core::chemical::PatchOperation Class Reference

A single operation that needs to be applied in a residue patch. More...

#include <PatchOperation.hh>

Inherits VirtualBase.

Inherited by core::chemical::AddAtom, core::chemical::AddAtomAlias, core::chemical::AddBond, core::chemical::AddBondType, core::chemical::AddChi, core::chemical::AddChiRotamer, core::chemical::AddConnect, core::chemical::AddConnectAndTrackingVirt, core::chemical::AddConnectDeleteChildProton, core::chemical::AddProperty, core::chemical::AddProtonChi, core::chemical::AppendMainchainAtom, core::chemical::ChangeAncestory, core::chemical::ChangeBondType, core::chemical::ChiralFlipAtoms, core::chemical::ChiralFlipNaming, core::chemical::ClearChiRotamers, core::chemical::ConnectSulfurAndMakeVirtualProton, core::chemical::DeleteActCoordAtom, core::chemical::DeleteAtom, core::chemical::DeleteChildProton, core::chemical::DeleteMetalbindingAtom, core::chemical::DeleteProperty, core::chemical::DeleteTerminalChi, core::chemical::DeleteVariantType, core::chemical::NCAARotLibBBTorsions, core::chemical::NCAARotLibNumRotamerBins, core::chemical::NCAARotLibPath, core::chemical::PrependMainchainAtom, core::chemical::RamaPreproFilename, core::chemical::RamaPreproResname, core::chemical::RedefineChi, core::chemical::RemoveRotamerSpecifications, core::chemical::RenameAtom, core::chemical::ReplaceMainchainAtom, core::chemical::ReplaceProtonWithBromine, core::chemical::ReplaceProtonWithChlorine, core::chemical::ReplaceProtonWithEthyl, core::chemical::ReplaceProtonWithFluorine, core::chemical::ReplaceProtonWithHydroxyl, core::chemical::ReplaceProtonWithIodine, core::chemical::ReplaceProtonWithMethoxy, core::chemical::ReplaceProtonWithMethyl, core::chemical::ReplaceProtonWithTrifluoromethyl, core::chemical::ResetBondLength, core::chemical::Set_AA, core::chemical::SetAllAtomsRepulsive, core::chemical::SetAtomicCharge, core::chemical::SetAtomType, core::chemical::SetBackboneHeavyatom, core::chemical::SetBaseName, core::chemical::SetDisulfideAtomName, core::chemical::SetFormalCharge, core::chemical::SetICoor, core::chemical::SetInterchangeabilityGroup_String, core::chemical::SetIO_String, core::chemical::SetMMAtomType, core::chemical::SetNbrAtom, core::chemical::SetNbrRadius, core::chemical::SetNetFormalCharge, core::chemical::SetOrientAtom, core::chemical::SetPolymerConnectAtom, core::chemical::SetVirtualShadow, core::chemical::VirtualizeAll, and core::chemical::VirtualizeSidechain.

Public Member Functions
	~PatchOperation () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
virtual std::string	name () const =0
	Returns the name of the patch operation. Useful for debugging. More...
virtual bool	apply (MutableResidueType &rsd) const =0
	Returns true to signal failure, false to indicate success. 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...

Detailed Description

A single operation that needs to be applied in a residue patch.

Constructor & Destructor Documentation

core::chemical::PatchOperation::~PatchOperation ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

Member Function Documentation

virtual utility::vector1< std::string > core::chemical::PatchOperation::adds_atoms ( )

inlinevirtual

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

Reimplemented in core::chemical::AddAtomAlias, and core::chemical::AddAtom.

virtual std::string core::chemical::PatchOperation::adds_property ( ) const

inlinevirtual

Which property, if any, is added.

Reimplemented in core::chemical::AddProperty.

virtual ResidueProperty core::chemical::PatchOperation::adds_property_enum ( ) const

inlinevirtual

Which property, if any, is added.

This returns an enum value.

Author

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

Reimplemented in core::chemical::AddProperty.

References core::chemical::NO_PROPERTY.

virtual bool core::chemical::PatchOperation::applies_to_placeholder ( ) const

inlinevirtual

Special – does this apply to 'minimal', placeholder types? Generally true, unless updating aa or name3.

