core::chemical::ChangeBondType Class Reference

A patch operation for changing the bond type of a given bond. More...

#include <PatchOperation.hh>

Inheritance diagram for core::chemical::ChangeBondType:

Public Member Functions
	ChangeBondType (std::string const &atom1_in, std::string const &atom2_in, std::string const &old_bond_type_in, std::string const &new_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 ("ChangeBondType"). 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_type () const
	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	old_bond_type_
std::string	new_bond_type_

Detailed Description

A patch operation for changing the bond type of a given bond.

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::ChangeBondType::ChangeBondType	(	std::string const &	atom1_in,
		std::string const &	atom2_in,
		std::string const &	old_bond_type_in,
		std::string const &	new_bond_type_in
	)

Member Function Documentation

bool core::chemical::ChangeBondType::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 atom1_, atom2_, core::chemical::MutableResidueType::change_bond_type(), core::chemical::convert_to_BondName(), and new_bond_type_.

std::string core::chemical::ChangeBondType::name ( ) const

overridevirtual

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

Author

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

Implements core::chemical::PatchOperation.

Member Data Documentation

std::string core::chemical::ChangeBondType::atom1_

private

Referenced by apply().

std::string core::chemical::ChangeBondType::atom2_

private

Referenced by apply().

std::string core::chemical::ChangeBondType::new_bond_type_

private

Referenced by apply().

std::string core::chemical::ChangeBondType::old_bond_type_

private

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

• src/core/chemical/PatchOperation.hh
• src/core/chemical/PatchOperation.cc