|
| class | Adduct |
| | Description of optional single-atom residue adducts. More...
|
| |
| class | Atom |
| |
| class | ICoorAtomID |
| | Atom 's ID in internal coordinates in a ResidueType. More...
|
| |
| class | AtomICoor |
| | A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More...
|
| |
| class | AtomProperties |
| |
| class | AtomPropertiesManager |
| |
| class | RefConvert |
| | An internal implementation class, to get around the fact that functions cannot be partially specialized. More...
|
| |
| class | RefConvert< VD > |
| |
| class | RefConvert< core::Size > |
| |
| class | RefConvert< std::string > |
| |
| class | AtomRefMapping |
| | A class for mapping ResidueType atom references from one to another. It's intended not only for intra ResidueType mapping, but also for mapping corresponding references from one ResidueType to another. More...
|
| |
| class | AtomType |
| | basic atom type More...
|
| |
| class | AtomTypeDatabaseIO |
| |
| class | AtomTypeSet |
| | a set of AtomTypes More...
|
| |
| class | AutomorphismIterator |
| | Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations. More...
|
| |
| class | Bond |
| | basic chemical Bond More...
|
| |
| class | CacheableResidueTypeSets |
| | A (Pose-cacheable) container for ResidueTypeSets. More...
|
| |
| class | ChemicalManager |
| | a class managing different sets of atom_type_set and residue_type_set More...
|
| |
| class | ElectronConfiguration |
| | describes the electron configuration of atoms More...
|
| |
| class | Element |
| | stores element properties More...
|
| |
| class | ElementSet |
| | A set of Bcl Elements. More...
|
| |
| class | GlobalResidueTypeSet |
| | A collection of ResidueType defined. More...
|
| |
| class | RerootRestypeVisitor |
| |
| class | RerootEdgeSorter |
| | Edge sorting: Return true if we should prefer edge1 over edge2. More...
|
| |
| class | IdealBondLengthSet |
| | A set of Elements. More...
|
| |
| class | Metapatch |
| | A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...
|
| |
| class | MMAtomType |
| | Basic MM atom type. More...
|
| |
| class | MMAtomTypeSet |
| | A set of MMAtomTypes. More...
|
| |
| class | MutableChiRecord |
| | A class containing bundled info about chis. More...
|
| |
| class | MutableICoorRecord |
| | A basic class containing basic info of internal coordinates needed for building an atom within a ResidueType This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor. More...
|
| |
| class | MutableResidueConnection |
| | A simple class marking atoms at inter-residue connections. More...
|
| |
| class | MutableResidueType |
| | A class for defining a type of residue, modifiable version. More...
|
| |
| class | Orbital |
| | basic chemical atom More...
|
| |
| class | PatchCase |
| | A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More...
|
| |
| class | Patch |
| | A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...
|
| |
| class | PatchOperation |
| | A single operation that needs to be applied in a residue patch. More...
|
| |
| class | DeleteAtom |
| | delete an atom More...
|
| |
| class | SetBackboneHeavyatom |
| | set an atom as backbone heavy atom More...
|
| |
| class | SetPolymerConnectAtom |
| | set an atom as polymer connection More...
|
| |
| class | AddConnect |
| |
| class | AddProperty |
| | add a property to ResidueType More...
|
| |
| class | 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 | DeleteVariantType |
| | A patch operation for deleting a VariantType from a ResidueType. More...
|
| |
| class | AddChi |
| | Add a chi angle to ResidueType. More...
|
| |
| class | AddProtonChi |
| |
| class | RedefineChi |
| | Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTMs. More...
|
| |
| class | DeleteTerminalChi |
| | Delete terminal chi angle Added by Andrew M. Watkins in April 2015. More...
|
| |
| class | DeleteMetalbindingAtom |
| | Delete a metal binding atom Added by Andrew M. Watkins in April 2015. More...
|
| |
| class | DeleteActCoordAtom |
| | Delete an act coord atom Added by Andrew M. Watkins in April 2015. More...
|
| |
| class | AddChiRotamer |
| | Add a rotamer sample to a chi angle of the ResidueType. More...
|
| |
| class | ClearChiRotamers |
| | A patch operation for clearing all rotamer bins from the chi of a ResidueType. More...
|
| |
| class | AddAtom |
| | add an atom to ResidueType More...
|
| |
| class | AddAtomAlias |
| | A patch operation for adding an atom alias to a ResidueType. More...
|
| |
| class | AddBond |
| | add a bond to ResidueType More...
|
| |
| class | AddBondType |
| | A patch operation for adding a specific type of bond to a ResidueType. More...
|
| |
| class | ChangeBondType |
| | A patch operation for changing the bond type of a given bond. More...
|
| |
| class | SetAtomicCharge |
| | set an atom's charge More...
|
| |
| class | SetFormalCharge |
| | A patch operation for setting the formal charge of a ResidueType's atom. More...
|
| |
| class | SetNetFormalCharge |
| | A patch operation for setting the net formal charge of a whole ResidueType. More...
|
| |
| class | SetAtomType |
| | set atom's chemical type More...
|
| |
| class | Set_AA |
| | set residue's aa More...
|
| |
| class | SetIO_String |
| | set residue's name1 and name3 More...
|
| |
| class | SetInterchangeabilityGroup_String |
| | set the interchangeability_group string for a ResidueType More...
|
| |
| class | SetMMAtomType |
| | set atom's MM chemical type More...
|
| |
| class | SetICoor |
| | set an atom's AtomICoord More...
|
| |
| class | ChangeAncestory |
| |
| class | ResetBondLength |
| | A patch operation for resetting the length of a bond within a ResidueType. More...
|
| |
| class | PrependMainchainAtom |
| | add a mainchain atom before the first mainchain atom More...
|
| |
| class | AppendMainchainAtom |
| | add a mainchain atom after the last mainchain atom More...
|
| |
| class | ReplaceMainchainAtom |
| | replace a mainchain atom More...
|
| |
| class | SetNbrAtom |
| | set the residue neighbor atom More...
|
| |
| class | SetNbrRadius |
| | set the residue neighbor radius More...
|
| |
| class | SetAllAtomsRepulsive |
| | set the residue neighbor radius More...
|
| |
| class | SetOrientAtom |
| | Set orient atom selection mode. More...
|
| |
| class | RemoveRotamerSpecifications |
| | Remove existing rotamer specifications (of any type). More...
|
| |
| class | RamaPreproFilename |
| | Set the filenames for RamaPrePro scoring tables. More...
|
| |
| class | RamaPreproResname |
| | Set the residue name for RamaPrePro scoring tables. More...
|
| |
| class | NCAARotLibPath |
| | set the path to a rotamer library for an NCAA that is not in dunbrack More...
|
| |
| class | NCAARotLibBBTorsions |
| | Set the mainchain torsion indices that a noncanonical rotamer library depends upon. More...
|
| |
| class | NCAARotLibNumRotamerBins |
| | Set the number of rotamer bins per chi for an NCAA that is not in dunbrack. More...
|
| |
| class | ConnectSulfurAndMakeVirtualProton |
| | Add a connection to the residue's sulfur and make a virtual proton to track the position of the connection atom. More...
|
| |
| class | SetBaseName |
| | Alter the base name. More...
|
| |
| class | ChiralFlipNaming |
| | Execute chiral flip (primarily: at CA) More...
|
| |
| class | ChiralFlipAtoms |
| | Execute chiral flip (primarily: at CA) More...
|
| |
| class | ReplaceProtonWithTrifluoromethyl |
| | replace proton with trifluoromethyl More...
|
| |
| class | ReplaceProtonWithMethyl |
| | replace proton with methyl More...
|
| |
| class | ReplaceProtonWithMethoxy |
| | replace proton with methoxy More...
|
| |
| class | ReplaceProtonWithEthyl |
| | replace proton with ethyl More...
|
| |
| class | ReplaceProtonWithChlorine |
| | replace proton with chlorine More...
|
| |
| class | ReplaceProtonWithFluorine |
| | replace proton with fluorine More...
|
| |
| class | ReplaceProtonWithBromine |
| | replace proton with bromine More...
|
| |
| class | ReplaceProtonWithIodine |
| | replace proton with iodine More...
|
| |
| class | ReplaceProtonWithHydroxyl |
| | replace proton with hydroxyl More...
|
| |
| class | AddConnectAndTrackingVirt |
| | add a connect and tracking virt to the atom More...
|
| |
| class | AddConnectDeleteChildProton |
| | add a connect to the atom, delete child proton More...
|
| |
| class | DeleteChildProton |
| | delete child proton More...
|
| |
| class | VirtualizeAll |
| | virtualize all More...
|
| |
| class | VirtualizeSidechain |
| | virtualize sidechain More...
|
| |
| class | SetVirtualShadow |
| | set virtual shadow atoms More...
|
| |
| class | RenameAtom |
| | rename atom More...
|
| |
| class | SetDisulfideAtomName |
| | set an atom as this residue's disulfide forming atom More...
