A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More...

#include <Patch.hh>

Inheritance diagram for core::chemical::PatchCase:

Public Member Functions
	~PatchCase () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

bool	applies_to (ResidueTypeBase const &rsd) const
	whether the PatchCase is applicable to this ResidueType? More...

virtual MutableResidueTypeOP	apply (ResidueType const &rsd_in, bool const instantiate=true) const
	returns patched residue, 0 if patch failed More...

virtual MutableResidueTypeOP	apply (MutableResidueType const &rsd_in, bool const instantiate=true) const
	returns patched residue, 0 if patch failed More...

void	add_operation (PatchOperationOP operation)
	add one more operation in this PatchCase More...

ResidueTypeSelector &	selector ()
	to which ResidueTypes this PatchCase applies to? More...

void	set_selector (ResidueTypeSelector const &selector)

utility::vector1< std::string >	adds_atoms () const
	returns list of added atom names, useful for identifying patches that go with PDB residues More...

utility::vector1< std::string >	deletes_atoms () const
	returns list of deleted atom names, useful for identifying patches that go with PDB residues More...

utility::vector1< std::string >	adds_properties () const
	returns list of added property names, useful for identifying patches that go with PDB residues More...

utility::vector1< ResidueProperty >	adds_properties_enums () const
	Returns list of added property enums. Useful for identifying patches that go with PDB residues. More...

utility::vector1< std::string >	deletes_properties () const
	returns list of deleted property names, useful for identifying patches that go with PDB residues More...

utility::vector1< ResidueProperty >	deletes_properties_enums () const
	Returns list of deleted property enums. Useful for identifying patches that go with PDB residues. More...

utility::vector1< std::string >	deletes_variants () const
	returns list of deleted variant names, useful for identifying patches that go with PDB residues More...

utility::vector1 < core::chemical::VariantType >	deletes_variants_by_enum () const
	Returns list of deleted VariantTypes. Doesn't support on-the-fly VariantTypes. More...

std::string	generates_new_name3 () const
	returns new name3, if changed More...

std::string	generates_interchangeability_group () const
	returns interchangeability group, if set. More...

bool	generates_base_residue_type () const
	Does this PatchCase result in a new base residue type? More...

bool	may_change_aa () const
	returns list of new interchangeability_group, useful for identifying patches that go with PDB residues More...

bool	changes_connections_on (ResidueType const &rsd_in, std::string const &atom) const
	Can the patch case change the connections for atom on the ResidueType? More...

Private Attributes
ResidueTypeSelector	selector_
	to which ResidueTypes this PatchCase applies to? More...

utility::vector1 < PatchOperationOP >	operations_
	operations to done in this PatchCase More...

bool	generates_base_residue_type_ = false
	Does this PatchCase result in a new base residue type? More...

Detailed Description

A single case of a patch, eg proline Nterminus is a case of NtermProteinFull.

Constructor & Destructor Documentation

core::chemical::PatchCase::~PatchCase ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

void core::chemical::PatchCase::add_operation ( PatchOperationOP operation )

add one more operation in this PatchCase

References generates_base_residue_type_, and operations_.

Referenced by core::chemical::apply_adducts_to_residue().

utility::vector1< std::string > core::chemical::PatchCase::adds_atoms ( ) const

returns list of added atom names, useful for identifying patches that go with PDB residues

Go through patch operations in this PatchCase, and compile list of any atom names that are added. Also, add any atom aliases for those atoms.

References operations_.

utility::vector1< std::string > core::chemical::PatchCase::adds_properties ( ) const

returns list of added property names, useful for identifying patches that go with PDB residues

Go through patch operations in this PatchCase, and compile list of any property names that are added.

References operations_.

utility::vector1< ResidueProperty > core::chemical::PatchCase::adds_properties_enums ( ) const

Returns list of added property enums. Useful for identifying patches that go with PDB residues.

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

Loop through patch operations in this PatchCase, and compile a list of any ResidueProperties that are added. Note that this version uses enums, and only works for canonical properties (not on-the-fly properties).

References core::chemical::NO_PROPERTY, operations_, and update_ResidueType_enum_files::properties.

bool core::chemical::PatchCase::applies_to ( ResidueTypeBase const & rsd ) const

inline

whether the PatchCase is applicable to this ResidueType?

References selector_.

MutableResidueTypeOP core::chemical::PatchCase::apply	(	ResidueType const &	rsd_in,
		bool const	instantiate = `true`
	)		const

virtual

returns patched residue, 0 if patch failed

Referenced by core::chemical::apply_adducts_to_residue().

MutableResidueTypeOP core::chemical::PatchCase::apply	(	MutableResidueType const &	rsd_in,
		bool const	instantiate = `true`
	)		const

virtual

returns patched residue, 0 if patch failed

First clone the base ResidueType. Then patching for this case is done by applying all the operations. finalize() is called after the VariantTypes and name are set by Patch::apply().

Note: If you call this method without calling finalize(), your ResidueType may not have the correct derived data!

References core::chemical::MutableResidueType::clone(), operations_, core::chemical::MutableResidueType::placeholder_clone(), and core::chemical::tr().

bool core::chemical::PatchCase::changes_connections_on	(	ResidueType const &	rsd_in,
		std::string const &	atom
	)		const

Can the patch case change the connections for atom on the ResidueType?

References operations_.

utility::vector1< std::string > core::chemical::PatchCase::deletes_atoms ( ) const

returns list of deleted atom names, useful for identifying patches that go with PDB residues

Go through patch operations in this PatchCase, and compile list of any atom names that are deleted.

References operations_.

utility::vector1< std::string > core::chemical::PatchCase::deletes_properties ( ) const

returns list of deleted property names, useful for identifying patches that go with PDB residues

Go through patch operations in this PatchCase, and compile list of any property names that are deleted.

References operations_.

utility::vector1< ResidueProperty > core::chemical::PatchCase::deletes_properties_enums ( ) const

Returns list of deleted property enums. Useful for identifying patches that go with PDB residues.

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

Loop through patch operations in this PatchCase, and compile a list of any ResidueProperties that are deleted. Note that this version uses enums, and only works for canonical properties (not on-the-fly properties).

References core::chemical::NO_PROPERTY, and operations_.

utility::vector1< std::string > core::chemical::PatchCase::deletes_variants ( ) const

returns list of deleted variant names, useful for identifying patches that go with PDB residues

Go through patch operations in this PatchCase, and compile list of any property names that are deleted.

References operations_.

utility::vector1< core::chemical::VariantType > core::chemical::PatchCase::deletes_variants_by_enum ( ) const

Returns list of deleted VariantTypes. Doesn't support on-the-fly VariantTypes.

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

Go through patch operations in this PatchCase, and compile list of any property names that are deleted. This version works by enum, and doesn't support on-the-fly VariantTypes.

References core::chemical::NO_VARIANT, operations_, and update_ResidueType_enum_files::variants.

bool core::chemical::PatchCase::generates_base_residue_type ( ) const

inline

Does this PatchCase result in a new base residue type?

References generates_base_residue_type_.

std::string core::chemical::PatchCase::generates_interchangeability_group ( ) const

returns interchangeability group, if set.

returns list of new interchangeability_group, useful for identifying patches that go with PDB residues

References operations_.

std::string core::chemical::PatchCase::generates_new_name3 ( ) const

returns new name3, if changed

returns list of new name3, useful for identifying patches that go with PDB residues