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Rosetta
2019.42
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta
2019.42
|
Namespaces | |
| carbohydrates | |
| element | |
| gasteiger | |
| mainchain_potential | |
| mmCIF | |
| NucleotideTools | |
| orbitals | |
| rings | |
| rna | |
| rotamers | |
| sdf | |
Classes | |
| class | AcceptorAtomFilter |
| The filter responsible for obtaining all acceptor atoms. 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 | AddChi |
| Add a chi angle to ResidueType. More... | |
| class | AddChiRotamer |
| Add a rotamer sample to a chi angle of the ResidueType. More... | |
| class | AddConnect |
| 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 | AddProperty |
| add a property to ResidueType More... | |
| class | AddProtonChi |
| class | Adduct |
| Description of optional single-atom residue adducts. More... | |
| class | APolarHydrogenFilter |
| The filter responsible for all apolar hydrogens. More... | |
| class | AppendMainchainAtom |
| add a mainchain atom after the last mainchain atom More... | |
| class | AromaticAtomFilter |
| The filter responsible for all aromatic atoms. More... | |
| class | Atom |
| class | AtomICoor |
| A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More... | |
| class | AtomProperties |
| class | AtomPropertiesManager |
| 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 | ChangeAncestory |
| class | ChangeBondType |
| A patch operation for changing the bond type of a given bond. More... | |
| class | ChemicalManager |
| a class managing different sets of atom_type_set and residue_type_set More... | |
| class | ChiralFlipAtoms |
| Execute chiral flip (primarily: at CA) More... | |
| class | ChiralFlipNaming |
| Execute chiral flip (primarily: at CA) More... | |
| class | ClearChiRotamers |
| A patch operation for clearing all rotamer bins from the chi of a ResidueType. 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 | CopyEdge |
| class | CopyVertex |
| class | DeleteActCoordAtom |
| Delete an act coord atom Added by Andrew M. Watkins in April 2015. More... | |
| class | DeleteAtom |
| delete an atom More... | |
| class | DeleteChildProton |
| delete child proton More... | |
| class | DeleteMetalbindingAtom |
| Delete a metal binding atom Added by Andrew M. Watkins in April 2015. 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 | DeleteTerminalChi |
| Delete terminal chi angle Added by Andrew M. Watkins in April 2015. More... | |
| class | DeleteVariantType |
| A patch operation for deleting a VariantType from a ResidueType. 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 | GraphvizPropertyWriter |
| Callback class for write_graphviz - outputs properties for the nodes and edges. More... | |
| class | HeavyAtomFilter |
| The filter responsible for obtaining all heavy atoms. More... | |
| class | HeavyAtomWithHydrogensFilter |
| The filter responsible for finding heavy atoms with hydrogens. More... | |
| class | HeavyAtomWithPolarHydrogensFilter |
| The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them. More... | |
| class | HydrogenAtomFilter |
| The filter responsible for all hydrogens. More... | |
| class | ICoorAtomID |
| Atom 's ID in internal coordinates in a ResidueType. More... | |
| class | IdealBondLengthSet |
| A set of Elements. More... | |
| class | MergeBehaviorManager |
| 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 | 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 | NCAARotLibPath |
| set the path to a rotamer library for an NCAA that is not in dunbrack More... | |
| class | Orbital |
| basic chemical atom More... | |
| class | Patch |
| A class patching basic ResidueType to create variant types, containing multiple PatchCase. More... | |
| class | PatchCase |
| A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More... | |
| class | PatchOperation |
| A single operation that needs to be applied in a residue patch. More... | |
| class | PolarHydrogenFilter |
| The filter responsible for all polar hydrogens. More... | |
| class | PoseResidueTypeSet |
| A ResidueTypeSet which can be cached in the Pose. More... | |
| class | PrependMainchainAtom |
| add a mainchain atom before the first mainchain atom More... | |
| class | RamaPreproFilename |
| Set the filenames for RamaPrePro scoring tables. More... | |
| class | RamaPreproResname |
| Set the residue name for RamaPrePro scoring tables. More... | |
| class | RealFilter |
| A filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds. More... | |
| class | RedefineChi |
| Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTMs. More... | |
| class | RemoveRotamerSpecifications |
| Remove existing rotamer specifications (of any type). More... | |
| class | RenameAtom |
| rename atom More... | |
| class | ReplaceMainchainAtom |
| replace a mainchain atom More... | |
| class | ReplaceProtonWithBromine |
| replace proton with bromine More... | |
| class | ReplaceProtonWithChlorine |
| replace proton with chlorine More... | |
| class | ReplaceProtonWithEthyl |
| replace proton with ethyl More... | |
| class | ReplaceProtonWithFluorine |
| replace proton with fluorine More... | |
| class | ReplaceProtonWithHydroxyl |
| replace proton with hydroxyl More... | |
| class | ReplaceProtonWithIodine |
| replace proton with iodine More... | |
| class | ReplaceProtonWithMethoxy |
| replace proton with methoxy More... | |
| class | ReplaceProtonWithMethyl |
| replace proton with methyl More... | |
| class | ReplaceProtonWithTrifluoromethyl |
| replace proton with trifluoromethyl More... | |
| class | RerootEdgeSorter |
| Edge sorting: Return true if we should prefer edge1 over edge2. More... | |
| class | RerootRestypeVisitor |
| 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 | ResetBondLength |
| A patch operation for resetting the length of a bond within a ResidueType. More... | |
| class | ResidueConnection |
| A simple class marking atoms at inter-residue connections. More... | |
| class | ResidueDatabaseIO |
| class | ResidueProperties |
| 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 | ResidueTypeSelector |
| A class picking out a subset of ResidueType by multiple criteria. More... | |
| class | ResidueTypeSelectorSingle |
| A base class for defining a ResidueTypeSelector by a single criterion. 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... | |
| 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 | Selector_AA |
| Does the residue belong to ANY of these AAs? More... | |
| class | Selector_BASENAME |
| Does the residue have to ANY of these basenames? 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_HAS_ATOMS |
| Does the residue have ALL of the listed atoms?: More... | |
| class | Selector_MATCH_VARIANTS |
| Does the residue have ALL of the variant types and no more. More... | |
| class | Selector_NAME1 |
| Does the residue belong to ANY of these one-letter codes? More... | |
| class | Selector_NAME3 |
| Does the residue have ANY of these three-letter codes? More... | |
| class | Selector_NO_VARIANTS |
| Does the residue have NO variant types? More... | |
| class | Selector_PROPERTY |
| Does the residue have ANY of these properties? More... | |
| class | Selector_UPPER_ATOM |
| Does the main chain of this residue follow from the given position label? More... | |
| class | Selector_VARIANT_TYPE |
| Does the residue have ANY of variant types? More... | |
| class | Set_AA |
| set residue's aa More... | |
| class | SetAllAtomsRepulsive |
| set the residue neighbor radius More... | |
| class | SetAtomicCharge |
| set an atom's charge More... | |
| class | SetAtomType |
| set atom's chemical type More... | |
| class | SetBackboneHeavyatom |
| set an atom as backbone heavy atom More... | |
| class | SetDisulfideAtomName |
| set an atom as this residue's disulfide forming atom More... | |
| class | SetFormalCharge |
| A patch operation for setting the formal charge of a ResidueType's atom. More... | |
| class | SetICoor |
| set an atom's AtomICoord More... | |
| class | SetInterchangeabilityGroup_String |
| set the interchangeability_group string for a ResidueType More... | |
| class | SetIO_String |
| set residue's name1 and name3 More... | |
| class | SetMMAtomType |
| set atom's MM chemical type More... | |
| class | SetNbrAtom |
| set the residue neighbor atom More... | |
| class | SetNbrRadius |
| set the residue neighbor radius More... | |
| class | SetNetFormalCharge |