|
| |
| class | AddAtomCreator |
| |
| class | DeleteAtomCreator |
| |
| class | AddAtomAliasCreator |
| |
| class | SetBackboneHeavyatomCreator |
| |
| class | SetDisulfideAtomNameCreator |
| |
| class | SetAACreator |
| |
| class | SetBaseNameCreator |
| |
| class | SetIOStringCreator |
| |
| class | SetInterchangeabilityGroupCreator |
| |
| class | NbrAtomCreator |
| |
| class | NbrRadiusCreator |
| |
| class | AddPropertyCreator |
| |
| class | DeletePropertyCreator |
| |
| class | DeleteVariantTypeCreator |
| |
| class | AddChiCreator |
| |
| class | AddProtonChiCreator |
| |
| class | RedefineChiCreator |
| |
| class | DeleteTerminalChiCreator |
| |
| class | DeleteMetalBindingAtomCreator |
| |
| class | DeleteActCoordAtomCreator |
| |
| class | AddChiRotamerCreator |
| |
| class | ClearChiRotamersCreator |
| |
| class | AddBondCreator |
| |
| class | AddBondTypeCreator |
| |
| class | ChangeBondTypeCreator |
| |
| class | AddConnectCreator |
| |
| class | SetAtomTypeCreator |
| |
| class | SetMMAtomTypeCreator |
| |
| class | SetFormalChargeCreator |
| |
| class | SetNetFormalChargeCreator |
| |
| class | SetAtomicChargeCreator |
| |
| class | SetPolymerConnectCreator |
| |
| class | SetICOORCreator |
| |
| class | SetAncestorCreator |
| |
| class | ResetBondLengthCreator |
| |
| class | PrependMainchainAtomCreator |
| |
| class | AppendMainchainAtomCreator |
| |
| class | ReplaceMainchainAtomCreator |
| |
| class | RamaPreproFilenameCreator |
| |
| class | RamaPreproResnameCreator |
| |
| class | RemoveRotamerSpecificationsCreator |
| |
| class | NCAARotlibPathCreator |
| |
| class | NCAARotlibBBTorsionsCreator |
| |
| class | NCAARotlibNumRotamerBinsCreator |
| |
| class | SetNbrAtomCreator |
| |
| class | SetNbrRadiusCreator |
| |
| class | SetOrientAtomCreator |
| |
| class | SetAllAtomsRepulsiveCreator |
| |
| class | ConnectSulfurAndMakeVirtualProtonCreator |
| |
| class | ReplaceProtonWithChlorineCreator |
| |
| class | ReplaceProtonWithFluorineCreator |
| |
| class | ReplaceProtonWithBromineCreator |
| |
| class | ReplaceProtonWithIodineCreator |
| |
| class | ReplaceProtonWithMethylCreator |
| |
| class | ReplaceProtonWithTrifluoromethylCreator |
| |
| class | ReplaceProtonWithHydroxylCreator |
| |
| class | ReplaceProtonWithMethoxyCreator |
| |
| class | ReplaceProtonWithEthylCreator |
| |
| class | AddConnectAndDeleteChildProtonCreator |
| |
| class | DeleteChildProtonCreator |
| |
| class | AddConnectAndTrackingVirtCreator |
| |
| class | ChiralFlipNamingCreator |
| |
| class | ChiralFlipAtomsCreator |
| |
| class | VirtualizeSidechainCreator |
| |
| class | VirtualizeAllCreator |
| |
| class | SetVirtualShadowCreator |
| |
| class | RenameAtomCreator |
| |
| class | PatchOperationCreator |
| | The PatchOperationCreator is responsible for creating a PatchOperation from input line(s) More...
|
| |
| class | PatchOperationRegistrator |
| | This templated class will register an instance of an PatchOperationCreator (class T) with the PatchOperationFactory. It will ensure that no PatchOperationCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
|
| |
| class | PatchOperationFactory |
| |
| class | PoseResidueTypeSet |
| | A ResidueTypeSet which can be cached in the Pose. More...
|
| |
| class | ResConnID |
| | The ResConnID could more properly be called the ResidueConnector. It stores the data necessary to describe how one ResidueConnection on a conformation::Residue is connected to the rest of the structure (Pose), by listing the other Residue's index and the ResidueConnection index. More...
|
| |
| class | GraphvizPropertyWriter |
| | Callback class for write_graphviz - outputs properties for the nodes and edges. More...
|
| |
| class | RigidDistanceVisitor |
| | Utility visitor for find_nbr_dist Will only traverse those atoms in the "rigid" portion of graph around the starting atom. "Rigid" includes direct neighbors and atoms connected by non-rotatable bonds e.g. all rings, all double/triple bonds, methyl groups, single atoms, etc. More...
|
| |
| class | VDDistanceMatrix |
| | Utility class for VD-indexed matrix. More...
|
| |
| class | ResidueConnection |
| | A simple class marking atoms at inter-residue connections. More...
|
| |
| class | ResidueDatabaseIO |
| |
| class | ResidueProperties |
| |
| class | RealFilter |
| | @default A filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds. More...
|
| |
| class | HeavyAtomFilter |
| | The filter responsible for obtaining all heavy atoms. More...
|
| |
| class | AcceptorAtomFilter |
| | The filter responsible for obtaining all acceptor atoms. More...
|
| |
| class | HeavyAtomWithPolarHydrogensFilter |
| | The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them. More...
|
| |
| class | HeavyAtomWithHydrogensFilter |
| | The filter responsible for finding heavy atoms with hydrogens. More...
|
| |
| class | HydrogenAtomFilter |
| | The filter responsible for all hydrogens. More...
|
| |
| class | AromaticAtomFilter |
| | The filter responsible for all aromatic atoms. More...
|
| |
| class | PolarHydrogenFilter |
| | The filter responsible for all polar hydrogens. More...
|
| |
| class | APolarHydrogenFilter |
| | The filter responsible for all apolar hydrogens. More...
|
| |
| class | CopyVertex |
| |
| class | CopyEdge |
| |
| class | ResidueType |
| | A class for defining a type of residue. More...
|
| |
| class | ResidueTypeBase |
| | A base class for definiting types of residues. More...
|
| |
| class | ResidueTypeFinder |
| |
| class | ResidueTypeKinWriter |
| |
| class | ResidueTypeSelectorSingle |
| | A base class for defining a ResidueTypeSelector by a single criterion. More...
|
| |
| class | Selector_AA |
| | Does the residue belong to ANY of these AAs? More...
|
| |
| class | Selector_CMDFLAG |
| | Is a certain string in the command-line option -chemical:allow_patch present ? this selector does actually not depend on the residuetype it is queried for. More...
|
| |
| class | Selector_BASENAME |
| | Does the residue have to ANY of these basenames? More...
|
| |
| class | Selector_NAME3 |
| | Does the residue have ANY of these three-letter codes? More...
|
| |
| class | Selector_HAS_ATOMS |
| | Does the residue have ALL of the listed atoms?: More...
|
| |
| class | Selector_PROPERTY |
| | Does the residue have ANY of these properties? More...
|
| |
| class | Selector_VARIANT_TYPE |
| | Does the residue have ANY of variant types? More...
|
| |
| class | Selector_UPPER_ATOM |
| | Does the main chain of this residue follow from the given position label? More...
|
| |
| class | Selector_MATCH_VARIANTS |
| | Does the residue have ALL of the variant types and no more. More...
|
| |
| class | Selector_NO_VARIANTS |
| | Does the residue have NO variant types? More...
|
| |
| class | Selector_NAME1 |
| | Does the residue belong to ANY of these one-letter codes? More...
|
| |
| class | ResidueTypeSelector |
| | A class picking out a subset of ResidueType by multiple criteria. More...
|
| |
| class | ResidueTypeSet |
| | An abstract interface to a set of ResidueTypes. More...
|
| |
| class | ResidueTypeSetCache |
| |
| struct | RestypeDestructionEvent |
| | special signal that the ResidueType is getting destroyed More...
|
| |
|
| typedef utility::pointer::shared_ptr< Adduct > | AdductOP |
| |
| typedef std::map< std::string, int > | AdductMap |
| |
| typedef utility::pointer::shared_ptr< Atom > | AtomOP |
| |
| typedef utility::pointer::shared_ptr< Atom const > | AtomCOP |
| |
| typedef utility::pointer::weak_ptr< Atom > | AtomAP |
| |
| typedef utility::vector1< AtomOP > | AtomOPs |
| |
| typedef utility::vector1< AtomCOP > | AtomCOPs |
| |
| typedef utility::vector1< AtomAP > | AtomAPs |
| |
| using | AtomMemo = basic::datacache::DataMapObj< std::set< std::string > > |
| |
| using | AtomMemoOP = utility::pointer::shared_ptr< AtomMemo > |
| |
| typedef utility::pointer::shared_ptr< AtomProperties > | AtomPropertiesOP |
| |
| typedef utility::pointer::shared_ptr< AtomProperties const > | AtomPropertiesCOP |
| |
| typedef AtomRefMapping< VD, VD > | VDVDMapping |
| |
| typedef AtomRefMapping< VD, core::Size > | VDIndexMapping |
| |
| typedef AtomRefMapping< core::Size, VD > | IndexVDMapping |
| |
| typedef AtomRefMapping< core::Size, core::Size > | IndexIndexMapping |
| |
| typedef AtomRefMapping< std::string, VD > | StringVDMapping |
| |
| typedef AtomRefMapping< VD, std::string > | VDStringMapping |
| |
| typedef AtomRefMapping< std::string, VD > | NameVDMapping |
| |
| typedef AtomRefMapping< VD, std::string > | VDNameMapping |
| |
| typedef AtomRefMapping< std::string, core::Size > | NameIndexMapping |
| |
| typedef AtomRefMapping< core::Size, std::string > | IndexNameMapping |
| |
| typedef utility::pointer::shared_ptr< AtomTypeDatabaseIO > | AtomTypeDatabaseIOOP |
| |
| typedef utility::pointer::shared_ptr< AtomTypeDatabaseIO const > | AtomTypeDatabaseIOCOP |
| |
| typedef utility::pointer::weak_ptr< AtomTypeSet > | AtomTypeSetAP |
