core::chemical::AddChi Class Reference

Add a chi angle to ResidueType. More...

#include <PatchOperation.hh>

Inheritance diagram for core::chemical::AddChi:

Public Member Functions
	AddChi (Size const &chino_in, std::string const &atom1_in, std::string const &atom2_in, std::string const &atom3_in, std::string const &atom4_in)
	Constructor for when the chi index is specified. More...
	AddChi (std::string const &atom1_in, std::string const &atom2_in, std::string const &atom3_in, std::string const &atom4_in)
	Constructor for when the chi index is not specified. More...
bool	apply (MutableResidueType &rsd) const override
	Add a chi angle. More...
std::string	name () const override
	Return the name of this PatchOperation ("AddChi"). 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
bool	no_index_
Size	chino_
std::string	atom1_
std::string	atom2_
std::string	atom3_
std::string	atom4_

Detailed Description

Add a chi angle to ResidueType.

Author

Added by Andy M. Chen in June 2009

This is needed for PTMs, which often result in one or more extra chi angles.

Constructor & Destructor Documentation

core::chemical::AddChi::AddChi	(	Size const &	chino_in,
		std::string const &	atom1_in,
		std::string const &	atom2_in,
		std::string const &	atom3_in,
		std::string const &	atom4_in
	)

Constructor for when the chi index is specified.

core::chemical::AddChi::AddChi	(	std::string const &	atom1_in,
		std::string const &	atom2_in,
		std::string const &	atom3_in,
		std::string const &	atom4_in
	)

Constructor for when the chi index is not specified.

In this case, the new chi will be added to the end of the list when this operation is applied.

Author

Labonte

Member Function Documentation

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

overridevirtual

Add a chi angle.

Implements core::chemical::PatchOperation.

References core::chemical::MutableResidueType::add_chi(), atom1_, atom2_, atom3_, atom4_, chino_, core::chemical::MutableResidueType::has(), core::chemical::ResidueTypeBase::name(), no_index_, and core::chemical::TR_PatchOperations().

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

overridevirtual

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

Author

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

Implements core::chemical::PatchOperation.

Member Data Documentation

std::string core::chemical::AddChi::atom1_

private

Referenced by apply().

std::string core::chemical::AddChi::atom2_

private

Referenced by apply().

std::string core::chemical::AddChi::atom3_

private

Referenced by apply().

std::string core::chemical::AddChi::atom4_

private

Referenced by apply().

Size core::chemical::AddChi::chino_

private

Referenced by apply().

bool core::chemical::AddChi::no_index_

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