::MutableResidueType::add_atom_alias(), core::chemical::MutableResidueType::add_canonical_atom_alias(), aliases_, preferred_alias_, and rosetta_atom_name_.

std::string core::chemical::AddAtomAlias::name ( ) const
overridevirtual

Return the name of this PatchOperation ("AddAtomAlias").

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Implements core::chemical::PatchOperation.

Member Data Documentation

utility::vector1< std::string > core::chemical::AddAtomAlias::aliases_
private

Referenced by adds_atoms(), and apply().

std::string core::chemical::AddAtomAlias::preferred_alias_
private

Referenced by apply().

std::string core::chemical::AddAtomAlias::rosetta_atom_name_
private

Referenced by apply().


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