| |
| typedef utility::pointer::weak_ptr< AtomTypeSet const > | AtomTypeSetCAP |
| |
| typedef utility::pointer::shared_ptr< AtomTypeSet > | AtomTypeSetOP |
| |
| typedef utility::pointer::shared_ptr< AtomTypeSet const > | AtomTypeSetCOP |
| |
| typedef utility::pointer::shared_ptr< AutomorphismIterator > | AutomorphismIteratorOP |
| |
| typedef utility::pointer::shared_ptr< AutomorphismIterator const > | AutomorphismIteratorCOP |
| |
| typedef utility::pointer::shared_ptr< CacheableResidueTypeSets > | CacheableResidueTypeSetsOP |
| |
| typedef utility::pointer::shared_ptr< CacheableResidueTypeSets const > | CacheableResidueTypeSetsCOP |
| |
| typedef utility::pointer::shared_ptr< Element > | ElementOP |
| |
| typedef utility::pointer::shared_ptr< Element const > | ElementCOP |
| |
| typedef utility::pointer::weak_ptr< ElementSet > | ElementSetAP |
| |
| typedef utility::pointer::weak_ptr< ElementSet const > | ElementSetCAP |
| |
| typedef utility::pointer::shared_ptr< ElementSet > | ElementSetOP |
| |
| typedef utility::pointer::shared_ptr< ElementSet const > | ElementSetCOP |
| |
| typedef utility::pointer::shared_ptr< GlobalResidueTypeSet > | GlobalResidueTypeSetOP |
| |
| typedef utility::pointer::shared_ptr< GlobalResidueTypeSet const > | GlobalResidueTypeSetCOP |
| |
| typedef utility::pointer::weak_ptr< GlobalResidueTypeSet const > | GlobalResidueTypeSetCAP |
| |
| typedef std::map< core::chemical::VD, core::kinematics::tree::AtomOP > | VdTreeatomMap |
| |
| typedef utility::pointer::weak_ptr< IdealBondLengthSet > | IdealBondLengthSetAP |
| |
| typedef utility::pointer::weak_ptr< IdealBondLengthSet const > | IdealBondLengthSetCAP |
| |
| typedef utility::pointer::shared_ptr< IdealBondLengthSet > | IdealBondLengthSetOP |
| |
| typedef utility::pointer::shared_ptr< IdealBondLengthSet const > | IdealBondLengthSetCOP |
| |
| typedef int | AtomTypeIndex |
| |
| typedef Real | BondLength |
| |
| typedef utility::pointer::shared_ptr< Metapatch > | MetapatchOP |
| |
| typedef utility::pointer::shared_ptr< Metapatch const > | MetapatchCOP |
| |
| typedef utility::pointer::shared_ptr< MMAtomType > | MMAtomTypeOP |
| |
| typedef utility::pointer::weak_ptr< MMAtomTypeSet > | MMAtomTypeSetAP |
| |
| typedef utility::pointer::weak_ptr< MMAtomTypeSet const > | MMAtomTypeSetCAP |
| |
| typedef utility::pointer::shared_ptr< MMAtomTypeSet > | MMAtomTypeSetOP |
| |
| typedef utility::pointer::shared_ptr< MMAtomTypeSet const > | MMAtomTypeSetCOP |
| |
| typedef utility::pointer::shared_ptr< MutableChiRecord > | MutableChiRecordOP |
| |
| typedef utility::pointer::shared_ptr< MutableChiRecord const > | MutableChiRecordCOP |
| |
| typedef utility::pointer::shared_ptr< MutableICoorRecord > | MutableICoorRecordOP |
| |
| typedef utility::pointer::shared_ptr< MutableICoorRecord const > | MutableICoorRecordCOP |
| |
| typedef utility::pointer::shared_ptr< MutableResidueType > | MutableResidueTypeOP |
| |
| typedef utility::pointer::shared_ptr< MutableResidueType const > | MutableResidueTypeCOP |
| |
| typedef utility::vector1< MutableResidueTypeOP > | MutableResidueTypeOPs |
| |
| typedef utility::vector1< MutableResidueTypeCOP > | MutableResidueTypeCOPs |
| |
| typedef utility::pointer::shared_ptr< Orbital > | OrbitalOP |
| |
| typedef utility::pointer::shared_ptr< Orbital const > | OrbitalCOP |
| |
| typedef utility::vector1< OrbitalOP > | OrbitalOPs |
| |
| typedef utility::vector1< OrbitalCOP > | OrbitalCOPs |
| |
| typedef utility::pointer::shared_ptr< PatchCase > | PatchCaseOP |
| |
| typedef utility::pointer::shared_ptr< Patch > | PatchOP |
| |
| typedef utility::pointer::shared_ptr< Patch const > | PatchCOP |
| |
| typedef utility::pointer::shared_ptr< PatchOperation > | PatchOperationOP |
| |
| typedef utility::pointer::shared_ptr< PatchOperationCreator > | PatchOperationCreatorOP |
| |
| typedef utility::pointer::shared_ptr< PatchOperationCreator const > | PatchOperationCreatorCOP |
| |
| typedef utility::pointer::shared_ptr< PoseResidueTypeSet > | PoseResidueTypeSetOP |
| |
| typedef utility::pointer::shared_ptr< PoseResidueTypeSet const > | PoseResidueTypeSetCOP |
| |
| typedef boost::undirected_graph< Atom, Bond > | ResidueGraph |
| |
| typedef ResidueGraph::vertex_descriptor | VD |
| |
| typedef ResidueGraph::edge_descriptor | ED |
| |
| typedef utility::vector1< VD > | VDs |
| |
| typedef boost::graph_traits< ResidueGraph >::vertex_iterator | VIter |
| |
| typedef std::pair< VIter, VIter > | VIterPair |
| |
| typedef boost::graph_traits< ResidueGraph >::edge_iterator | EIter |
| |
| typedef std::pair< EIter, EIter > | EIterPair |
| |
| typedef boost::graph_traits< ResidueGraph >::out_edge_iterator | OutEdgeIter |
| |
| typedef std::pair< OutEdgeIter, OutEdgeIter > | OutEdgeIterPair |
| |
| typedef boost::graph_traits< ResidueGraph >::adjacency_iterator | AdjacentIter |
| |
| typedef std::pair< AdjacentIter, AdjacentIter > | AdjacentIterPair |
| |
| typedef std::map< std::string, VD > | NameVDMap |
| |
| typedef std::pair< std::string, VD > | NameVDPair |
| |
| typedef std::pair< NameVDMap::iterator, bool > | NameVDInserted |
| |
| typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, boost::property< boost::vertex_name_t, core::chemical::VD >, boost::property< boost::edge_name_t, core::chemical::ED > > | LightWeightResidueGraph |
| |
| typedef boost::graph_traits< LightWeightResidueGraph >::vertex_descriptor | lwrg_VD |
| |
| typedef boost::graph_traits< LightWeightResidueGraph >::edge_descriptor | lwrg_ED |
| |
| typedef boost::graph_traits< LightWeightResidueGraph >::vertex_iterator | lwrg_vd_iter |
| |
| typedef std::pair< lwrg_vd_iter, lwrg_vd_iter > | lwrg_vd_pair_iter |
| |
| typedef boost::graph_traits< LightWeightResidueGraph >::edge_iterator | lwrg_edge_iter |
| |
| typedef boost::graph_traits< LightWeightResidueGraph >::out_edge_iterator | lwrg_out_edge_iter |
| |
| typedef std::pair< lwrg_out_edge_iter, lwrg_out_edge_iter > | lwrg_out_edge_iter_pair |
| |
| typedef utility::pointer::shared_ptr< ResidueProperties > | ResiduePropertiesOP |
| |
| typedef utility::pointer::shared_ptr< ResidueProperties const > | ResiduePropertiesCOP |
| |
| typedef boost::filtered_graph< ResidueGraph, RealFilter, RealFilter > | RealResidueGraph |
| |
| typedef RealResidueGraph::vertex_descriptor | RealResidueVD |
| |
| typedef RealResidueGraph::edge_descriptor | RealResidueED |
| |
| typedef boost::graph_traits< RealResidueGraph >::vertex_iterator | RealResidueVIter |
| |
| typedef boost::graph_traits< RealResidueGraph >::edge_iterator | RealResidueEIter |
| |
| typedef boost::graph_traits< RealResidueGraph >::out_edge_iterator | RealResidueOutEdgeIter |
| |
| typedef std::pair< RealResidueOutEdgeIter, RealResidueOutEdgeIter > | RealResidueOutEdgeIterPair |
| |
| typedef std::pair< RealResidueVIter, RealResidueVIter > | RealResidueVIterPair |
| |
| typedef boost::graph_traits< RealResidueGraph >::adjacency_iterator | RealResidueAdjacentIter |
| |
| typedef std::pair< RealResidueAdjacentIter, RealResidueAdjacentIter > | RealResidueAdjacentIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, HeavyAtomFilter > | HeavyAtomGraph |
| |
| typedef HeavyAtomGraph::vertex_descriptor | HeavyAtomVD |
| |
| typedef HeavyAtomGraph::edge_descriptor | HeavyAtomED |
| |
| typedef boost::graph_traits< HeavyAtomGraph >::vertex_iterator | HeavyAtomVIter |
| |
| typedef boost::graph_traits< HeavyAtomGraph >::edge_iterator | HeavyAtomEIter |
| |
| typedef boost::graph_traits< HeavyAtomGraph >::out_edge_iterator | HeavyAtomOutEdgeIter |
| |
| typedef std::pair< HeavyAtomOutEdgeIter, HeavyAtomOutEdgeIter > | HeavyAtomOutEdgeIterPair |
| |
| typedef std::pair< HeavyAtomVIter, HeavyAtomVIter > | HeavyAtomVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, AcceptorAtomFilter > | AcceptorAtomGraph |
| |
| typedef boost::graph_traits< AcceptorAtomGraph >::vertex_iterator | AcceptorAtomVIter |
| |
| typedef boost::graph_traits< AcceptorAtomGraph >::edge_iterator | AcceptorAtomEIter |
| |
| typedef std::pair< AcceptorAtomVIter, AcceptorAtomVIter > | AcceptorAtomVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, HeavyAtomWithPolarHydrogensFilter > | HeavyAtomWithPolarHydrogensGraph |
| |
| typedef boost::graph_traits< HeavyAtomWithPolarHydrogensGraph >::vertex_iterator | HeavyAtomWithPolarHydrogensVIter |
| |
| typedef boost::graph_traits< HeavyAtomWithPolarHydrogensGraph >::edge_iterator | HeavyAtomWithPolarHydrogensEIter |
| |
| typedef std::pair< HeavyAtomWithPolarHydrogensVIter, HeavyAtomWithPolarHydrogensVIter > | HeavyAtomWithPolarHydrogensVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, HeavyAtomWithHydrogensFilter > | HeavyAtomWithHydrogensGraph |
| |
| typedef boost::graph_traits< HeavyAtomWithHydrogensGraph >::vertex_iterator | HeavyAtomWithHydrogensVIter |
| |
| typedef boost::graph_traits< HeavyAtomWithHydrogensGraph >::edge_iterator | HeavyAtomWithHydrogensEIter |
| |
