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core::chemical::AddBondType Class Reference

A patch operation for adding a specific type of bond to a ResidueType. More...

#include <PatchOperation.hh>

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

 AddBondType (std::string const &atom1_in, std::string const &atom2_in, std::string const &bond_type_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 ("AddBondType"). More...
 
- Public Member Functions inherited from core::chemical::PatchOperation
 ~PatchOperation () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
virtual utility::vector1
< std::string > 
adds_atoms ()
 Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues. 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 atom1_
 
std::string atom2_
 
std::string bond_type_
 

Detailed Description

A patch operation for adding a specific type of bond to a ResidueType.

Note
See residue_io.cc for a description of bond types.
Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Constructor & Destructor Documentation

core::chemical::AddBondType::AddBondType ( std::string const &  atom1_in,
std::string const &  atom2_in,
std::string const &  bond_type_in 
)

Member Function Documentation

bool core::chemical::AddBondType::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_bond(), atom1_, atom2_, bond_type_, and core::chemical::convert_to_BondName().

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

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

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

Implements core::chemical::PatchOperation.

Member Data Documentation

std::string core::chemical::AddBondType::atom1_
private

Referenced by apply().

std::string core::chemical::AddBondType::atom2_
private

Referenced by apply().

std::string core::chemical::AddBondType::bond_type_
private

Referenced by apply().


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