| A patch operation for setting the net formal charge of a whole ResidueType. More... | |
| class | SetOrientAtom |
| Set orient atom selection mode. More... | |
| class | SetPolymerConnectAtom |
| set an atom as polymer connection More... | |
| class | SetVirtualShadow |
| set virtual shadow atoms More... | |
| class | VirtualizeAll |
| virtualize all More... | |
| class | VirtualizeSidechain |
| virtualize sidechain More... | |
Typedefs | |
| 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 utility::pointer::shared_ptr < AtomDatabaseIO > | AtomDatabaseIOOP |
| typedef utility::pointer::shared_ptr < AtomDatabaseIO const > | AtomDatabaseIOCOP |
| 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 < MergeBehaviorManager > | MergeBehaviorManagerOP |
| typedef utility::pointer::shared_ptr < MergeBehaviorManager const > | MergeBehaviorManagerCOP |
| 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 < 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... | |
Functions | |
| 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_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... | |
| 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) |
| void | pretty_print_atomicoor (std::ostream &out, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent) |
| 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) |
| 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) |
| 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.MergeBehaviorManager") |
| MergeBehaviorManager::AtomRenamingMap | mrb_map_from_correspondence (std::string const &correspondence) |
| merge_residue_behavior | mrb_from_name (std::string const &mrb) |
| 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) |
| 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) |
| PatchOperationOP | 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... | |
| 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) |
| 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... | |
| 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) |
| 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) |
| 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) |
| 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... | |
| static basic::Tracer | TR ("core.chemical.residue_support") |
| ObjexxFCL::FArray2D_int | get_residue_path_distances (ResidueType const &res) |
| relies on class Graph to find all pairs shortest path information More... | |
| 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... | |
| 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... | |
| 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... | |
| void | real_to_virtual (MutableResidueType &restype) |
| Virtualize convert the MutableResidueType to a virtual type NOTE: This function does not rename the residue type. More... | |
| LightWeightResidueGraph | convert_residuetype_to_light_graph (MutableResidueType const &res) |
| 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... | |
| void | calculate_rigid_matrix (MutableResidueType const &res, utility::vector1< utility::vector1< core::Real > > &distances) |
| Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square. More... | |
| 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... | |
| void | rosetta_recharge_fullatom (MutableResidueType &res) |
| Apply molfile_to_params style partial charges to the ResidueType. More... | |
| MutableResidueTypeOP | make_centroid (ResidueType const &res) |
| Make a centroid version of the fullatom ResidueType passed in. More... | |
| MutableResidueTypeOP | make_centroid (MutableResidueType const &res) |
| bool | residue_type_bases_identical (ResidueTypeBase const &r1, ResidueTypeBase const &r2) |
| 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... | |
| 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... | |
| 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... | |
| bool | has (ResidueGraph const &graph, VD vd) |
| Does a ResidueGraph have a given vertex descriptor? More... | |
| bool | has (ResidueGraph const &graph, ED ed) |
| Does a ResidueGraph have a given edge descriptor? More... | |
| 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... | |
| std::ostream & | operator<< (std::ostream &output, ResidueProperties const &object_to_output) |
| std::ostream & | operator<< (std::ostream &output, ResidueProperty const &object_to_output) |
| ResidueProperty & | operator++ (ResidueProperty &property) |
| VariantType & | operator++ (VariantType &variant) |
| ResiduePropertiesOP | deep_copy (ResidueProperties const &source) |
| std::map< std::string, ResidueProperty > const * | generate_string_to_property_map () |
| static const std::map < std::string, ResidueProperty > *const | PROPERTY_MAP (generate_string_to_property_map()) |
| utility::vector1< std::string > const * | generate_property_to_string_vector () |
| static const utility::vector1 < std::string > *const | STRING_LIST (generate_property_to_string_vector()) |
| RealResidueGraph | make_real_residue_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| HeavyAtomGraph | make_heavy_atom_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| AcceptorAtomGraph | make_acceptor_atom_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| HeavyAtomWithPolarHydrogensGraph | make_heavy_atom_with_polar_hydrogens_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| HeavyAtomWithHydrogensGraph | make_heavy_atom_with_hydrogens_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| HydrogenAtomGraph | make_hydrogen_atom_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| AromaticAtomGraph | make_aromatic_atom_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| PolarHydrogenGraph | make_polar_hydrogen_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| APolarHydrogenGraph | make_apolar_hydrogen_graph (MutableResidueType const &restype) |
| Convenience constructor. More... | |
| static basic::Tracer | TR ("core.chemical.ResidueType") |
| std::ostream & | operator<< (std::ostream &output, ResidueType const &object_to_output) |
| static basic::Tracer | TR ("core.chemical.ResidueTypeBase") |
| std::string | get_element_color (std::string const &element) |
| static basic::Tracer | TR ("core.chemical.ResidueTypeSelector") |
| ResidueTypeSelectorSingleOP | residue_selector_single_from_line (std::string const &line) |
| create a singe ResidueTypeSelector from an input line. More... | |
| static basic::Tracer | TR ("core.chemical.ResidueTypeSet") |
| static std::string const | chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz") |
| static basic::Tracer | TR ("core.chemical.util") |
| core::chemical::ResidueTypeSetCAP | rsd_set_from_cmd_line () |
| Return a constant access pointer to the ResidueTypeSet specified by the command-line options. More... | |
| 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... | |
| 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... | |
| std::string | formatted_icoord_tree (core::chemical::ResidueType const &restype) |
| Return a string representing the internal coordinates tree of this ResidueType. More... | |
| std::string | formatted_icoord_tree (core::chemical::MutableResidueType const &restype) |
| Return a string representing the internal coordinates tree of this MutableResidueType (if any) More... | |
| void | print_chis (std::ostream &out, ResidueType const &res) |
| Utility to examine chi output. More... | |
| void | print_chis (std::ostream &out, MutableResidueType const &res) |
| Utility to examine chi output. More... | |
| std::string | fixup_patches (std::string const &string_in) |
| Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":". More... | |
| 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... | |
| utility::vector1< VariantType > | pH_mode_exceptions () |
| check if user has set -pH_mode. More... | |
| bool | variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2) |
| Are these two residues patched in exactly the same way? More... | |
| bool | nonadduct_variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2) |
| Similar to variants_match(), but allows different adduct-modified states. More... | |
| utility::vector1< VariantType > | get_terminal_varianttypes () |
| Get a list of those VariantTypes that affect termini. More... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| 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) |
| 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... | |