Reimplemented in core::chemical::ChiralFlipNaming, core::chemical::SetIO_String, and core::chemical::Set_AA.

virtual bool core::chemical::PatchOperation::apply ( MutableResidueType &  rsd ) const

pure virtual

Returns true to signal failure, false to indicate success.

Implemented in core::chemical::SetDisulfideAtomName, core::chemical::RenameAtom, core::chemical::SetVirtualShadow, core::chemical::VirtualizeSidechain, core::chemical::VirtualizeAll, core::chemical::DeleteChildProton, core::chemical::AddConnectDeleteChildProton, core::chemical::AddConnectAndTrackingVirt, core::chemical::ReplaceProtonWithHydroxyl, core::chemical::ReplaceProtonWithIodine, core::chemical::ReplaceProtonWithBromine, core::chemical::ReplaceProtonWithFluorine, core::chemical::ReplaceProtonWithChlorine, core::chemical::ReplaceProtonWithEthyl, core::chemical::ReplaceProtonWithMethoxy, core::chemical::ReplaceProtonWithMethyl, core::chemical::ReplaceProtonWithTrifluoromethyl, core::chemical::ChiralFlipAtoms, core::chemical::ChiralFlipNaming, core::chemical::SetBaseName, core::chemical::ConnectSulfurAndMakeVirtualProton, core::chemical::NCAARotLibNumRotamerBins, core::chemical::NCAARotLibBBTorsions, core::chemical::NCAARotLibPath, core::chemical::RamaPreproResname, core::chemical::RamaPreproFilename, core::chemical::RemoveRotamerSpecifications, core::chemical::SetOrientAtom, core::chemical::SetAllAtomsRepulsive, core::chemical::SetNbrRadius, core::chemical::SetNbrAtom, core::chemical::ReplaceMainchainAtom, core::chemical::AppendMainchainAtom, core::chemical::PrependMainchainAtom, core::chemical::ResetBondLength, core::chemical::ChangeAncestory, core::chemical::SetICoor, core::chemical::SetMMAtomType, core::chemical::SetInterchangeabilityGroup_String, core::chemical::SetIO_String, core::chemical::Set_AA, core::chemical::SetAtomType, core::chemical::SetNetFormalCharge, core::chemical::SetFormalCharge, core::chemical::SetAtomicCharge, core::chemical::ChangeBondType, core::chemical::AddBondType, core::chemical::AddBond, core::chemical::AddAtomAlias, core::chemical::AddAtom, core::chemical::ClearChiRotamers, core::chemical::AddChiRotamer, core::chemical::DeleteActCoordAtom, core::chemical::DeleteMetalbindingAtom, core::chemical::DeleteTerminalChi, core::chemical::RedefineChi, core::chemical::AddProtonChi, core::chemical::AddChi, core::chemical::DeleteVariantType, core::chemical::DeleteProperty, core::chemical::AddProperty, core::chemical::AddConnect, core::chemical::SetPolymerConnectAtom, core::chemical::SetBackboneHeavyatom, and core::chemical::DeleteAtom.

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

inlinevirtual

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 in core::chemical::AddConnectDeleteChildProton, core::chemical::AddConnectAndTrackingVirt, core::chemical::ConnectSulfurAndMakeVirtualProton, core::chemical::AddConnect, and core::chemical::SetPolymerConnectAtom.

virtual std::string core::chemical::PatchOperation::deletes_atom ( )

inlinevirtual

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

Reimplemented in core::chemical::DeleteAtom.

virtual std::string core::chemical::PatchOperation::deletes_property ( ) const

inlinevirtual

Which property, if any, is deleted.

Reimplemented in core::chemical::DeleteProperty.

virtual ResidueProperty core::chemical::PatchOperation::deletes_property_enum ( ) const

inlinevirtual

Which property, if any, is deleted.

This returns an enum value.

Author

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

Reimplemented in core::chemical::DeleteProperty.

References core::chemical::NO_PROPERTY.

virtual std::string core::chemical::PatchOperation::deletes_variant ( ) const

inlinevirtual

Which variant, if any, is deleted.