| typedef std::pair< HeavyAtomWithHydrogensVIter, HeavyAtomWithHydrogensVIter > | HeavyAtomWithHydrogensVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, HydrogenAtomFilter > | HydrogenAtomGraph |
| |
| typedef HydrogenAtomGraph::vertex_descriptor | HydrogenAtomVD |
| |
| typedef HydrogenAtomGraph::edge_descriptor | HydrogenAtomED |
| |
| typedef boost::graph_traits< HydrogenAtomGraph >::vertex_iterator | HydrogenAtomVIter |
| |
| typedef boost::graph_traits< HydrogenAtomGraph >::edge_iterator | HHydrogenAtomEIter |
| |
| typedef boost::graph_traits< HydrogenAtomGraph >::out_edge_iterator | HydrogenAtomOutEdgeIter |
| |
| typedef std::pair< HydrogenAtomOutEdgeIter, HydrogenAtomOutEdgeIter > | HydrogenAtomOutEdgeIterPair |
| |
| typedef std::pair< HydrogenAtomVIter, HydrogenAtomVIter > | HydrogenAtomVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, AromaticAtomFilter > | AromaticAtomGraph |
| |
| typedef boost::graph_traits< AromaticAtomGraph >::vertex_iterator | AromaticAtomVIter |
| |
| typedef boost::graph_traits< AromaticAtomGraph >::edge_iterator | AromaticAtomEIter |
| |
| typedef std::pair< AromaticAtomVIter, AromaticAtomVIter > | AromaticAtomVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, PolarHydrogenFilter > | PolarHydrogenGraph |
| |
| typedef boost::graph_traits< PolarHydrogenGraph >::vertex_iterator | PolarHydrogenVIter |
| |
| typedef boost::graph_traits< PolarHydrogenGraph >::edge_iterator | PolarHydrogenEIter |
| |
| typedef std::pair< PolarHydrogenVIter, PolarHydrogenVIter > | PolarHydrogenVIterPair |
| |
| typedef boost::filtered_graph< ResidueGraph, boost::keep_all, APolarHydrogenFilter > | APolarHydrogenGraph |
| |
| typedef boost::graph_traits< APolarHydrogenGraph >::vertex_iterator | APolarHydrogenVIter |
| |
| typedef boost::graph_traits< APolarHydrogenGraph >::edge_iterator | APolarHydrogenEIter |
| |
| typedef std::pair< APolarHydrogenVIter, APolarHydrogenVIter > | APolarHydrogenVIterPair |
| |
| typedef utility::pointer::weak_ptr< ResidueType > | ResidueTypeAP |
| |
| typedef utility::pointer::weak_ptr< ResidueType const > | ResidueTypeCAP |
| |
| typedef utility::pointer::shared_ptr< ResidueType > | ResidueTypeOP |
| |
| typedef utility::pointer::shared_ptr< ResidueType const > | ResidueTypeCOP |
| |
| typedef utility::vector1< ResidueTypeOP > | ResidueTypeOPs |
| |
| typedef utility::vector1< ResidueTypeCAP > | ResidueTypeCAPs |
| |
| typedef utility::vector1< ResidueTypeCOP > | ResidueTypeCOPs |
| |
| typedef utility::vector1< Size > | AtomIndices |
| |
| typedef utility::vector1< Size > | OrbitalIndices |
| |
| typedef utility::keys::Key2Tuple< Size, Size > | two_atom_set |
| |
| typedef utility::keys::Key3Tuple< Size, Size, Size > | three_atom_set |
| |
| typedef utility::keys::Key3Tuple< Size, Size, Size > | bondangle_atom_set |
| |
| typedef utility::keys::Key4Tuple< Size, Size, Size, Size > | dihedral_atom_set |
| |
| typedef utility::pointer::weak_ptr< ResidueTypeBase > | ResidueTypeBaseAP |
| |
| typedef utility::pointer::weak_ptr< ResidueTypeBase const > | ResidueTypeBaseCAP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeBase > | ResidueTypeBaseOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeBase const > | ResidueTypeBaseCOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeFinder > | ResidueTypeFinderOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeFinder const > | ResidueTypeFinderCOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeKinWriter > | ResidueTypeKinWriterOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeKinWriter const > | ResidueTypeKinWriterCOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeSelectorSingle > | ResidueTypeSelectorSingleOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeSelector > | ResidueTypeSelectorOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeSet > | ResidueTypeSetOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeSet const > | ResidueTypeSetCOP |
| |
| typedef utility::pointer::weak_ptr< ResidueTypeSet const > | ResidueTypeSetCAP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeSetCache > | ResidueTypeSetCacheOP |
| |
| typedef utility::pointer::shared_ptr< ResidueTypeSetCache const > | ResidueTypeSetCacheCOP |
| |
| typedef std::pair< AA, std::pair< utility::vector1< std::string >, utility::vector1< VariantType > > > | AA_VariantsExceptions |
| |
| typedef std::tuple< ResidueTypeCOP, utility::vector1< VariantType >, utility::vector1< std::string >, utility::vector1< VariantType >, bool > | Restype_Variants_VariantStrings_Exceptions |
| | A type for key lookup. This consists of a BASE TYPE ResidueTypeCOP, a list of variants (by enum), a list of custom variants (by string), a list of variant exceptions (by enum), and a bool for whether to turn off metapatches. More...
|
| |
|
| enum | AA {
aa_none = 0
, aa_ala = 1
, first_l_aa = aa_ala
, aa_cys
,
aa_asp
, aa_glu
, aa_phe
, aa_gly
,
aa_his
, aa_ile
, aa_lys
, aa_leu
,
aa_met
, aa_asn
, aa_pro
, aa_gln
,
aa_arg
, aa_ser
, aa_thr
, aa_val
,
aa_trp
, aa_tyr
, num_canonical_aas = aa_tyr
, na_ade
,
first_DNA_aa = na_ade
, na_cyt
, na_gua
, na_thy
,
last_DNA_aa = na_thy
, na_rgu
, na_rad
, na_rcy
,
na_ura
, aa_dal
, first_D_aa = aa_dal
, aa_dcs
,
aa_das
, aa_dgu
, aa_dph
, aa_dhi
,
aa_dil
, aa_dly
, aa_dle
, aa_dme
,
aa_dan
, aa_dpr
, aa_dgn
, aa_dar
,
aa_dse
, aa_dth
, aa_dva
, aa_dtr
,
aa_dty
, last_D_aa = aa_dty
, aa_b3a
, first_beta3_aa = aa_b3a
,
aa_b3c
, aa_b3d
, aa_b3e
, aa_b3f
,
aa_b3g
, aa_b3h
, aa_b3i
, aa_b3k
,
aa_b3l
, aa_b3m
, aa_b3n
, aa_b3p
,
aa_b3q
, aa_b3r
, aa_b3s
, aa_b3t
,
aa_b3v
, aa_b3w
, aa_b3y
, aa_b3cisACPC
,
aa_b3transACPC
, aa_b3cisACHC
, last_beta3_aa = aa_b3cisACHC
, aa_b2a
,
first_beta2_aa = aa_b2a
, last_beta2_aa = aa_b2a
, na_lra
, na_lrc
,
na_lrg
, na_lur
, ou3_ala
, first_oligourea = ou3_ala
,
ou3_cys
, ou3_asp
, ou3_glu
, ou3_phe
,
ou3_gly
, ou3_his
, ou3_ile
, ou3_lys
,
ou3_leu
, ou3_met
, ou3_asn
, ou3_pro
,
ou3_gln
, ou3_arg
, ou3_ser
, ou3_thr
,
ou3_val
, ou3_trp
, ou3_tyr
, ou3_aib
,
last_oligourea = ou3_aib
, aa_h2o
, aa_vrt
, aa_unp
,
aa_unk
, num_aa_types = aa_unk
} |
| | enumeration for amino acids and nucleotides types with the total number as num_aa_types More...
|
| |
| enum class | ICoordAtomIDType { INTERNAL = 1
, POLYMER_LOWER
, POLYMER_UPPER
, CONNECT
} |
| | ICoordAtomIDType. More...
|
| |
| enum | AtomProperty {
NO_ATOM_PROPERTY = 0
, FIRST_ATOM_PROPERTY = 1
, H_DONOR
, H_ACCEPTOR
,
POLAR_HYDROGEN
, AROMATIC_HYDROGEN
, HAS_ORBITALS
, VIRTUAL_ATOM
,
REPULSIVE
, AROMATIC_CARBON_WITH_FREE_VALENCE
, N_ATOM_PROPERTIES = AROMATIC_CARBON_WITH_FREE_VALENCE
} |
| | Enumerators for all the properties that can be assigned to a chemical::Atom. More...
|
| |
| enum | BondName {
UnknownBond =0
, SingleBond =1
, DoubleBond =2
, TripleBond =3
,
AromaticBond =4
, OrbitalBond =5
, PseudoBond =99
} |
| |
| enum | BondOrder {
UnknownBondOrder =0
, SingleBondOrder =1
, DoubleBondOrder =2
, TripleBondOrder =3
,
OrbitalBondOrder
, DeleteBondOrder
, PseudoBondOrder =99
} |
| |
| enum | BondConjugability { UnknownConjugability
, NotConjugableBond
, ConjugableBond
} |
| | As with the BCL, bond conjugability is more about the atom types on either end of the bond than about the bond itself. A conjugatable bond is one where it is known that the atoms on both sides of the bond can participate in a conjugated system. Double, triple and aromatic bonds are always conjugatable, and single bonds are conjugatable if both atoms are in other triple, double, or aromatic systems. More...
|
| |
| enum | BondRingness { UnknownRingness
, BondNotInRing
, BondInRing
} |
| |
| enum | BondAromaticity { UnknownAromaticity
, NonaromaticBond
, IsAromaticBond
} |
| | Proper aromaticity implies participation in a 4n+2 electron ring system. For simple single-double alternation, see conjugatable bond. More...
|
| |
| enum | BondIsometry { UnknownIsometry
, NoBondIsometry
, EIsometry
, ZIsometry
} |
| |
| enum | TypeSetMode {
INVALID_t = 0
, FULL_ATOM_t = 1
, DEFAULT_t
, CENTROID_t
,
CENTROID_ROT_t
, HYBRID_FA_STANDARD_CENTROID_t
, COARSE_RNA_t
, MIXED_t
,
TYPE_SET_MODES_LENGTH = MIXED_t
} |
| | A type set category is the "compatibility class" of a type set. That is, all e.g. ResidueTypes of a given TypeSetMode should be "compatible" with the scale of modeling resolution, indepenent of if they're in the same ResidueTypeSet. More...
|
| |
| enum | GreekDistance {
PRIMARY_ATOM = 0
, ALPHA_ATOM
, BETA_ATOM
, GAMMA_ATOM
,
DELTA_ATOM
, EPSILON_ATOM
, ZETA_ATOM
, ETA_ATOM
,
THETA_ATOM
, IOTA_ATOM
, KAPPA_ATOM
, LAMBDA_ATOM
,
MU_ATOM
, NU_ATOM
, XI_ATOM
, OMICRON_ATOM
,
PI_ATOM
, SIGMA_ATOM
, TAU_ATOM
, UPSILON_ATOM
,
PHI_ATOM
, CHI_ATOM
, PSI_ATOM
, NA_GREEK_DISTANCE = 1023
} |
| | Enumerators for the Greek distance from the atom with the functional group of highest priority. More...
|
| |
| enum | Ancestor { anc_parent
, anc_grandparent
, anc_greatgrandparent
} |
| | Change the parent, grandparent, or great-grandparent of an atom. More...