| bool | is_mainchain_torsion_also_ring_torsion (ResidueType const &res_type, uint torsion_index) |
| Are these main-chain torsions also ring torsions? More... | |
| std::map< std::string, VariantType > const * | generate_string_to_variant_map () |
| static const std::map < std::string, VariantType > *const | VARIANT_MAP (generate_string_to_variant_map()) |
| utility::vector1< std::string > const * | generate_variant_to_string_vector () |
| static const utility::vector1 < std::string > *const | STRING_LIST (generate_variant_to_string_vector()) |
Variables | |
| Real const | MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 } |
| Maximum distance between a heavy atom and a hydrogen atom to which it is chemically bound Set in .cc file. More... | |
| std::string const | FA_STANDARD |
| std::string const | CENTROID |
| std::string const | CENTROID_ROT |
| std::string const | HYBRID_FA_STANDARD_CENTROID |
| std::string const | COARSE_RNA |
| std::string const | PATCH_LINKER = ":" |
| the string used to create new residue names after patching More... | |
| typedef std::pair< AA, std::pair< utility::vector1< std::string >, utility::vector1< VariantType > > > core::chemical::AA_VariantsExceptions |
| typedef boost::graph_traits<AcceptorAtomGraph>::edge_iterator core::chemical::AcceptorAtomEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, AcceptorAtomFilter> core::chemical::AcceptorAtomGraph |
| typedef boost::graph_traits<AcceptorAtomGraph>::vertex_iterator core::chemical::AcceptorAtomVIter |
| typedef std::pair<AcceptorAtomVIter, AcceptorAtomVIter> core::chemical::AcceptorAtomVIterPair |
| typedef std::map< std::string, int > core::chemical::AdductMap |
| typedef utility::pointer::shared_ptr< Adduct > core::chemical::AdductOP |
| typedef boost::graph_traits<ResidueGraph>::adjacency_iterator core::chemical::AdjacentIter |
| typedef std::pair<AdjacentIter, AdjacentIter> core::chemical::AdjacentIterPair |
| typedef boost::graph_traits<APolarHydrogenGraph>::edge_iterator core::chemical::APolarHydrogenEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, APolarHydrogenFilter> core::chemical::APolarHydrogenGraph |
| typedef boost::graph_traits<APolarHydrogenGraph>::vertex_iterator core::chemical::APolarHydrogenVIter |
| typedef std::pair<APolarHydrogenVIter, APolarHydrogenVIter> core::chemical::APolarHydrogenVIterPair |
| typedef boost::graph_traits<AromaticAtomGraph>::edge_iterator core::chemical::AromaticAtomEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, AromaticAtomFilter> core::chemical::AromaticAtomGraph |
| typedef boost::graph_traits<AromaticAtomGraph>::vertex_iterator core::chemical::AromaticAtomVIter |
| typedef std::pair<AromaticAtomVIter, AromaticAtomVIter> core::chemical::AromaticAtomVIterPair |
| typedef utility::pointer::weak_ptr< Atom > core::chemical::AtomAP |
| typedef utility::vector1< AtomAP > core::chemical::AtomAPs |
| typedef utility::pointer::shared_ptr< Atom const > core::chemical::AtomCOP |
| typedef utility::vector1< AtomCOP > core::chemical::AtomCOPs |
| typedef utility::pointer::shared_ptr< AtomDatabaseIO const > core::chemical::AtomDatabaseIOCOP |
| typedef utility::pointer::shared_ptr< AtomDatabaseIO > core::chemical::AtomDatabaseIOOP |
| typedef utility::vector1< Size > core::chemical::AtomIndices |
| using core::chemical::AtomMemo = typedef basic::datacache::DataMapObj<std::set<std::string> > |
| using core::chemical::AtomMemoOP = typedef utility::pointer::shared_ptr<AtomMemo> |
| typedef utility::pointer::shared_ptr< Atom > core::chemical::AtomOP |
| typedef utility::vector1< AtomOP > core::chemical::AtomOPs |
| typedef utility::pointer::shared_ptr< AtomProperties const > core::chemical::AtomPropertiesCOP |
| typedef utility::pointer::shared_ptr< AtomProperties > core::chemical::AtomPropertiesOP |
| typedef int core::chemical::AtomTypeIndex |
| typedef utility::pointer::weak_ptr< AtomTypeSet > core::chemical::AtomTypeSetAP |
| typedef utility::pointer::weak_ptr< AtomTypeSet const > core::chemical::AtomTypeSetCAP |
| typedef utility::pointer::shared_ptr< AtomTypeSet const > core::chemical::AtomTypeSetCOP |
| typedef utility::pointer::shared_ptr< AtomTypeSet > core::chemical::AtomTypeSetOP |
| typedef utility::pointer::shared_ptr< AutomorphismIterator const > core::chemical::AutomorphismIteratorCOP |
| typedef utility::pointer::shared_ptr< AutomorphismIterator > core::chemical::AutomorphismIteratorOP |
| typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::bondangle_atom_set |
| typedef Real core::chemical::BondLength |
| typedef utility::pointer::shared_ptr< CacheableResidueTypeSets const > core::chemical::CacheableResidueTypeSetsCOP |
| typedef utility::pointer::shared_ptr< CacheableResidueTypeSets > core::chemical::CacheableResidueTypeSetsOP |
| typedef utility::keys::Key4Tuple< Size, Size, Size, Size > core::chemical::dihedral_atom_set |
| typedef ResidueGraph::edge_descriptor core::chemical::ED |
| typedef boost::graph_traits<ResidueGraph>::edge_iterator core::chemical::EIter |
| typedef std::pair<EIter, EIter> core::chemical::EIterPair |
| typedef utility::pointer::shared_ptr< Element const > core::chemical::ElementCOP |
| typedef utility::pointer::shared_ptr< Element > core::chemical::ElementOP |
| typedef utility::pointer::weak_ptr< ElementSet > core::chemical::ElementSetAP |
| typedef utility::pointer::weak_ptr< ElementSet const > core::chemical::ElementSetCAP |
| typedef utility::pointer::shared_ptr< ElementSet const > core::chemical::ElementSetCOP |
| typedef utility::pointer::shared_ptr< ElementSet > core::chemical::ElementSetOP |
| typedef utility::pointer::weak_ptr< GlobalResidueTypeSet const > core::chemical::GlobalResidueTypeSetCAP |
| typedef utility::pointer::shared_ptr< GlobalResidueTypeSet const > core::chemical::GlobalResidueTypeSetCOP |
| typedef utility::pointer::shared_ptr< GlobalResidueTypeSet > core::chemical::GlobalResidueTypeSetOP |
| typedef HeavyAtomGraph::edge_descriptor core::chemical::HeavyAtomED |
| typedef boost::graph_traits<HeavyAtomGraph>::edge_iterator core::chemical::HeavyAtomEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HeavyAtomFilter> core::chemical::HeavyAtomGraph |
| typedef boost::graph_traits<HeavyAtomGraph>::out_edge_iterator core::chemical::HeavyAtomOutEdgeIter |
| typedef std::pair<HeavyAtomOutEdgeIter, HeavyAtomOutEdgeIter> core::chemical::HeavyAtomOutEdgeIterPair |
| typedef HeavyAtomGraph::vertex_descriptor core::chemical::HeavyAtomVD |
| typedef boost::graph_traits<HeavyAtomGraph>::vertex_iterator core::chemical::HeavyAtomVIter |
| typedef std::pair<HeavyAtomVIter, HeavyAtomVIter> core::chemical::HeavyAtomVIterPair |
| typedef boost::graph_traits<HeavyAtomWithHydrogensGraph>::edge_iterator core::chemical::HeavyAtomWithHydrogensEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HeavyAtomWithHydrogensFilter> core::chemical::HeavyAtomWithHydrogensGraph |
| typedef boost::graph_traits<HeavyAtomWithHydrogensGraph>::vertex_iterator core::chemical::HeavyAtomWithHydrogensVIter |
| typedef std::pair<HeavyAtomWithHydrogensVIter, HeavyAtomWithHydrogensVIter> core::chemical::HeavyAtomWithHydrogensVIterPair |
| typedef boost::graph_traits<HeavyAtomWithPolarHydrogensGraph>::edge_iterator core::chemical::HeavyAtomWithPolarHydrogensEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HeavyAtomWithPolarHydrogensFilter> core::chemical::HeavyAtomWithPolarHydrogensGraph |
| typedef boost::graph_traits<HeavyAtomWithPolarHydrogensGraph>::vertex_iterator core::chemical::HeavyAtomWithPolarHydrogensVIter |
| typedef std::pair<HeavyAtomWithPolarHydrogensVIter, HeavyAtomWithPolarHydrogensVIter> core::chemical::HeavyAtomWithPolarHydrogensVIterPair |
| typedef boost::graph_traits<HydrogenAtomGraph>::edge_iterator core::chemical::HHydrogenAtomEIter |
| typedef HydrogenAtomGraph::edge_descriptor core::chemical::HydrogenAtomED |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HydrogenAtomFilter> core::chemical::HydrogenAtomGraph |
| typedef boost::graph_traits<HydrogenAtomGraph>::out_edge_iterator core::chemical::HydrogenAtomOutEdgeIter |
| typedef std::pair<HydrogenAtomOutEdgeIter, HydrogenAtomOutEdgeIter> core::chemical::HydrogenAtomOutEdgeIterPair |
| typedef HydrogenAtomGraph::vertex_descriptor core::chemical::HydrogenAtomVD |
| typedef boost::graph_traits<HydrogenAtomGraph>::vertex_iterator core::chemical::HydrogenAtomVIter |
| typedef std::pair<HydrogenAtomVIter, HydrogenAtomVIter> core::chemical::HydrogenAtomVIterPair |
