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PatchOperation.hh File Reference

Polymorphic classes representing the contents of a residue-type patch file. More...

#include <core/chemical/PatchOperation.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/MutableResidueType.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueProperties.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/VirtualBase.hh>
#include <map>

Classes

class  core::chemical::PatchOperation
 A single operation that needs to be applied in a residue patch. More...
 
class  core::chemical::DeleteAtom
 delete an atom More...
 
class  core::chemical::SetBackboneHeavyatom
 set an atom as backbone heavy atom More...
 
class  core::chemical::SetPolymerConnectAtom
 set an atom as polymer connection More...
 
class  core::chemical::AddConnect
 
class  core::chemical::AddProperty
 add a property to ResidueType More...
 
class  core::chemical::DeleteProperty
 delete a property from ResidueType Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM's (e.g. methylation) Rewritten by Vikram K. Mulligan on 25 Aug. 2016 to use enums wherever possible for speed. More...
 
class  core::chemical::DeleteVariantType
 A patch operation for deleting a VariantType from a ResidueType. More...
 
class  core::chemical::AddChi
 Add a chi angle to ResidueType. More...
 
class  core::chemical::AddProtonChi
 
class  core::chemical::RedefineChi
 Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTMs. More...
 
class  core::chemical::DeleteTerminalChi
 Delete terminal chi angle Added by Andrew M. Watkins in April 2015. More...
 
class  core::chemical::DeleteMetalbindingAtom
 Delete a metal binding atom Added by Andrew M. Watkins in April 2015. More...
 
class  core::chemical::DeleteActCoordAtom
 Delete an act coord atom Added by Andrew M. Watkins in April 2015. More...
 
class  core::chemical::AddChiRotamer
 Add a rotamer sample to a chi angle of the ResidueType. More...
 
class  core::chemical::ClearChiRotamers
 A patch operation for clearing all rotamer bins from the chi of a ResidueType. More...
 
class  core::chemical::AddAtom
 add an atom to ResidueType More...
 
class  core::chemical::AddAtomAlias
 A patch operation for adding an atom alias to a ResidueType. More...
 
class  core::chemical::AddBond
 add a bond to ResidueType More...
 
class  core::chemical::AddBondType
 A patch operation for adding a specific type of bond to a ResidueType. More...
 
class  core::chemical::ChangeBondType
 A patch operation for changing the bond type of a given bond. More...
 
class  core::chemical::SetAtomicCharge
 set an atom's charge More...
 
class  core::chemical::SetFormalCharge
 A patch operation for setting the formal charge of a ResidueType's atom. More...
 
class  core::chemical::SetNetFormalCharge
 A patch operation for setting the net formal charge of a whole ResidueType. More...
 
class  core::chemical::SetAtomType
 set atom's chemical type More...
 
class  core::chemical::Set_AA
 set residue's aa More...
 
class  core::chemical::SetIO_String
 set residue's name1 and name3 More...
 
class  core::chemical::SetInterchangeabilityGroup_String
 set the interchangeability_group string for a ResidueType More...
 
class  core::chemical::SetMMAtomType
 set atom's MM chemical type More...
 
class  core::chemical::SetICoor
 set an atom's AtomICoord More...
 
class  core::chemical::ChangeAncestory
 
class  core::chemical::ResetBondLength
 A patch operation for resetting the length of a bond within a ResidueType. More...
 
class  core::chemical::PrependMainchainAtom
 add a mainchain atom before the first mainchain atom More...
 
class  core::chemical::AppendMainchainAtom
 add a mainchain atom after the last mainchain atom More...
 
class  core::chemical::ReplaceMainchainAtom
 replace a mainchain atom More...
 
class  core::chemical::SetNbrAtom
 set the residue neighbor atom More...
 
class  core::chemical::SetNbrRadius
 set the residue neighbor radius More...
 
class  core::chemical::SetAllAtomsRepulsive
 set the residue neighbor radius More...
 
class  core::chemical::SetOrientAtom
 Set orient atom selection mode. More...
 
class  core::chemical::RemoveRotamerSpecifications
 Remove existing rotamer specifications (of any type). More...
 
class  core::chemical::RamaPreproFilename
 Set the filenames for RamaPrePro scoring tables. More...
 
class  core::chemical::RamaPreproResname
 Set the residue name for RamaPrePro scoring tables. More...
 
class  core::chemical::NCAARotLibPath
 set the path to a rotamer library for an NCAA that is not in dunbrack More...
 
class  core::chemical::NCAARotLibBBTorsions
 Set the mainchain torsion indices that a noncanonical rotamer library depends upon. More...
 
class  core::chemical::NCAARotLibNumRotamerBins
 Set the number of rotamer bins per chi for an NCAA that is not in dunbrack. More...
 
class  core::chemical::ConnectSulfurAndMakeVirtualProton
 Add a connection to the residue's sulfur and make a virtual proton to track the position of the connection atom. More...
 
class  core::chemical::ChiralFlipNaming
 Execute chiral flip (primarily: at CA) More...
 
class  core::chemical::ChiralFlipAtoms
 Execute chiral flip (primarily: at CA) More...
 
class  core::chemical::ReplaceProtonWithTrifluoromethyl
 replace proton with trifluoromethyl More...
 
class  core::chemical::ReplaceProtonWithMethyl
 replace proton with methyl More...
 
class  core::chemical::ReplaceProtonWithMethoxy
 replace proton with methoxy More...
 
class  core::chemical::ReplaceProtonWithEthyl
 replace proton with ethyl More...
 
class  core::chemical::ReplaceProtonWithChlorine
 replace proton with chlorine More...
 
class  core::chemical::ReplaceProtonWithFluorine
 replace proton with fluorine More...
 
class  core::chemical::ReplaceProtonWithBromine
 replace proton with bromine More...
 
class  core::chemical::ReplaceProtonWithIodine
 replace proton with iodine More...
 
class  core::chemical::ReplaceProtonWithHydroxyl
 replace proton with hydroxyl More...
 
class  core::chemical::AddConnectAndTrackingVirt
 add a connect and tracking virt to the atom More...
 
class  core::chemical::AddConnectDeleteChildProton
 add a connect to the atom, delete child proton More...
 
class  core::chemical::DeleteChildProton
 delete child proton More...
 
class  core::chemical::VirtualizeAll
 virtualize all More...
 
class  core::chemical::VirtualizeSidechain
 virtualize sidechain More...
 
class  core::chemical::SetVirtualShadow
 set virtual shadow atoms More...
 
class  core::chemical::RenameAtom
 rename atom More...
 
class  core::chemical::SetDisulfideAtomName
 set an atom as this residue's disulfide forming atom More...
 

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::chemical
 

Enumerations

enum  core::chemical::Ancestor { core::chemical::anc_parent, core::chemical::anc_grandparent, core::chemical::anc_greatgrandparent }
 Change the parent, grandparent, or great-grandparent of an atom. More...
 

Functions

PatchOperationOP core::chemical::patch_operation_from_patch_file_line (std::string const &line, std::map< std::string, Real > const &atomic_charge_reassignments)
 Virtual constructor, returns 0 if no match. More...
 

Detailed Description

Polymorphic classes representing the contents of a residue-type patch file.

Author
Phil Bradley