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Rosetta
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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 <utility/vector1.hh>#include <utility/VirtualBase.hh>#include <map>#include <core/chemical/ResidueProperty.hh>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::SetBaseName |
| Alter the base name. 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... | |
Polymorphic classes representing the contents of a residue-type patch file.
1.9.1