| typedef utility::pointer::weak_ptr< IdealBondLengthSet > core::chemical::IdealBondLengthSetAP |
| typedef utility::pointer::weak_ptr< IdealBondLengthSet const > core::chemical::IdealBondLengthSetCAP |
| typedef utility::pointer::shared_ptr< IdealBondLengthSet const > core::chemical::IdealBondLengthSetCOP |
| typedef utility::pointer::shared_ptr< IdealBondLengthSet > core::chemical::IdealBondLengthSetOP |
| 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> > core::chemical::LightWeightResidueGraph |
Light weight graph typedefs The light weight graph is a graph that holds a pointer to the edge descriptor and vertex descriptor or the ResidueGraph. We generate the light weight graph so that we can do rapid things like look for rings ina small molecule. Also
| typedef boost::graph_traits<LightWeightResidueGraph>::edge_descriptor core::chemical::lwrg_ED |
| typedef boost::graph_traits<LightWeightResidueGraph>::edge_iterator core::chemical::lwrg_edge_iter |
| typedef boost::graph_traits<LightWeightResidueGraph>::out_edge_iterator core::chemical::lwrg_out_edge_iter |
| typedef std::pair<lwrg_out_edge_iter, lwrg_out_edge_iter> core::chemical::lwrg_out_edge_iter_pair |
| typedef boost::graph_traits<LightWeightResidueGraph>::vertex_descriptor core::chemical::lwrg_VD |
| typedef boost::graph_traits<LightWeightResidueGraph>::vertex_iterator core::chemical::lwrg_vd_iter |
| typedef std::pair<lwrg_vd_iter, lwrg_vd_iter> core::chemical::lwrg_vd_pair_iter |
| typedef utility::pointer::shared_ptr< MergeBehaviorManager const > core::chemical::MergeBehaviorManagerCOP |
| typedef utility::pointer::shared_ptr< MergeBehaviorManager > core::chemical::MergeBehaviorManagerOP |
| typedef utility::pointer::shared_ptr< Metapatch const > core::chemical::MetapatchCOP |
| typedef utility::pointer::shared_ptr< Metapatch > core::chemical::MetapatchOP |
| typedef utility::pointer::shared_ptr< MMAtomType > core::chemical::MMAtomTypeOP |
| typedef utility::pointer::weak_ptr< MMAtomTypeSet > core::chemical::MMAtomTypeSetAP |
| typedef utility::pointer::weak_ptr< MMAtomTypeSet const > core::chemical::MMAtomTypeSetCAP |
| typedef utility::pointer::shared_ptr< MMAtomTypeSet const > core::chemical::MMAtomTypeSetCOP |
| typedef utility::pointer::shared_ptr< MMAtomTypeSet > core::chemical::MMAtomTypeSetOP |
| typedef utility::pointer::shared_ptr< MutableChiRecord const > core::chemical::MutableChiRecordCOP |
| typedef utility::pointer::shared_ptr< MutableChiRecord > core::chemical::MutableChiRecordOP |
| typedef utility::pointer::shared_ptr< MutableICoorRecord const > core::chemical::MutableICoorRecordCOP |
| typedef utility::pointer::shared_ptr< MutableICoorRecord > core::chemical::MutableICoorRecordOP |
| typedef utility::pointer::shared_ptr< MutableResidueType const > core::chemical::MutableResidueTypeCOP |
| typedef utility::vector1< MutableResidueTypeCOP > core::chemical::MutableResidueTypeCOPs |
| typedef utility::pointer::shared_ptr< MutableResidueType > core::chemical::MutableResidueTypeOP |
| typedef utility::vector1< MutableResidueTypeOP > core::chemical::MutableResidueTypeOPs |
| typedef std::pair<NameVDMap::iterator, bool> core::chemical::NameVDInserted |
| typedef std::map< std::string, VD > core::chemical::NameVDMap |
| typedef std::pair<std::string, VD> core::chemical::NameVDPair |
| typedef utility::pointer::shared_ptr< Orbital const > core::chemical::OrbitalCOP |
| typedef utility::vector1< OrbitalCOP > core::chemical::OrbitalCOPs |
| typedef utility::vector1<Size> core::chemical::OrbitalIndices |
| typedef utility::pointer::shared_ptr< Orbital > core::chemical::OrbitalOP |
| typedef utility::vector1< OrbitalOP > core::chemical::OrbitalOPs |
| typedef boost::graph_traits<ResidueGraph>::out_edge_iterator core::chemical::OutEdgeIter |
| typedef std::pair<OutEdgeIter, OutEdgeIter> core::chemical::OutEdgeIterPair |
| typedef utility::pointer::shared_ptr< PatchCase > core::chemical::PatchCaseOP |
| typedef utility::pointer::shared_ptr< Patch const > core::chemical::PatchCOP |
| typedef utility::pointer::shared_ptr< Patch > core::chemical::PatchOP |
| typedef utility::pointer::shared_ptr< PatchOperation > core::chemical::PatchOperationOP |
| typedef boost::graph_traits<PolarHydrogenGraph>::edge_iterator core::chemical::PolarHydrogenEIter |
| typedef boost::filtered_graph<ResidueGraph, boost::keep_all, PolarHydrogenFilter> core::chemical::PolarHydrogenGraph |
| typedef boost::graph_traits<PolarHydrogenGraph>::vertex_iterator core::chemical::PolarHydrogenVIter |
| typedef std::pair<PolarHydrogenVIter, PolarHydrogenVIter> core::chemical::PolarHydrogenVIterPair |
| typedef utility::pointer::shared_ptr< PoseResidueTypeSet const > core::chemical::PoseResidueTypeSetCOP |
| typedef utility::pointer::shared_ptr< PoseResidueTypeSet > core::chemical::PoseResidueTypeSetOP |
| typedef boost::graph_traits<RealResidueGraph>::adjacency_iterator core::chemical::RealResidueAdjacentIter |
| typedef std::pair<RealResidueAdjacentIter, RealResidueAdjacentIter> core::chemical::RealResidueAdjacentIterPair |
| typedef RealResidueGraph::edge_descriptor core::chemical::RealResidueED |
| typedef boost::graph_traits<RealResidueGraph>::edge_iterator core::chemical::RealResidueEIter |
| typedef boost::filtered_graph<ResidueGraph, RealFilter, RealFilter> core::chemical::RealResidueGraph |
| typedef boost::graph_traits<RealResidueGraph>::out_edge_iterator core::chemical::RealResidueOutEdgeIter |
| typedef std::pair<RealResidueOutEdgeIter, RealResidueOutEdgeIter> core::chemical::RealResidueOutEdgeIterPair |
| typedef RealResidueGraph::vertex_descriptor core::chemical::RealResidueVD |
| typedef boost::graph_traits<RealResidueGraph>::vertex_iterator core::chemical::RealResidueVIter |
| typedef std::pair<RealResidueVIter, RealResidueVIter> core::chemical::RealResidueVIterPair |
| typedef boost::undirected_graph< Atom, Bond > core::chemical::ResidueGraph |
| typedef utility::pointer::shared_ptr< ResidueProperties const > core::chemical::ResiduePropertiesCOP |
| typedef utility::pointer::shared_ptr< ResidueProperties > core::chemical::ResiduePropertiesOP |
| typedef utility::pointer::weak_ptr< ResidueType > core::chemical::ResidueTypeAP |
| typedef utility::pointer::weak_ptr< ResidueTypeBase > core::chemical::ResidueTypeBaseAP |
| typedef utility::pointer::weak_ptr< ResidueTypeBase const > core::chemical::ResidueTypeBaseCAP |
| typedef utility::pointer::shared_ptr< ResidueTypeBase const > core::chemical::ResidueTypeBaseCOP |
| typedef utility::pointer::shared_ptr< ResidueTypeBase > core::chemical::ResidueTypeBaseOP |
| typedef utility::pointer::weak_ptr< ResidueType const > core::chemical::ResidueTypeCAP |
| typedef utility::vector1< ResidueTypeCAP > core::chemical::ResidueTypeCAPs |
| typedef utility::pointer::shared_ptr< ResidueType const > core::chemical::ResidueTypeCOP |
| typedef utility::vector1< ResidueTypeCOP > core::chemical::ResidueTypeCOPs |
| typedef utility::pointer::shared_ptr< ResidueTypeFinder const > core::chemical::ResidueTypeFinderCOP |
| typedef utility::pointer::shared_ptr< ResidueTypeFinder > core::chemical::ResidueTypeFinderOP |
| typedef utility::pointer::shared_ptr< ResidueTypeKinWriter const > core::chemical::ResidueTypeKinWriterCOP |
| typedef utility::pointer::shared_ptr< ResidueTypeKinWriter > core::chemical::ResidueTypeKinWriterOP |
| typedef utility::pointer::shared_ptr< ResidueType > core::chemical::ResidueTypeOP |
| typedef utility::vector1< ResidueTypeOP > core::chemical::ResidueTypeOPs |
| typedef utility::pointer::shared_ptr< ResidueTypeSelector > core::chemical::ResidueTypeSelectorOP |
| typedef utility::pointer::shared_ptr< ResidueTypeSelectorSingle > core::chemical::ResidueTypeSelectorSingleOP |
| typedef utility::pointer::shared_ptr< ResidueTypeSetCache const > core::chemical::ResidueTypeSetCacheCOP |
| typedef utility::pointer::shared_ptr< ResidueTypeSetCache > core::chemical::ResidueTypeSetCacheOP |
| typedef utility::pointer::weak_ptr< ResidueTypeSet const > core::chemical::ResidueTypeSetCAP |
| typedef utility::pointer::shared_ptr< ResidueTypeSet const > core::chemical::ResidueTypeSetCOP |
| typedef utility::pointer::shared_ptr< ResidueTypeSet > core::chemical::ResidueTypeSetOP |
| typedef std::tuple< ResidueTypeCOP, utility::vector1< VariantType >, utility::vector1< std::string >, utility::vector1< VariantType >, bool > core::chemical::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.
| typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::three_atom_set |
| typedef utility::keys::Key2Tuple< Size, Size > core::chemical::two_atom_set |
| typedef ResidueGraph::vertex_descriptor core::chemical::VD |
| typedef utility::vector1< VD > core::chemical::VDs |
| typedef std::map< core::chemical::VD, core::kinematics::tree::AtomOP > core::chemical::VdTreeatomMap |
| typedef boost::graph_traits<ResidueGraph>::vertex_iterator core::chemical::VIter |
| typedef std::pair<VIter, VIter> core::chemical::VIterPair |
| enum core::chemical::AA |
enumeration for amino acids and nucleotides types with the total number as num_aa_types
Enumerators for all the properties that can be assigned to a chemical::Atom.
| Enumerator | |
|---|---|
| NO_ATOM_PROPERTY | |
| FIRST_ATOM_PROPERTY | |
| H_DONOR | |
| H_ACCEPTOR | |
| POLAR_HYDROGEN | |
| AROMATIC_HYDROGEN | |
| HAS_ORBITALS | |
| VIRTUAL_ATOM | |
| REPULSIVE | |
| AROMATIC_CARBON_WITH_FREE_VALENCE | |
| N_ATOM_PROPERTIES | |
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.
| Enumerator | |
|---|---|
| UnknownConjugability | |
| NotConjugableBond | |
| ConjugableBond | |
Enumerators for the Greek distance from the atom with the functional group of highest priority.
|
strong |
ICoordAtomIDType.
If you add anything to this enum, be sure to update the string_to_icoord_type() function.
| Enumerator | |
|---|---|
| INTERNAL | |
| POLYMER_LOWER | |
| POLYMER_UPPER | |
| CONNECT | |
Enumerators for all the properties that can be assigned to a ResidueType.
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.
| Enumerator | |
|---|---|
| INVALID_t |
Don't use this as a mode - it exists as an error signal only. |
| FULL_ATOM_t |
Full atom modeling - all atoms are represented. |
| DEFAULT_t |
For type sets where there really isn't a clear distinction between fullatom and centroid. |
| CENTROID_t |
Standard Rosetta Centroid: amino acid sidechains are represented by a "superatom", and other atoms are represented by a unified-atom model. (No apolar hydrogens.) |
| CENTROID_ROT_t |
A modification of the Centroid mode, where the amino acid sidechains have additional degrees of freedom. |
| HYBRID_FA_STANDARD_CENTROID_t |
??? |
| COARSE_RNA_t |
??? |
| MIXED_t |
MIXED is not an actual mode, but is instead used for a a mixed TypeSetMode situation. |
| TYPE_SET_MODES_LENGTH | |
Enumerators for all the ResidueType variants.
VariantTypes are primarily utilized by the patch system. All the type does is add an identifier that can be used later on in different protocols. It also helps the patch system keep track of which residues are patched with which patches.
|
inline |
|
inline |
vector that maps AA enum to one letter char
References setup_aa2oneletter().
Referenced by oneletter_code_from_aa().
| AA core::chemical::aa_from_name | ( | std::string const & | name | ) |
Give an AA string 3-letter code, return its enum type.
References core::sequence::end, and name2aa().
Referenced by core::chemical::ResidueTypeBase::aa(), aa_from_one_or_three(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::splice::Splice::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), core::pack::task::operation::RestrictYSDesign::apply(), core::chemical::ResidueTypeBase::backbone_aa(), core::chemical::ResidueTypeBase::base_analogue(), protocols::simple_moves::WaterBoxMover::build_backbone_rotamer_clouds(), protocols::motifs::Motif::build_rotamers(), core::chemical::rotamers::CenrotRotamerLibrarySpecification::CenrotRotamerLibrarySpecification(), core::pack::dunbrack::cenrot::CenrotLibrary::create_centroid_rotamer_libraries_from_ASCII(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), core::chemical::rotamers::DunbrackRotamerLibrarySpecification::DunbrackRotamerLibrarySpecification(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_oneletter_codes(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::match::Matcher::initialize_from_file(), core::io::mmtf::make_current_group(), protocols::motifs::make_dna_mutations(), protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop(), core::chemical::ResidueTypeBase::na_analogue(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_filters::NeighborTypeFilter::parse_my_tag(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::P_AA::read_P_AA(), core::scoring::P_AA::read_P_AA_n(), core::scoring::P_AA::read_P_AA_pp(), core::scoring::P_AA_ss::read_P_AA_ss(), core::scoring::Ramachandran::read_rama_map_file_shapovalov(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), and setup_patch_atomic_charge_reassignments_from_commandline().
| AA core::chemical::aa_from_one_or_three | ( | std::string const & | name | ) |
References aa_from_name(), and aa_from_oneletter_code().
Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), and protocols::antibody::design::CDRSeqDesignOptionsParser::set_disallow_amino_acids().
| AA core::chemical::aa_from_oneletter_code | ( | char | onelettercode | ) |
give a 1 letter code and return the string name
References aa_unk, core::sequence::end, and oneletter2aa().
Referenced by core::sequence::AnnotatedSequence::aa(), aa_from_one_or_three(), protocols::noesy_assign::ResonanceList::aa_from_resid(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT::aas_to_keep(), core::scoring::abego3aa_to_index(), protocols::simple_moves::RepeatPropagationMover::add_cap_seq(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), protocols::forge::components::BDR::allowed_surface_aa(), protocols::forge::remodel::RemodelMover::allowed_surface_aa(), core::conformation::Residue::annotated_name(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::task_operations::ConservativeDesignOperation::apply(), protocols::task_operations::ThreadSequenceOperation::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::pose_creation::MergePDBatOverlapMover::assign_seq(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::enzymes::get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position(), protocols::recon_design::get_candidate_AAs(), protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains(), core::conformation::get_residue_from_name1(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::task_operations::DsspDesignOperation::get_restrictions(), protocols::flxbb::LayerDesignOperation::get_restrictions(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), protocols::sasa_scores::help_load_data(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::sequence::ProfSimScoringScheme::initialize_parameters(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs(), protocols::antibody::design::MutateFrameworkForCluster::load_data(), protocols::task_operations::ConservativeDesignOperation::load_data_from_db(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::optimize_weights::IterativeOptEDriver::load_pssm_data(), core::scoring::dna::DNA_EnvPairPotential::load_score_tables(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::denovo_design::task_operations::make_aa_bitmap_from_allowed_aas(), protocols::denovo_design::task_operations::make_aa_bitmap_from_forbidden_aas(), protocols::pmut_scan::PointMutScanDriver::make_mutant_structure(), protocols::membrane::MPMutateRelaxMover::make_mutations(), core::fragment::make_pose_from_sequence_(), protocols::tcr::match_template_and_target_sequence(), protocols::analysis::InterfaceAnalyzerMover::mut_to_gly(), core::scoring::nv::NVlookup::NVlookup(), core::fragment::picking_old::vall::VallResidue::order_vector(), protocols::frag_picker::VallResidue::order_vector(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter(), protocols::mean_field::AAMatrix::parse_aa_line(), core::pack::task::operation::DesignRestrictions::parse_tag(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset(), core::scoring::motif::Xfres::place_sidechain_in_pose(), protocols::multistate_design::PosType::PosType(), protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::forge::components::BDR::process_continuous_design_string(), protocols::forge::remodel::RemodelMover::process_continuous_design_string(), protocols::forge::components::BDR::process_insert_design_string(), protocols::forge::remodel::RemodelMover::process_insert_design_string(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), protocols::dna::DnaInterfacePacker::protein_scan(), core::sequence::MatrixScoringScheme::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::sequence::SequenceProfile::read_from_binary_chk(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::read_in_mutations(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), core::pose::residue_types_from_sequence(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), core::sequence::MatrixScoringScheme::score(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), protocols::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(), protocols::forge::remodel::RemodelLoopMover::set_starting_sequence(), protocols::hydrate::set_task_and_movemap(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), protocols::simple_moves::ResTypeFragmentMover::swap_residue_types(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile(), protocols::antibody::design::transform_sequence_to_mutation_set(), and core::sequence::MatrixScoringScheme::values_for_aa().
| void core::chemical::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.