|
| |
| enum | ResidueProperty {
NO_PROPERTY = 0
, FIRST_PROPERTY = 1
, POLYMER = 1
, LIGAND
,
PROTEIN
, CANONICAL_AA
, CANONICAL_NUCLEIC
, DNA
,
RNA
, TNA
, PNA
, PEPTOID
,
OLIGOUREA
, ARAMID
, ORTHO_ARAMID
, META_ARAMID
,
PARA_ARAMID
, PRE_METHYLENE_ORTHO_ARAMID
, PRE_METHYLENE_META_ARAMID
, PRE_METHYLENE_PARA_ARAMID
,
POST_METHYLENE_ORTHO_ARAMID
, POST_METHYLENE_META_ARAMID
, POST_METHYLENE_PARA_ARAMID
, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID
,
PRE_METHYLENE_POST_METHYLENE_META_ARAMID
, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID
, CARBOHYDRATE
, LIPID
,
TERPENE
, NUCLEOTIDE_DIPHOSPHATE
, SRI
, TRIAZOLE_LINKER
,
METAL
, SURFACE
, WATER
, TP3
,
VIRTUALIZABLE_BY_PACKER
, SOLVENT
, VIRTUAL_RESIDUE
, VRT1
,
INVERTED_VIRTUAL_RESIDUE
, LOWER_TERMINUS
, UPPER_TERMINUS
, BRANCH_POINT
,
TERMINUS
, LOWERTERM_TRUNC
, UPPERTERM_TRUNC
, COARSE
,
ADDUCT
, SC_ORBITALS
, FRAGMENT
, UPPERTERM_CAP
,
LOWERTERM_CAP
, POLAR
, HYDROPHOBIC
, CHARGED
,
NEGATIVE_CHARGE
, POSITIVE_CHARGE
, AROMATIC
, ALIPHATIC
,
CYCLIC
, BETA_BRANCHED_SIDECHAIN
, METALBINDING
, SIDECHAIN_THIOL
,
DISULFIDE_BONDED
, ELECTROPHILE
, SIDECHAIN_AMINE
, N_METHYLATED
,
MEMBRANE
, PHOSPHONATE
, PHOSPHONATE_UPPER
, ACETYLATED_NTERMINUS
,
METHYLATED_CTERMINUS
, DIMETHYLATED_CTERMINUS
, ALPHA_AA
, BETA_AA
,
GAMMA_AA
, L_AA
, D_AA
, ACHIRAL_BACKBONE
,
ACHIRAL_SIDECHAIN
, R_PEPTOID
, S_PEPTOID
, TAUTOMER
,
PURINE
, PYRIMIDINE
, L_RNA
, D_RNA
,
METHYLATED_NA
, TRIOSE
, TETROSE
, PENTOSE
,
HEXOSE
, HEPTOSE
, OCTOSE
, NONOSE
,
ALDOSE
, KETOSE
, L_SUGAR
, D_SUGAR
,
OXIROSE
, OXETOSE
, FURANOSE
, PYRANOSE
,
SEPTANOSE
, ALPHA_SUGAR
, BETA_SUGAR
, SIALIC_ACID
,
C1_MODIFIED
, C2_MODIFIED
, C3_MODIFIED
, C4_MODIFIED
,
C5_MODIFIED
, C6_MODIFIED
, C7_MODIFIED
, C8_MODIFIED
,
C9_MODIFIED
, GLYCOSIDE
, ALDONIC_ACID
, URONIC_ACID
,
DEOXY_SUGAR
, AMINO_SUGAR
, ACETYLAMINO_SUGAR
, GLYCOLYLAMINO_SUGAR
,
ACETYL_SUGAR
, BUTYRYL_SUGAR
, LACTYL_SUGAR
, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
,
PHOSPHORYLATED_SUGAR
, SULFATED_SUGAR
, SULFOAMINO_SUGAR
, THIO_SUGAR
,
C_METHYLATED_SUGAR
, PROPARGYL_SUGAR
, FLUORO_SUGAR
, METHYL_SUGAR
,
PHOSPHATE
, SPINLABEL
, DIAMAGNETIC
, PARAMAGNETIC
,
N_PROPERTIES = PARAMAGNETIC
} |
| | Enumerators for all the properties that can be assigned to a ResidueType. More...
|
| |
| enum | Hybridization {
SP2_HYBRID = 1
, SP3_HYBRID
, RING_HYBRID
, UNKNOWN_HYBRID
,
HYBRID_MAX = UNKNOWN_HYBRID
} |
| |
| enum | VariantType {
NO_VARIANT = 0
, FIRST_VARIANT = 1
, UPPER_TERMINUS_VARIANT = 1
, LOWER_TERMINUS_VARIANT
,
UPPERTERM_TRUNC_VARIANT
, LOWERTERM_TRUNC_VARIANT
, PHOSPHONATE_UPPER_VARIANT
, CUTPOINT_LOWER
,
CUTPOINT_UPPER
, NTERM_CONNECT
, CTERM_CONNECT
, DISULFIDE
,
SC_BRANCH_POINT
, C1_BRANCH_POINT
, C2_BRANCH_POINT
, C3_BRANCH_POINT
,
C4_BRANCH_POINT
, C5_BRANCH_POINT
, C6_BRANCH_POINT
, C7_BRANCH_POINT
,
C8_BRANCH_POINT
, C9_BRANCH_POINT
, SIDECHAIN_CONJUGATION
, SG_CONNECT
,
NE2_CONNECT
, ZN_CONNECT
, VIRTUAL_METAL_CONJUGATION
, METHYLATED_NTERM_VARIANT
,
ACETYLATED_NTERMINUS_VARIANT
, ACETYLATED_NTERMINUS_CONNECTION_VARIANT
, METHYLATED_CTERMINUS_VARIANT
, DIMETHYLATED_CTERMINUS_VARIANT
,
OOP_PRE
, OOP_POST
, HBS_PRE
, HBS_POST
,
A3B_HBS_PRE
, A3B_HBS_POST
, CA_CONNECT
, CA_CONNECT2
,
CA_CONNECT3
, CA_CONNECT4
, CA_CONNECT5
, CA_CONNECT6
,
CA_CONNECT7
, OE1_CONNECT
, OE2_CONNECT
, OD1_CONNECT
,
OD2_CONNECT
, O_CONNECT
, OG_CONNECT
, OG1_CONNECT
,
PROTONATED
, DEPROTONATED
, ALTERNATIVE_PROTONATION
, METHYLATION
,
DIMETHYLATION
, TRIMETHYLATION
, ACETYLATION
, PHOSPHORYLATION
,
SULFATION
, HYDROXYLATION
, HYDROXYLATION1
, HYDROXYLATION2
,
CARBOXYLATION
, DIIODINATION
, N_METHYLATION
, VIRTUAL_BB
,
VIRTUAL_SIDE_CHAIN
, VIRTUAL_RESIDUE_VARIANT
, VIRTUAL_NTERM
, VIRTUAL_PHOSPHATE
,
VIRTUAL_DNA_PHOSPHATE
, REPLS_BB
, REPLONLY
, REPL_PHOSPHATE
,
VIRTUAL_RIBOSE
, VIRTUAL_BACKBONE_EXCEPT_C1PRIME
, VIRTUAL_BASE
, VIRTUAL_BASE_HEAVY_ATOM
,
VIRTUAL_RNA_RESIDUE
, VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE
, BULGE
, VIRTUAL_O2PRIME_HYDROGEN
,
THREE_PRIME_END_OH
, THREE_PRIME_PHOSPHATE
, THREE_PRIME_AZIDE
, THREE_PRIME_DEOXY
,
FIVE_PRIME_END_OH
, FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE
, FIVE_PRIME_END_PHOSPHATE
, FIVE_PRIME_PHOSPHATE
,
FIVE_PRIME_RME_PHOSPHATE
, FIVEPRIME_CAP
, THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE
, DEOXY_O2PRIME
,
UPPER_CONNECTION_RNA
, THREE_PRIME_PACKABLE_PHOSPHATE
, FIVE_PRIME_PACKABLE_PHOSPHATE
, FIVE_PRIME_PACKABLE_TRIPHOSPHATE
,
PROTONATED_N1
, PROTONATED_N3
, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE
, BLOCK_STACK_ABOVE
,
BLOCK_STACK_BELOW
, N_ACETYLATION
, N_FORMYLATION
, C_METHYLAMIDATION
,
CTERM_AMIDATION
, C5_METHYLATED_NA
, ALDONIC_ACID_VARIANT
, C2_KETOALDONIC_ACID
,
C3_KETOALDONIC_ACID
, C4_KETOALDONIC_ACID
, C5_KETOALDONIC_ACID
, C6_KETOALDONIC_ACID
,
C7_KETOALDONIC_ACID
, C8_KETOALDONIC_ACID
, URONIC_ACID_VARIANT
, C1_DEOXY_SUGAR
,
C2_DEOXY_SUGAR
, C3_DEOXY_SUGAR
, C4_DEOXY_SUGAR
, C5_DEOXY_SUGAR
,
C6_DEOXY_SUGAR
, C7_DEOXY_SUGAR
, C8_DEOXY_SUGAR
, C9_DEOXY_SUGAR
,
C1_AMINO_SUGAR
, C2_AMINO_SUGAR
, C3_AMINO_SUGAR
, C4_AMINO_SUGAR
,
C5_AMINO_SUGAR
, C6_AMINO_SUGAR
, C7_AMINO_SUGAR
, C8_AMINO_SUGAR
,
C9_AMINO_SUGAR
, C1_ACETYLAMINO_SUGAR
, C2_ACETYLAMINO_SUGAR
, C3_ACETYLAMINO_SUGAR
,
C4_ACETYLAMINO_SUGAR
, C5_ACETYLAMINO_SUGAR
, C6_ACETYLAMINO_SUGAR
, C7_ACETYLAMINO_SUGAR
,
C8_ACETYLAMINO_SUGAR
, C9_ACETYLAMINO_SUGAR
, C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
,
C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
,
C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
, C1_PHOSPHORYLATED_SUGAR
,
C2_PHOSPHORYLATED_SUGAR
, C3_PHOSPHORYLATED_SUGAR
, C4_PHOSPHORYLATED_SUGAR
, C5_PHOSPHORYLATED_SUGAR
,
C6_PHOSPHORYLATED_SUGAR
, C7_PHOSPHORYLATED_SUGAR
, C8_PHOSPHORYLATED_SUGAR
, C9_PHOSPHORYLATED_SUGAR
,
C1_SULFATED_SUGAR
, C2_SULFATED_SUGAR
, C3_SULFATED_SUGAR
, C4_SULFATED_SUGAR
,
C5_SULFATED_SUGAR
, C6_SULFATED_SUGAR
, C7_SULFATED_SUGAR
, C8_SULFATED_SUGAR
,
C9_SULFATED_SUGAR
, C1_SULFOAMINO_SUGAR
, C2_SULFOAMINO_SUGAR
, C3_SULFOAMINO_SUGAR
,
C4_SULFOAMINO_SUGAR
, C5_SULFOAMINO_SUGAR
, C6_SULFOAMINO_SUGAR
, C7_SULFOAMINO_SUGAR
,
C8_SULFOAMINO_SUGAR
, C9_SULFOAMINO_SUGAR
, C1_THIO_SUGAR
, C2_THIO_SUGAR
,
C3_THIO_SUGAR
, C4_THIO_SUGAR
, C5_THIO_SUGAR
, C6_THIO_SUGAR
,
C7_THIO_SUGAR
, C8_THIO_SUGAR
, C9_THIO_SUGAR
, C1_METHYLATED_SUGAR
,
C2_METHYLATED_SUGAR
, C3_METHYLATED_SUGAR
, C4_METHYLATED_SUGAR
, C5_METHYLATED_SUGAR
,
C6_METHYLATED_SUGAR
, C7_METHYLATED_SUGAR
, C8_METHYLATED_SUGAR
, C9_METHYLATED_SUGAR
,
C1_PHOSPHATE
, C2_PHOSPHATE
, C3_PHOSPHATE
, C4_PHOSPHATE
,
C5_PHOSPHATE
, C6_PHOSPHATE
, C7_PHOSPHATE
, C8_PHOSPHATE
,
C9_PHOSPHATE
, O1_ACETYL_SUGAR
, O2_ACETYL_SUGAR
, O3_ACETYL_SUGAR
,
O4_ACETYL_SUGAR
, O5_ACETYL_SUGAR
