core::chemical::AddConnect Class Reference

#include <PatchOperation.hh>

Inheritance diagram for core::chemical::AddConnect:

Public Member Functions
	AddConnect (std::string const &connect_atom, Real const phi, Real const theta, Real const d, std::string const &parent_atom, std::string const &angle_atom, std::string const &torsion_atom)
bool	apply (MutableResidueType &rsd) const override
	add a property More...
bool	changes_connections_on (ResidueType const &rsd_type, std::string const &atom) const override
	Can this case change connections for the atom on the residue? More...
std::string	name () const override
	Return the name of this PatchOperation ("AddConnect"). More...
Public Member Functions inherited from core::chemical::PatchOperation
	~PatchOperation () override
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
virtual std::string	adds_atom ()
	Which atom, if any, is 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 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	connect_atom_
Real	phi_
Real	theta_
Real	d_
std::string	parent_atom_
std::string	angle_atom_
std::string	torsion_atom_

Constructor & Destructor Documentation

core::chemical::AddConnect::AddConnect	(	std::string const &	connect_atom,
		Real const	phi,
		Real const	theta,
		Real const	d,
		std::string const &	parent_atom,
		std::string const &	angle_atom,
		std::string const &	torsion_atom
	)

Member Function Documentation

bool core::chemical::AddConnect::apply ( MutableResidueType &  rsd ) const

overridevirtual

add a property

Implements core::chemical::PatchOperation.

References core::chemical::MutableResidueType::add_residue_connection(), angle_atom_, connect_atom_, d_, core::chemical::MutableResidueType::has(), parent_atom_, phi_, core::chemical::MutableResidueType::set_icoor(), theta_, and torsion_atom_.

Referenced by core::chemical::ConnectSulfurAndMakeVirtualProton::apply().

bool core::chemical::AddConnect::changes_connections_on ( ResidueType const &  , std::string const &    ) const

overridevirtual

Can this case change connections for the atom on the residue?

• Be a little careful, as the passed atom name string may not have the same whitespace padding as any internal atom name.

Reimplemented from core::chemical::PatchOperation.

References connect_atom_, and core::chemical::ResidueType::has().

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

overridevirtual

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

Author

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

Implements core::chemical::PatchOperation.

Member Data Documentation

std::string core::chemical::AddConnect::angle_atom_

private

Referenced by apply().

std::string core::chemical::AddConnect::connect_atom_

private

Referenced by apply(), and changes_connections_on().

Real core::chemical::AddConnect::d_

private

Referenced by apply().

std::string core::chemical::AddConnect::parent_atom_

private

Referenced by apply().

Real core::chemical::AddConnect::phi_

private

Referenced by apply().

Real core::chemical::AddConnect::theta_

private

Referenced by apply().

std::string core::chemical::AddConnect::torsion_atom_

private

Referenced by apply().

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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