Called by ChemicalManager at time of AtomTypeSet creation.
References core::chemical::AtomTypeSet::add_parameters_from_file(), protocols::abinitio::filename(), and TR().
Referenced by core::chemical::ChemicalManager::create_atom_type_set().
| void core::chemical::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.
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::bond(), core::chemical::MutableResidueType::bonded_neighbors(), core::chemical::MutableResidueType::chi_atom_vds(), protocols::sparta::contains(), core::chemical::Bond::cut_bond(), core::chemical::Atom::is_backbone(), core::chemical::MutableResidueType::lower_connect_atom(), core::chemical::MutableResidueType::lower_connect_id(), protocols::sic_dock::scores::nbr, core::chemical::MutableResidueType::nchi(), core::chemical::MutableResidueType::upper_connect_atom(), and core::chemical::MutableResidueType::upper_connect_id().
Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().
| MutableResidueTypeOP core::chemical::apply_adducts_to_residue | ( | ResidueType const & | rsd, |
| utility::vector1< bool > & | add_mask | ||
| ) |
Apply adducts to residue using a boolean mask.
References core::chemical::PatchCase::add_operation(), ADDUCT_VARIANT, core::chemical::PatchCase::apply(), core::chemical::ResidueTypeBase::defined_adducts(), core::chemical::ResidueTypeBase::name(), and TR().
Referenced by create_adduct_combinations().
| void core::chemical::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).
Ugh. Special-case logic.
Referenced by read_topology_file().
| gasteiger::GasteigerAtomTypeData::Properties core::chemical::bond_order_to_property | ( | const core::Size & | BOND_ORDER_OR_AROMATIC | ) |
convert bond order or aromatic into the corresponding radius
| BOND_ORDER_OR_AROMATIC | bond type in notation: 1=single, 2=double, 3=triple, 4=aromatic |
References core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusAromaticBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusDoubleBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusSingleBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusTripleBond, update_ResidueType_enum_files::properties, and core::chemical::gasteiger::GasteigerAtomTypeData::VdWaalsRadiusCSD.
Referenced by create_bond_length().
| void core::chemical::calculate_rigid_matrix | ( | MutableResidueType const & | res, |
| utility::vector1< utility::vector1< core::Real > > & | distances | ||
| ) |
Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square.
Calculate the rigid matrix for neighbor atom finding Assume that distances has been initialized to some really large value, and is square.
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::atom_iterators(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::graph(), core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::natoms(), and TR().
Referenced by find_nbr_dist().
| PatchCaseOP core::chemical::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
add selector_ from lines enclosed by "BEGIN_SELECTOR" and "END_SELECTOR".
add operations_ from each input line containing a single operation
References patch_operation_from_patch_file_line(), setup_patch_atomic_charge_reassignments_from_commandline(), and tag_from_line().
Referenced by core::chemical::Metapatch::get_one_patch(), core::chemical::Metapatch::read_file(), and core::chemical::Patch::read_file().
| std::string const core::chemical::CENTROID | ( | "centroid" | ) |
tag name for querying fullatom chemical type set.
| std::string const core::chemical::CENTROID_ROT | ( | "centroid_rot" | ) |
tag name for querying centroid_rot chemical type set.
| void core::chemical::check_residue_has_atom | ( | std::string const & | atom_name, |
| core::chemical::MutableResidueType const & | rsd, | ||
| std::string const & | location | ||
| ) |
References core::chemical::MutableResidueType::has(), INTERNAL, core::chemical::ResidueTypeBase::name(), and string_to_icoord_type().
Referenced by core::chemical::SetICoor::apply().
|
static |
Referenced by core::pose::full_model_info::figure_out_conventional_chains_from_full_model_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_chainIDs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), and core::pack::task::ResfileContents::parse_resid().
| void core::chemical::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.)
Assumes that all of the xyz coordinates are updated.
References core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_iterators(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::MutableICoorRecord::d(), core::chemical::MutableResidueType::icoor(), core::chemical::Atom::ideal_xyz(), INTERNAL, core::chemical::MutableResidueType::lower_connect_id(), core::chemical::ResidueTypeBase::name(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::MutableResidueType::set_icoor(), core::chemical::MutableICoorRecord::stub_atom1(), core::chemical::MutableICoorRecord::stub_atom2(), core::chemical::MutableICoorRecord::stub_type1(), core::chemical::MutableICoorRecord::stub_type2(), core::chemical::MutableICoorRecord::stub_type3(), core::chemical::MutableICoorRecord::theta(), TR(), core::chemical::MutableResidueType::upper_connect_id(), walk_back_to_find_usable_base(), and core::chemical::MutableICoorRecord::xyz().
Referenced by core::chemical::SetPolymerConnectAtom::apply().
| std::string const core::chemical::COARSE_RNA | ( | "coarse_rna" | ) |
tag name for querying COARSE_RNA chemical type set.
| bool core::chemical::compare_atom_icoor | ( | AtomICoor const & | aic1, |
| AtomICoor const & | aic2, | ||
| bool | fuzzy | ||
| ) |
Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue.
References core::chemical::AtomICoor::built_atom(), core::chemical::AtomICoor::d(), core::chemical::AtomICoor::phi(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), and core::chemical::AtomICoor::theta().
Referenced by compare_residue_connection(), and residue_types_identical().
| bool core::chemical::compare_residue_connection | ( | ResidueConnection const & | rc1, |
| ResidueConnection const & | rc2, | ||
| bool | fuzzy | ||
| ) |
Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue.
References core::chemical::ResidueConnection::atomno(), compare_atom_icoor(), core::chemical::ResidueConnection::icoor(), and core::chemical::ResidueConnection::index().
Referenced by residue_types_identical().
| void core::chemical::complex_ring_detection | ( | MutableResidueType & | res | ) |
| LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph | ( | MutableResidueType const & | res | ) |
References protocols::forge::methods::add_vertex(), and core::chemical::MutableResidueType::graph().
Referenced by complex_ring_detection().
| BondName core::chemical::convert_to_BondName | ( | std::string const & | id | ) |
References AromaticBond, DoubleBond, OrbitalBond, PseudoBond, SingleBond, TripleBond, and UnknownBond.
Referenced by core::chemical::AddBondType::apply(), core::chemical::ChangeBondType::apply(), and read_topology_file().
| std::string core::chemical::correct_conn | ( | std::string const & | old, |
| core::Size const | conn_id_deleted | ||
| ) |
A short utility function for update_icoors_after_connection_deletion()
References CONNECT, get_connection_number(), string_to_icoord_type(), and core::id::to_string().
Referenced by core::chemical::MutableResidueType::update_icoors_after_connection_deletion().
| MutableResidueTypeOPs core::chemical::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.
References apply_adducts_to_residue(), and core::chemical::ResidueTypeBase::defined_adducts().
Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().
| Real core::chemical::create_bond_length | ( | gasteiger::GasteigerAtomTypeData const & | atom1, |
| gasteiger::GasteigerAtomTypeData const & | atom2, | ||
| BondName | bond_type | ||
| ) |
| AtomPropertiesOP core::chemical::deep_copy | ( | AtomProperties const & | source | ) |
| ResiduePropertiesOP core::chemical::deep_copy | ( | ResidueProperties const & | source | ) |
| void core::chemical::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.
References core::chemical::AtomTypeSet::atom_type_index(), and core::chemical::AtomTypeSet::n_atomtypes().