, O6_ACETYL_SUGAR
, O7_ACETYL_SUGAR
,
O8_ACETYL_SUGAR
, O9_ACETYL_SUGAR
, O1_BUTYRYL_SUGAR
, O2_BUTYRYL_SUGAR
,
O3_BUTYRYL_SUGAR
, O4_BUTYRYL_SUGAR
, O5_BUTYRYL_SUGAR
, O6_BUTYRYL_SUGAR
,
O7_BUTYRYL_SUGAR
, O8_BUTYRYL_SUGAR
, O9_BUTYRYL_SUGAR
, O1_PROPARGYL_SUGAR
,
O2_PROPARGYL_SUGAR
, O3_PROPARGYL_SUGAR
, O4_PROPARGYL_SUGAR
, O5_PROPARGYL_SUGAR
,
O6_PROPARGYL_SUGAR
, O7_PROPARGYL_SUGAR
, O8_PROPARGYL_SUGAR
, O9_PROPARGYL_SUGAR
,
O1_LACTYL_SUGAR
, O2_LACTYL_SUGAR
, O3_LACTYL_SUGAR
, O4_LACTYL_SUGAR
,
O5_LACTYL_SUGAR
, O6_LACTYL_SUGAR
, O7_LACTYL_SUGAR
, O8_LACTYL_SUGAR
,
O9_LACTYL_SUGAR
, C1_GLYCOLYLAMINO_SUGAR
, C2_GLYCOLYLAMINO_SUGAR
, C3_GLYCOLYLAMINO_SUGAR
,
C4_GLYCOLYLAMINO_SUGAR
, C5_GLYCOLYLAMINO_SUGAR
, C6_GLYCOLYLAMINO_SUGAR
, C7_GLYCOLYLAMINO_SUGAR
,
C8_GLYCOLYLAMINO_SUGAR
, C9_GLYCOLYLAMINO_SUGAR
, C1_FLUORO_SUGAR
, C2_FLUORO_SUGAR
,
C3_FLUORO_SUGAR
, C4_FLUORO_SUGAR
, C5_FLUORO_SUGAR
, C6_FLUORO_SUGAR
,
C7_FLUORO_SUGAR
, C8_FLUORO_SUGAR
, C9_FLUORO_SUGAR
, O1_METHYL_SUGAR
,
O2_METHYL_SUGAR
, O3_METHYL_SUGAR
, O4_METHYL_SUGAR
, O5_METHYL_SUGAR
,
O6_METHYL_SUGAR
, O7_METHYL_SUGAR
, O8_METHYL_SUGAR
, O9_METHYL_SUGAR
,
METHYL_GLYCOSIDE
, TRIAZOLAMERN
, TRIAZOLAMERC
, CA2_COORDINATION
,
MG2_COORDINATION
, CU2_COORDINATION
, CO2_COORDINATION
, FE2_COORDINATION
,
FE3_COORDINATION
, MN2_COORDINATION
, LA3_COORDINATION
, LU3_COORDINATION
,
TB3_COORDINATION
, TM3_COORDINATION
, DY3_COORDINATION
, YB3_COORDINATION
,
ADDUCT_VARIANT
, CENTROID_WITH_HA
, SPECIAL_ROT
, SC_FRAGMENT
,
SHOVE_BB
, N_VARIANTS = SHOVE_BB
} |
| | Enumerators for all the ResidueType variants. More...
|
| |
|
| std::map< std::string, AA > | setup_name2aa () |
| | setup the map that converts string name to AA enum More...
|
| |
| std::map< char, AA > | setup_oneletter2aa () |
| | setup the map the converts one letter char to AA enum More...
|
| |
| std::map< std::string, AA > const & | name2aa () |
| | map that converts string name to AA enum More...
|
| |
| std::map< char, AA > const & | oneletter2aa () |
| | map that converts one letter char to AA enum More...
|
| |
| utility::vector1< std::string > | setup_aa2name () |
| | setup the vector that maps AA enum to string name More...
|
| |
| utility::vector1< std::string > const & | aa2name () |
| | vector that maps AA enum to string name More...
|
| |
| utility::vector1< char > | setup_aa2oneletter () |
| | setup the vector that maps AA enum to one letter char More...
|
| |
| utility::vector1< char > const & | aa2oneletter () |
| | vector that maps AA enum to one letter char More...
|
| |
| AA | aa_from_name (std::string const &name) |
| | Give an AA string 3-letter code, return its enum type. More...
|
| |
| AA | aa_from_one_or_three (std::string const &name) |
| |
| bool | is_canonical_D_aa (AA const aa) |
| | Give an enum type, return true if and only if it is a D-amino acid that is the mirror image of a canonical alpha-L-amino acid. More...
|
| |
| bool | is_canonical_L_aa_excluding_gly (AA const aa) |
| | Give an enum type, return true if and only if it is an L-amino acid of a canonical type. More...
|
| |
| bool | is_canonical_L_aa_or_gly (AA const aa) |
| | Given an enum type, return true if and only if it is a canonical L-amino acid. Rocco approves. More...
|
| |
| bool | is_canonical_beta3_aa (AA const aa) |
| | Given an enum type, return true if and only if it is a canonical beta-amino acid. More...
|
| |
| bool | is_aa_name_unknown (std::string const &name) |
| | Given aa three letter string, return true if it is an unknown aa. More...
|
| |
| AA | get_L_equivalent (AA const aa) |
| | Given an enum type for a D-amino acid with a canonical side-chain, return the enum type for the corresponding L-amino acid (or aa_unk if the corresponding L-amino acid cannot be determined). More...
|
| |
| AA | get_D_equivalent (AA const aa) |
| | Given an enum type for a L-amino acid with a canonical side-chain, return the enum type for the corresponding D-amino acid (or aa_unk if the corresponding D-amino acid cannot be determined). More...
|
| |
| std::istream & | operator>> (std::istream &is, AA &aa) |
| | input operator for AA enum type More...
|
| |
| std::ostream & | operator<< (std::ostream &os, AA const &aa) |
| | output operator for AA enum type More...
|
| |
| std::string | name_from_aa (AA aa) |
| | give a enum type and return the string name More...
|
| |
| std::string | full_name_from_aa (AA aa) |
| | give the canonical "full" ResidueType name for given AA More...
|
| |
| char | oneletter_code_from_aa (AA aa) |
| | give a enum type and return the string name More...
|
| |
| AA | aa_from_oneletter_code (char onelettercode) |
| | give a 1 letter code and return the string name More...
|
| |
| bool | oneletter_code_specifies_aa (char onelettercode) |
| |
| std::map< std::string, int > | parse_adduct_string (utility::options::StringVectorOption &add_vec) |
| | Convert input string to map of adducts->max usage. More...
|
| |
| void | error_check_requested_adducts (std::map< std::string, int > const &add_map, ResidueTypeCOPs const &rsd_types) |
| | Make sure any adducts requested actually exist. More...
|
| |
| MutableResidueTypeOP | apply_adducts_to_residue (ResidueType const &rsd, utility::vector1< bool > &add_mask) |
| | Apply adducts to residue using a boolean mask. More...
|
| |
| MutableResidueTypeOPs | create_adduct_combinations (ResidueType const &rsd, AdductMap ref_map, AdductMap count_map, utility::vector1< bool > add_mask, utility::vector1< Adduct >::const_iterator work_iter) |
| | Create correct combinations of adducts for a residue type. More...
|
| |
| void | error_check_requested_adducts (AdductMap const &add_map, ResidueTypeCOPs const &rsd_types) |
| | Make sure requested adducts exist in some residue. More...
|
| |
| static basic::Tracer | TR ("core.chemical.Atom") |
| |
| std::ostream & | operator<< (std::ostream &out, Atom const &atom) |
| |
| static basic::Tracer | TR ("core.chemical.AtomICoor") |
| |
| ICoordAtomIDType | string_to_icoord_type (std::string const &) |
| | Convert a string designation into the corresponding ICoordAtomIDType enum. More...
|
| |
| Size | get_connection_number (std::string const &) |
| | Get the connection number from a string representing an CONNECT type (e.g. 4 from CONN4) More...
|
| |
| void | pretty_print_atomicoor (std::ostream &out, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent, AtomMemoOP memo) |
| |
| void | pretty_print_atomicoor (std::ostream &out, ResidueType const &rsd_type) |
| | print the icoord table starting at the root. More...
|
| |
| void | pretty_print_atomicoor (std::ostream &out, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent=0) |
| | print the icoord table starting with the given icoord record More...