Reimplemented in core::chemical::DeleteVariantType.

virtual VariantType core::chemical::PatchOperation::deletes_variant_enum ( ) const

inlinevirtual

Which variant, if any, is deleted, by enum.

Reimplemented in core::chemical::DeleteVariantType.

References core::chemical::NO_VARIANT.

virtual bool core::chemical::PatchOperation::generates_base_residue_type ( ) const

inlinevirtual

Generates base residue – legacy for D_AA – do not use otherwise.

Reimplemented in core::chemical::ChiralFlipNaming, and core::chemical::SetBaseName.

virtual std::string core::chemical::PatchOperation::generates_interchangeability_group ( )

inlinevirtual

Generates interchangeability_group.

Reimplemented in core::chemical::SetInterchangeabilityGroup_String.

virtual std::string core::chemical::PatchOperation::generates_name3 ( )

inlinevirtual

Generates name3.

Reimplemented in core::chemical::SetIO_String.

virtual bool core::chemical::PatchOperation::may_change_aa ( )

inlinevirtual

Generates a new aa.

Reimplemented in core::chemical::ChiralFlipNaming, core::chemical::SetBaseName, and core::chemical::Set_AA.

virtual std::string core::chemical::PatchOperation::name ( ) const

pure virtual

Returns the name of the patch operation. Useful for debugging.

Author

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

Implemented in core::chemical::SetDisulfideAtomName, core::chemical::RenameAtom, core::chemical::SetVirtualShadow, core::chemical::VirtualizeSidechain, core::chemical::VirtualizeAll, core::chemical::DeleteChildProton, core::chemical::AddConnectDeleteChildProton, core::chemical::AddConnectAndTrackingVirt, core::chemical::ReplaceProtonWithHydroxyl, core::chemical::ReplaceProtonWithIodine, core::chemical::ReplaceProtonWithBromine, core::chemical::ReplaceProtonWithFluorine, core::chemical::ReplaceProtonWithChlorine, core::chemical::ReplaceProtonWithEthyl, core::chemical::ReplaceProtonWithMethoxy, core::chemical::ReplaceProtonWithMethyl, core::chemical::ReplaceProtonWithTrifluoromethyl, core::chemical::ChiralFlipAtoms, core::chemical::ChiralFlipNaming, core::chemical::SetBaseName, core::chemical::ConnectSulfurAndMakeVirtualProton, core::chemical::NCAARotLibNumRotamerBins, core::chemical::NCAARotLibBBTorsions, core::chemical::NCAARotLibPath, core::chemical::RamaPreproResname, core::chemical::RamaPreproFilename, core::chemical::RemoveRotamerSpecifications, core::chemical::SetOrientAtom, core::chemical::SetAllAtomsRepulsive, core::chemical::SetNbrRadius, core::chemical::SetNbrAtom, core::chemical::ReplaceMainchainAtom, core::chemical::AppendMainchainAtom, core::chemical::PrependMainchainAtom, core::chemical::ResetBondLength, core::chemical::ChangeAncestory, core::chemical::SetICoor, core::chemical::SetMMAtomType, core::chemical::SetInterchangeabilityGroup_String, core::chemical::SetIO_String, core::chemical::Set_AA, core::chemical::SetAtomType, core::chemical::SetNetFormalCharge, core::chemical::SetFormalCharge, core::chemical::SetAtomicCharge, core::chemical::ChangeBondType, core::chemical::AddBondType, core::chemical::AddBond, core::chemical::AddAtomAlias, core::chemical::AddAtom, core::chemical::ClearChiRotamers, core::chemical::AddChiRotamer, core::chemical::DeleteActCoordAtom, core::chemical::DeleteMetalbindingAtom, core::chemical::DeleteTerminalChi, core::chemical::RedefineChi, core::chemical::AddProtonChi, core::chemical::AddChi, core::chemical::DeleteVariantType, core::chemical::DeleteProperty, core::chemical::AddProperty, core::chemical::AddConnect, core::chemical::SetPolymerConnectAtom, core::chemical::SetBackboneHeavyatom, and core::chemical::DeleteAtom.

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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