Referenced by enlarge_h_lj_wdepth(), core::scoring::etable::Etable::initialize_from_input_atomset(), and core::chemical::AtomTypeSet::legacy_command_line_post_processing().
| void core::chemical::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.
References enlarge_h_lj_wdepth(), and core::chemical::AtomTypeSet::n_atomtypes().
| void core::chemical::error_check_requested_adducts | ( | std::map< std::string, int > const & | add_map, |
| ResidueTypeCOPs const & | rsd_types | ||
| ) |
Make sure requested adducts exist in some residue.
Make sure requested adducts exist in some residue.
References core::chemical::ResidueTypeBase::defined_adducts().
Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().
| void core::chemical::error_check_requested_adducts | ( | std::map< std::string, int > const & | add_map, |
| ResidueTypeCOPs const & | rsd_types | ||
| ) |
Make sure any adducts requested actually exist.
Make sure requested adducts exist in some residue.
References core::chemical::ResidueTypeBase::defined_adducts().
Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().
| std::string core::chemical::expand_icoor_atom_name | ( | std::string | name, |
| MutableResidueType const & | rsd | ||
| ) |
References core::chemical::MutableResidueType::n_possible_residue_connections().
Referenced by core::chemical::SetICoor::apply().
| std::string const core::chemical::FA_STANDARD | ( | "fa_standard" | ) |
tag name for querying fullatom chemical type set.
| void core::chemical::fill_ideal_xyz_from_icoor | ( | core::chemical::MutableResidueType & | restype, |
| core::chemical::ResidueGraph const & | graph | ||
| ) |
Contains logic originally from read_topology_file()
References core::pose::motif::a(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::MutableICoorRecord::build_xyz(), core::kinematics::Stub::create_orthogonal(), core::chemical::MutableResidueType::has(), has_assigned_coords(), core::chemical::MutableResidueType::icoor(), core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::set_ideal_xyz(), protocols::fldsgn::potentials::sspot::spherical(), and TR().
Referenced by core::chemical::MutableResidueType::fill_ideal_xyz_from_icoor(), and core::chemical::ResidueDatabaseIO::read_residue_type_icoor().
| ResidueTypeCOP core::chemical::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
taken out of build_pose_as_is1 rsd_type should have all the atoms present in xyz try to minimize atoms missing from xyz
References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::has(), and core::chemical::ResidueType::natoms().
Referenced by core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names().
| void core::chemical::find_bonds_in_rings | ( | MutableResidueType & | res, |
| bool const | complex_ring | ||
| ) |
Determine which bonds are in rings, and set the BondRingness property of each.
References core::chemical::MutableResidueType::bond(), BondNotInRing, complex_ring_detection(), core::chemical::MutableResidueType::graph(), quick_ring_detection(), and core::chemical::Bond::ringness().
Referenced by core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), and reroot_restype().
| utility::vector1< VDs > core::chemical::find_chi_bonds | ( | MutableResidueType const & | restype | ) |
Find which bonds are rotatatable (chi) bonds Returns a list of four vds representing the chi.
Assumes:
References core::pose::motif::a(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_base(), core::chemical::MutableResidueType::atom_name(), protocols::match::upstream::b, core::chemical::MutableResidueType::bond(), core::chemical::MutableResidueType::bond_iterators(), BondInRing, core::chemical::element::C, core::pack::dunbrack::c, core::chemical::Atom::element_type(), core::chemical::MutableResidueType::graph(), core::chemical::element::H, core::chemical::Bond::order(), core::chemical::MutableResidueType::root_atom(), SingleBond, core::id::swap(), TR(), and TripleBondOrder.
Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().
| core::Real core::chemical::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.
The neighbor distance here is adjusted for rotatable bonds - It should be at least as large as the maximum neighbor distance in any torsional rotamer If the neighbor atom is not provided, the atom chosen will be a multiply-bonded heavy atom.
Assumes:
All ring bonds have been annotated
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_index(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bonded_neighbor_iterators(), calculate_rigid_matrix(), core::chemical::Atom::element_type(), core::sequence::end, core::chemical::element::H, core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::null_vertex, and TR().
Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().
| std::string core::chemical::fixup_patches | ( | std::string const & | string_in | ) |
Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":".
References PATCH_LINKER.
Referenced by core::chemical::ResidueTypeSet::has_name(), core::chemical::ResidueTypeSet::name_mapOP(), core::chemical::ResidueTypeSet::name_mapOP_write_locked(), and core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().
| std::string core::chemical::formatted_icoord_tree | ( | core::chemical::ResidueType const & | restype | ) |
Return a string representing the internal coordinates tree of this ResidueType.
References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::icoor(), and core::chemical::ResidueType::natoms().
Referenced by print_chis().
| std::string core::chemical::formatted_icoord_tree | ( | core::chemical::MutableResidueType const & | restype | ) |
Return a string representing the internal coordinates tree of this MutableResidueType (if any)
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::MutableResidueType::has(), core::chemical::MutableResidueType::icoor(), core::chemical::MutableResidueType::null_vertex, and core::chemical::MutableResidueType::root_atom().
| utility::vector1< std::string > const* core::chemical::generate_property_to_string_vector | ( | ) |
References ACETYL_SUGAR, ACETYLAMINO_SUGAR, ACETYLATED_NTERMINUS, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN, ADDUCT, ALDONIC_ACID, ALDOSE, ALIPHATIC, ALPHA_AA, ALPHA_SUGAR, AMINO_SUGAR, ARAMID, AROMATIC, BETA_AA, BETA_SUGAR, BRANCH_POINT, C1_MODIFIED, C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED, C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED, C_METHYLATED_SUGAR, CANONICAL_AA, CANONICAL_NUCLEIC, CARBOHYDRATE, CHARGED, COARSE, CYCLIC, D_AA, D_RNA, D_SUGAR, DEOXY_SUGAR, DIAMAGNETIC, DIMETHYLATED_CTERMINUS, DISULFIDE_BONDED, DNA, ELECTROPHILE, FRAGMENT, FURANOSE, GAMMA_AA, GLYCOSIDE, HEPTOSE, HEXOSE, HYDROPHOBIC, INVERTED_VIRTUAL_RESIDUE, KETOSE, L_AA, L_RNA, L_SUGAR, LIGAND, LIPID, LOWER_TERMINUS, LOWERTERM_CAP, LOWERTERM_TRUNC, MEMBRANE, META_ARAMID, METAL, METALBINDING, METHYLATED_CTERMINUS, N_METHYLATED, N_PROPERTIES, NEGATIVE_CHARGE, NONOSE, NUCLEOTIDE_DIPHOSPHATE, OCTOSE, OLIGOUREA, ORTHO_ARAMID, OXETOSE, OXIROSE, PARA_ARAMID, PARAMAGNETIC, PENTOSE, PEPTOID, PHOSPHATE, PHOSPHONATE, PHOSPHONATE_UPPER, PNA, POLAR, POLYMER, POSITIVE_CHARGE, POST_METHYLENE_META_ARAMID, POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, PROTEIN, PURINE, PYRANOSE, PYRIMIDINE, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, R_PEPTOID, RNA, S_PEPTOID, SC_ORBITALS, SEPTANOSE, SIALIC_ACID, SIDECHAIN_AMINE, SIDECHAIN_THIOL, SOLVENT, SPINLABEL, SRI, SULFATED_SUGAR, SULFOAMINO_SUGAR, SURFACE, TAUTOMER, TERMINUS, TERPENE, TETROSE, TNA, TP3, TRIAZOLE_LINKER, TRIOSE, UPPER_TERMINUS, UPPERTERM_CAP, UPPERTERM_TRUNC, URONIC_ACID, VIRTUAL_RESIDUE, VIRTUALIZABLE_BY_PACKER, VRT1, and WATER.