|
| |
| std::ostream & | operator<< (std::ostream &out, ICoordAtomIDType type) |
| |
| std::ostream & | operator<< (std::ostream &output, AtomProperties const &object_to_output) |
| |
| AtomProperty & | operator++ (AtomProperty &property) |
| |
| AtomPropertiesOP | deep_copy (AtomProperties const &source) |
| |
| template<class FromRef , class ToRef > |
| std::ostream & | operator<< (std::ostream &out, AtomRefMapping< FromRef, ToRef > const &map) |
| |
| template<class ARef , class BRef , class CRef > |
| AtomRefMapping< ARef, CRef > | combine (AtomRefMapping< ARef, BRef > const &first, AtomRefMapping< BRef, CRef > const &second) |
| |
| std::ostream & | operator<< (std::ostream &out, const AtomType &atom_type) |
| |
| bool | retype_is_aromatic (VD const &atom, ResidueGraph const &graph) |
| | An atom is aromatic if it has any aromatic bonds to a non-virtual atom. TODO: We need better aromatic ring detection. More...
|
| |
| void | rosetta_retype_fullatom (MutableResidueType &restype, bool preserve) |
| | Reassign Rosetta atom types based on the current fullatom heuristics. More...
|
| |
| static basic::Tracer | tr ("core.chemical.AtomTypeSet") |
| |
| static basic::Tracer | TR ("core.chemical.Bond") |
| |
| BondName | convert_to_BondName (std::string const &id) |
| |
| std::ostream & | operator<< (std::ostream &out, Bond const &bond) |
| |
| static basic::Tracer | TR ("core.chemical.bond_support") |
| |
| gasteiger::GasteigerAtomTypeData::Properties | bond_order_to_property (const core::Size &BOND_ORDER_OR_AROMATIC) |
| | convert bond order or aromatic into the corresponding radius More...
|
| |
| void | find_bonds_in_rings (MutableResidueType &res, bool const complex_ring_detection=false) |
| | Determine which bonds are in rings, and set the BondRingness property of each. More...
|
| |
| void | complex_ring_detection (MutableResidueType &res) |
| |
| void | quick_ring_detection (MutableResidueType &res) |
| |
| utility::vector1< VD > | get_connecting_atoms (MutableResidueType const &res, ED const &edge) |
| |
| utility::vector1< VD > | get_connecting_atoms (ResidueGraph const &graph, ED const &edge) |
| |
| ED | get_bond (MutableResidueType const &res, VD const &source, VD const &target) |
| |
| Real | create_bond_length (gasteiger::GasteigerAtomTypeData const &atom1, gasteiger::GasteigerAtomTypeData const &atom2, BondName bond_type) |
| | this will create a bond length based on gasteiger atom type definitions of bonds More...
|
| |
| utility::vector1< VDs > | find_chi_bonds (MutableResidueType const &restype) |
| | Find which bonds are rotatatable (chi) bonds Returns a list of four vds representing the chi. More...
|
| |
| bool | is_sp2_proton_chi (core::Size chi, MutableResidueType const &restype) |
| | Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom? More...
|
| |
| static basic::Tracer | TR ("core.chemical.ChemicalManager") |
| |
| std::string const | FA_STANDARD ("fa_standard") |
| | tag name for querying fullatom chemical type set. More...
|
| |
| std::string const | CENTROID ("centroid") |
| | tag name for querying fullatom chemical type set. More...
|
| |
| std::string const | CENTROID_ROT ("centroid_rot") |
| | tag name for querying centroid_rot chemical type set. More...
|
| |
| std::string const | HYBRID_FA_STANDARD_CENTROID ("hybrid_fa_standard_centroid") |
| | tag name for querying hybrid fullatom+centroid chemical type set. More...
|
| |
| std::string const | COARSE_RNA ("coarse_rna") |
| | tag name for querying COARSE_RNA chemical type set. More...
|
| |
| TypeSetMode | type_set_mode_from_string (std::string const &mode, bool fail) |
| |
| std::string | string_from_type_set_mode (TypeSetMode mode) |
| |
| std::ostream & | operator<< (std::ostream &out, TypeSetMode mode) |
| |
| std::ostream & | operator<< (std::ostream &out, ElectronConfiguration const &obj) |
| |
| std::istream & | operator>> (std::istream &in, ElectronConfiguration &obj) |
| |
| std::ostream & | operator<< (std::ostream &out, Element const &obj) |
| |
| std::istream & | operator>> (std::istream &in, Element &obj) |
| |
| static basic::Tracer | tr ("core.chemical.ElementSet") |
| |
| static basic::Tracer | TR ("core.chemical.GlobalResidueTypeSet") |
| |
| bool | sort_patchop_by_name (PatchOP p, PatchOP q) |
| |
| static basic::Tracer | TR ("core.chemical.icoor_support") |
| |
| VD | walk_back_to_find_usable_base (core::chemical::MutableResidueType const &restype, VD start, utility::vector1< VD > const &exclusions) |
| | Walk up the icoor tree to find alternate reference atoms Utility function for clean_up_dangling_connect() – we only go up the tree to make sure we don't get cycles. Won't choose atoms in exclusions (or the start) More...
|
| |
| void | clean_up_dangling_connect (core::chemical::MutableResidueType &restype, ICoordAtomIDType remove_type) |
| | Attempt to find new ICOOR definitions for entries in the ResidueType which rely on a now-deleted upper/lower connection (Connection type is specified by the passed type.) More...
|
| |
| void | reroot_restype (core::chemical::MutableResidueType &restype, core::chemical::ResidueGraph const &graph, core::chemical::VD root) |
| | Reroot the Icoord records of a ResidueType on the given atom We need direct access to the ResidueGraph, so this function can only be called by ResidueType itself. More...
|
| |
| bool | has_assigned_coords (std::string const &stub, std::set< VD > const &assigned, core::chemical::MutableResidueType const &restype) |
| | Utility function for fill_ideal_xyz_from_icoor() – does this ICoorAtomID have all the dependancies filled? More...
|
| |
| void | fill_ideal_xyz_from_icoor (core::chemical::MutableResidueType &restype, core::chemical::ResidueGraph const &graph) |
| |
| static basic::Tracer | tr ("core.chemical") |
| |
| static basic::Tracer | tr ("core.chemical") |
| |
| static basic::Tracer | tr ("core.chemical") |
| |
| static basic::Tracer | TR ("core.chemical.MutableChiRecord") |
| |
| static basic::Tracer | TR ("core.chemical.MutableICoorRecord") |
| |
| std::ostream & | operator<< (std::ostream &out, MutableICoorRecord const &icoor) |
| |
| static basic::Tracer | TR ("core.chemical.MutableResidueType") |
| |
| utility::vector1< VD > | remap_vect (utility::vector1< VD > const &vect, std::map< VD, VD > const &old_to_new) |
| |
| std::string | correct_conn (std::string const &old, core::Size const conn_id_deleted) |
| | A short utility function for update_icoors_after_connection_deletion() More...
|
| |
| std::ostream & | operator<< (std::ostream &output, MutableResidueType const &object_to_output) |
| |
| std::ostream & | operator<< (std::ostream &out, const Orbital &orbital) |
| |
| OrbitalOP | deep_copy (Orbital const &source) |
| |
| static basic::Tracer | tr ("core.chemical.Patch") |
| |
| std::string | tag_from_line (std::string const &line) |
| | handy function, return the first word from a line More...
|
| |
| std::string | residue_type_base_name (ResidueTypeBase const &rsd_type) |
| | helper function, returns the base residue name prior to any patching More...
|
| |
| std::string | residue_type_all_patches_name (ResidueType const &rsd_type) |
| | helper function, returns the name of all added patches More...
|
| |
| utility::vector1< std::string > | get_patch_names (ResidueType const &rsd_type) |
| |
| void | setup_patch_atomic_charge_reassignments_from_commandline (std::string const &patch_name, TypeSetMode rsd_type_set_mode, ResidueTypeSelector const &rsd_selector, std::map< std::string, Real > &atomic_charge_reassignments) |
| | override patch partial charges with values from commandline More...
|
| |
| PatchCaseOP | case_from_lines (utility::vector1< std::string > const &lines, TypeSetMode res_type_set_mode, std::string const &patch_name) |
| | create a PatchCase from input lines More...
|
| |
| static basic::Tracer | tr ("core.chemical") |
| |
| static basic::Tracer | TR_PatchOperations ("core.chemical.PatchOperations.hh") |
| |
| std::string | expand_icoor_atom_name (std::string name, MutableResidueType const &rsd) |
| |
| void | check_residue_has_atom (std::string const &atom_name, core::chemical::MutableResidueType const &rsd, std::string const &location) |
| |
| static basic::Tracer | TR ("core.chemical.PatchOperationFactory") |
| |
| bool | operator< (ResConnID const &lhs, ResConnID const &rhs) |
| |
| bool | operator== (ResConnID const &lhs, ResConnID const &rhs) |
| |
| bool | operator!= (ResConnID const &lhs, ResConnID const &rhs) |
| |
| static basic::Tracer | tr ("core.chemical") |
| |
| MutableResidueTypeOP | read_topology_file (std::string const &filename, chemical::ResidueTypeSetCOP rsd_type_set) |
| | function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set More...
|
| |
| MutableResidueTypeOP | read_topology_file (utility::io::izstream &istream, chemical::ResidueTypeSetCOP rsd_type_set) |
| | function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
|
| |
| MutableResidueTypeOP | read_topology_file (std::istream &istream, std::string const &filename, chemical::ResidueTypeSetCOP rsd_type_set) |
| | function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
|
| |
| MutableResidueTypeOP | read_topology_file (std::string const &filename, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types) |
| | function to convert params files into ResidueType objects (repackages string filename into istream) More...
|
| |
| MutableResidueTypeOP | read_topology_file (std::istream &data, std::string const &filename, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types) |
| | main function to convert params files into ResidueType objects More...
|
| |
| void | write_topology_file (ResidueType const &rsd, std::string filename="") |
| | writes a .params file from a given ResidueType object More...
|
| |
| void | write_graphviz (ResidueType const &rsd, std::ostream &out, bool header) |
| | Produces a graphviz dot representation of the ResidueType to the given output stream If header is true (the default) a line with an explanitory message will be printed first. More...
|
| |
| void | write_graphviz (MutableResidueType const &rsd, std::ostream &out, bool header) |
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| void | set_up_mapfile_reassignments_from_commandline (ResidueTypeBaseOP rsd) |
| | Certain commandline flags override the default RamaPrePro maps used by the 20 canonical amino acids. This function applies those overrides. More...
