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core::chemical::PatchCase Class Reference

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

#include <Patch.hh>

Inheritance diagram for core::chemical::PatchCase:
Inheritance graph
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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...
 
ResidueTypeSelectorselector ()
 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< ResiduePropertyadds_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< ResiduePropertydeletes_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 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...
 

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)
inline

add one more operation in this PatchCase

References 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.

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

References operations_.

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

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

References operations_.

ResidueTypeSelector& core::chemical::PatchCase::selector ( )
inline

to which ResidueTypes this PatchCase applies to?

References selector_.

Referenced by set_selector().

void core::chemical::PatchCase::set_selector ( ResidueTypeSelector const &  selector)
inline

References selector(), and selector_.

Member Data Documentation

utility::vector1< PatchOperationOP > core::chemical::PatchCase::operations_
private
ResidueTypeSelector core::chemical::PatchCase::selector_
private

to which ResidueTypes this PatchCase applies to?

Referenced by applies_to(), selector(), and set_selector().


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