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| void | setup_atom_type_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, std::string > &atom_type_reassignments) |
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| void | setup_atomic_charge_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, Real > &atomic_charge_reassignments) |
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| void | setup_icoor_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, utility::vector1< std::string > > &icoor_reassignments) |
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| void | apply_symm_b3g_corrections (std::string const &child_atom, core::Real &phi, core::Real &theta, core::Real &d, std::string &, std::string &, std::string &torsion_atom) |
| | Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option). More...
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| void | apply_symm_gly_corrections (std::string const &child_atom, core::Real &phi, core::Real &, core::Real &d, std::string &, std::string &, std::string &torsion_atom) |
| | Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option). More...
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| static basic::Tracer | TR ("core.chemical.residue_support") |
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| ObjexxFCL::FArray2D_int | get_residue_path_distances (ResidueType const &res) |
| | relies on class Graph to find all pairs shortest path information More...
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| utility::vector1< VD > | mainchain_path (MutableResidueType const &res) |
| | Figure out the shortest path between the upper and lower connect atoms (inclusive) Will return an empty vector if one does not exist. More...
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| utility::vector1< VD > | shortest_path (MutableResidueType const &res, VD start, VD end) |
| | Figure out the shortest path between two atoms (inclusive) Will return an empty vector if one does not exist. More...
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| void | annotate_backbone (MutableResidueType &restype) |
| | Annotate "backbone" atoms. For the purpose of this function, backbone atoms are any atoms which are connected to another backbone atom by a non-rotatable, non-cut bond. Atoms connected to the upper and/or lower connect points are always backbone. Important - if Chis/cuts aren't properly annotated, all atoms will be backbone. More...
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| void | real_to_virtual (MutableResidueType &restype) |
| | Virtualize convert the MutableResidueType to a virtual type NOTE: This function does not rename the residue type. More...
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| LightWeightResidueGraph | convert_residuetype_to_light_graph (MutableResidueType const &res) |
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| void | rename_atoms (MutableResidueType &res, bool preserve) |
| | Rename atoms in the residue type such that their names are unique. If preserve is true, only rename those which have no names or who have name conflicts. (Both of the conflicting atoms will be renamed.) More...
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| void | calculate_rigid_matrix (MutableResidueType const &res, VDDistanceMatrix &distances) |
| | Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square. More...
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| core::Real | find_nbr_dist (MutableResidueType const &res, VD &nbr_atom) |
| | Find the neighbor distance to the given neighbor atom. If nbr_atom is null_vertex, give the smallest neighbor distance, and set nbr_atom to the atom for that distance. More...
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| void | rosetta_recharge_fullatom (MutableResidueType &res) |
| | Apply molfile_to_params style partial charges to the ResidueType. More...
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| MutableResidueTypeOP | make_centroid (ResidueType const &res) |
| | Make a centroid version of the fullatom ResidueType passed in. More...
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| MutableResidueTypeOP | make_centroid (MutableResidueType const &res) |
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| bool | residue_type_bases_identical (ResidueTypeBase const &r1, ResidueTypeBase const &r2) |
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| bool | residue_types_identical (ResidueType const &res1, ResidueType const &res2) |
| | Are two ResidueTypes equivalent? This is here rather than as an operator on ResidueType because it's not the sort of thing one should be doing normally. This looks for exact equivalence, including atom order. More...
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| bool | compare_residue_connection (ResidueConnection const &rc1, ResidueConnection const &rc2, bool fuzzy=false) |
| | Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue. More...
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| bool | compare_atom_icoor (AtomICoor const &aic1, AtomICoor const &aic2, bool fuzzy=false) |
| | Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue. More...
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| bool | has (ResidueGraph const &graph, VD vd) |
| | Does a ResidueGraph have a given vertex descriptor? More...
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| bool | has (ResidueGraph const &graph, ED ed) |
| | Does a ResidueGraph have a given edge descriptor? More...
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| template<typename Graph > |
| void | regenerate_graph_vertex_index (Graph &graph) |
| | When adding and deleting nodes in a graph, sometimes the inner counting of nodes/edges gets outdated. Run this to fix the problem. More...
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| std::ostream & | operator<< (std::ostream &output, ResidueProperties const &object_to_output) |
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| std::ostream & | operator<< (std::ostream &output, ResidueProperty const &object_to_output) |
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| ResidueProperty & | operator++ (ResidueProperty &property) |
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| VariantType & | operator++ (VariantType &variant) |
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| ResiduePropertiesOP | deep_copy (ResidueProperties const &source) |
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| std::map< std::string, ResidueProperty > const * | generate_string_to_property_map () |
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| static const std::map< std::string, ResidueProperty > *const | PROPERTY_MAP (generate_string_to_property_map()) |
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| utility::vector1< std::string > const * | generate_property_to_string_vector () |
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| static const utility::vector1< std::string > *const | STRING_LIST (generate_property_to_string_vector()) |
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| template<class Graph > |
| core::Size | filtered_num_vertices (Graph const &graph) |
| | It's a frustrating truth, but num_vertices doesn't give the number of filtered vertices for filtered graphs, but instead gives the number of underlying vertices ... this gets the true number of filtered vertices. More...
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| RealResidueGraph | make_real_residue_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| HeavyAtomGraph | make_heavy_atom_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| AcceptorAtomGraph | make_acceptor_atom_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| HeavyAtomWithPolarHydrogensGraph | make_heavy_atom_with_polar_hydrogens_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| HeavyAtomWithHydrogensGraph | make_heavy_atom_with_hydrogens_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| HydrogenAtomGraph | make_hydrogen_atom_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| AromaticAtomGraph | make_aromatic_atom_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| PolarHydrogenGraph | make_polar_hydrogen_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| APolarHydrogenGraph | make_apolar_hydrogen_graph (MutableResidueType const &restype) |
| | Convenience constructor. More...
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| static basic::Tracer | TR ("core.chemical.ResidueType") |
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| std::ostream & | operator<< (std::ostream &output, ResidueType const &object_to_output) |
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| static basic::Tracer | TR ("core.chemical.ResidueTypeBase") |
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| std::string | get_element_color (std::string const &element) |
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| static basic::Tracer | TR ("core.chemical.ResidueTypeSelector") |
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| ResidueTypeSelectorSingleOP | residue_selector_single_from_line (std::string const &line) |
| | create a singe ResidueTypeSelector from an input line. More...
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| static basic::Tracer | TR ("core.chemical.ResidueTypeSet") |
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| static std::string const | chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz") |
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| std::string | one_indexed_chr_chains () |
| | pad chr_chains with a dummy char in the first element so that it can be indexed starting at 1 More...
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| static basic::Tracer | TR ("core.chemical.util") |
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| core::chemical::ResidueTypeSetCAP | rsd_set_from_cmd_line () |
| | Return a constant access pointer to the ResidueTypeSet specified by the command-line options. More...
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| void | add_atom_type_set_parameters_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set) |
| | Add additional parameter files not present in <atom-set-name>/extras.txt. More...
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| |
| void | add_mm_atom_type_set_parameters_from_command_line (std::string const &mm_atom_type_set_tag, MMAtomTypeSet &atom_type_set) |
| | Add additional mm atom parameters not present in <mm-atom-type-set-name>/mm_atom_properties.txt. More...
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| |
| void | add_atom_types_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set) |
| | Add additional atomy types not present in <atom-set-name>/atom_properties.txt. More...
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| |
| void | modify_atom_properties_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set) |
| | Modify atom_type properties from the command line. More...
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| |
| std::string | formatted_icoord_tree (core::chemical::ResidueType const &restype) |
| | Return a string representing the internal coordinates tree of this ResidueType. More...
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| std::string | formatted_icoord_tree (core::chemical::MutableResidueType const &restype) |
| | Return a string representing the internal coordinates tree of this MutableResidueType (if any) More...
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| void | print_chis (std::ostream &out, ResidueType const &res) |
| | Utility to examine chi output. More...
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| void | print_chis (std::ostream &out, MutableResidueType const &res) |
| | Utility to examine chi output. More...
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| std::string | fixup_patches (std::string const &string_in) |
| | Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":". More...
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| bool | variants_match_with_exceptions (ResidueTypeBase const &res1, ResidueTypeBase const &res2, utility::vector1< VariantType > list_of_variants_to_ignore) |
| | Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions? More...
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| utility::vector1< VariantType > | pH_mode_exceptions () |
| | check if user has set -pH_mode. More...
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| |
| bool | variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2) |
| | Are these two residues patched in exactly the same way? More...
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| bool | nonadduct_variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2) |
| | Similar to variants_match(), but allows different adduct-modified states. More...
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| |
| utility::vector1< VariantType > | get_terminal_varianttypes () |
| | Get a list of those VariantTypes that affect termini. More...
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| ResidueTypeCOP | find_best_match (ResidueTypeCOPs const &rsd_type_list, utility::vector1< std::string > const &atom_names, bool const ignore_atom_named_H) |
| | look for best match to atom_names More...
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| |
| void | enlarge_h_lj_wdepth (utility::vector1< Real > &lj_wdepth, AtomTypeSet const &atom_type_set) |
| | Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA. More...
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| void | enlarge_h_lj_wdepth (AtomTypeSet &atom_type_set) |
| | Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA. More...
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| |
| void | unset_acceptor_ether_oxygens (AtomTypeSet &atom_type_set) |
| | Rhiju. O3', O4', O5' in nucleic acids are ethers – turn them off as acceptors for H-bonds. More...
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| void | detect_ld_chirality_from_polymer_residue (core::chemical::MutableResidueType const &restype, bool &is_d_aa, bool &is_l_aa) |
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| void | detect_ld_chirality_from_polymer_residue (std::map< std::string, Vector > const &xyz, std::string const &name3, bool &is_d_aa, bool &is_l_aa) |
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| bool | heavy_atom_names_match (ResidueType const &first, ResidueType const &second) |
| | Return true if the two residues have the same number and name of heavy atoms. More...
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| bool | is_mainchain_torsion_also_ring_torsion (ResidueType const &res_type, uint torsion_index) |
| | Are these main-chain torsions also ring torsions? More...
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| std::map< std::string, VariantType > const * | generate_string_to_variant_map () |
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| static const std::map< std::string, VariantType > *const | VARIANT_MAP (generate_string_to_variant_map()) |
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| utility::vector1< std::string > const * | generate_variant_to_string_vector () |
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| static const utility::vector1< std::string > *const | STRING_LIST (generate_variant_to_string_vector()) |
| |