| std::map< std::string, ResidueProperty > const* core::chemical::generate_string_to_property_map | ( | ) |
References ACETYL_SUGAR, ACETYLAMINO_SUGAR, ACETYLATED_NTERMINUS, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN, ADDUCT, ALDONIC_ACID, ALDOSE, ALIPHATIC, ALPHA_AA, ALPHA_SUGAR, AMINO_SUGAR, ARAMID, AROMATIC, BETA_AA, BETA_SUGAR, BRANCH_POINT, C1_MODIFIED, C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED, C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED, C_METHYLATED_SUGAR, CANONICAL_AA, CANONICAL_NUCLEIC, CARBOHYDRATE, CHARGED, COARSE, CYCLIC, D_AA, D_RNA, D_SUGAR, DEOXY_SUGAR, DIAMAGNETIC, DIMETHYLATED_CTERMINUS, DISULFIDE_BONDED, DNA, ELECTROPHILE, FRAGMENT, FURANOSE, GAMMA_AA, GLYCOSIDE, HEPTOSE, HEXOSE, HYDROPHOBIC, INVERTED_VIRTUAL_RESIDUE, KETOSE, L_AA, L_RNA, L_SUGAR, LIGAND, LIPID, LOWER_TERMINUS, LOWERTERM_CAP, LOWERTERM_TRUNC, MEMBRANE, META_ARAMID, METAL, METALBINDING, METHYLATED_CTERMINUS, N_METHYLATED, NEGATIVE_CHARGE, NO_PROPERTY, NONOSE, NUCLEOTIDE_DIPHOSPHATE, OCTOSE, OLIGOUREA, ORTHO_ARAMID, OXETOSE, OXIROSE, PARA_ARAMID, PARAMAGNETIC, PENTOSE, PEPTOID, PHOSPHATE, PHOSPHONATE, PHOSPHONATE_UPPER, PNA, POLAR, POLYMER, POSITIVE_CHARGE, POST_METHYLENE_META_ARAMID, POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, PROTEIN, PURINE, PYRANOSE, PYRIMIDINE, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, R_PEPTOID, RNA, S_PEPTOID, SC_ORBITALS, SEPTANOSE, SIALIC_ACID, SIDECHAIN_AMINE, SIDECHAIN_THIOL, SOLVENT, SPINLABEL, SRI, SULFATED_SUGAR, SULFOAMINO_SUGAR, SURFACE, TAUTOMER, TERMINUS, TERPENE, TETROSE, TNA, TP3, TRIAZOLE_LINKER, TRIOSE, UPPER_TERMINUS, UPPERTERM_CAP, UPPERTERM_TRUNC, URONIC_ACID, VIRTUAL_RESIDUE, VIRTUALIZABLE_BY_PACKER, VRT1, and WATER.
| std::map< std::string, VariantType > const* core::chemical::generate_string_to_variant_map | ( | ) |
References A3B_HBS_POST, A3B_HBS_PRE, ACETYLATED_NTERMINUS_VARIANT, ACETYLATION, ADDUCT_VARIANT, ALDONIC_ACID_VARIANT, ALTERNATIVE_PROTONATION, BLOCK_STACK_ABOVE, BLOCK_STACK_BELOW, BULGE, C1_ACETYLAMINO_SUGAR, C1_AMINO_SUGAR, C1_BRANCH_POINT, C1_DEOXY_SUGAR, C1_METHYLATED_SUGAR, C1_PHOSPHATE, C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_SULFATED_SUGAR, C1_SULFOAMINO_SUGAR, C2_ACETYLAMINO_SUGAR, C2_AMINO_SUGAR, C2_BRANCH_POINT, C2_DEOXY_SUGAR, C2_KETOALDONIC_ACID, C2_METHYLATED_SUGAR, C2_PHOSPHATE, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_SULFATED_SUGAR, C2_SULFOAMINO_SUGAR, C3_ACETYLAMINO_SUGAR, C3_AMINO_SUGAR, C3_BRANCH_POINT, C3_DEOXY_SUGAR, C3_KETOALDONIC_ACID, C3_METHYLATED_SUGAR, C3_PHOSPHATE, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_SULFATED_SUGAR, C3_SULFOAMINO_SUGAR, C4_ACETYLAMINO_SUGAR, C4_AMINO_SUGAR, C4_BRANCH_POINT, C4_DEOXY_SUGAR, C4_KETOALDONIC_ACID, C4_METHYLATED_SUGAR, C4_PHOSPHATE, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C4_SULFATED_SUGAR, C4_SULFOAMINO_SUGAR, C5_ACETYLAMINO_SUGAR, C5_AMINO_SUGAR, C5_BRANCH_POINT, C5_DEOXY_SUGAR, C5_KETOALDONIC_ACID, C5_METHYLATED_SUGAR, C5_PHOSPHATE, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_SULFATED_SUGAR, C5_SULFOAMINO_SUGAR, C6_ACETYLAMINO_SUGAR, C6_AMINO_SUGAR, C6_BRANCH_POINT, C6_DEOXY_SUGAR, C6_KETOALDONIC_ACID, C6_METHYLATED_SUGAR, C6_PHOSPHATE, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_SULFATED_SUGAR, C6_SULFOAMINO_SUGAR, C7_ACETYLAMINO_SUGAR, C7_AMINO_SUGAR, C7_BRANCH_POINT, C7_DEOXY_SUGAR, C7_KETOALDONIC_ACID, C7_METHYLATED_SUGAR, C7_PHOSPHATE, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_SULFATED_SUGAR, C7_SULFOAMINO_SUGAR, C8_ACETYLAMINO_SUGAR, C8_AMINO_SUGAR, C8_BRANCH_POINT, C8_DEOXY_SUGAR, C8_KETOALDONIC_ACID, C8_METHYLATED_SUGAR, C8_PHOSPHATE, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C8_SULFATED_SUGAR, C8_SULFOAMINO_SUGAR, C9_ACETYLAMINO_SUGAR, C9_AMINO_SUGAR, C9_BRANCH_POINT, C9_DEOXY_SUGAR, C9_METHYLATED_SUGAR, C9_PHOSPHATE, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_SULFATED_SUGAR, C9_SULFOAMINO_SUGAR, C_METHYLAMIDATION, CA2_COORDINATION, CA_CONNECT, CA_CONNECT2, CA_CONNECT3, CA_CONNECT4, CA_CONNECT5, CA_CONNECT6, CA_CONNECT7, CARBOXYLATION, CENTROID_WITH_HA, CO2_COORDINATION, CTERM_AMIDATION, CTERM_CONNECT, CU2_COORDINATION, CUTPOINT_LOWER, CUTPOINT_UPPER, DEOXY_O2PRIME, DEPROTONATED, DIIODINATION, DIMETHYLATED_CTERMINUS_VARIANT, DIMETHYLATION, DISULFIDE, DY3_COORDINATION, FE2_COORDINATION, FE3_COORDINATION, FIVE_PRIME_END_OH, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PACKABLE_TRIPHOSPHATE, FIVE_PRIME_PHOSPHATE, FIVE_PRIME_RME_PHOSPHATE, FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE, FIVEPRIME_CAP, HBS_POST, HBS_PRE, HYDROXYLATION, HYDROXYLATION1, HYDROXYLATION2, LA3_COORDINATION, LOWER_TERMINUS_VARIANT, LOWERTERM_TRUNC_VARIANT, LU3_COORDINATION, METHYL_GLYCOSIDE, METHYLATED_CTERMINUS_VARIANT, METHYLATED_NTERM_VARIANT, METHYLATION, MG2_COORDINATION, MN2_COORDINATION, N_ACETYLATION, N_FORMYLATION, N_METHYLATION, NE2_CONNECT, NO_VARIANT, NTERM_CONNECT, 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, O_CONNECT, OD1_CONNECT, OD2_CONNECT, OE1_CONNECT, OE2_CONNECT, OG1_CONNECT, OG_CONNECT, OOP_POST, OOP_PRE, PHOSPHONATE_UPPER_VARIANT, PHOSPHORYLATION, PROTONATED, PROTONATED_N1, PROTONATED_N3, REPL_PHOSPHATE, REPLONLY, REPLS_BB, SC_BRANCH_POINT, SC_FRAGMENT, SG_CONNECT, SHOVE_BB, SIDECHAIN_CONJUGATION, SPECIAL_ROT, SULFATION, TB3_COORDINATION, THREE_PRIME_AZIDE, THREE_PRIME_DEOXY, THREE_PRIME_END_OH, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, THREE_PRIME_PACKABLE_PHOSPHATE, THREE_PRIME_PHOSPHATE, THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE, TM3_COORDINATION, TRIAZOLAMERC, TRIAZOLAMERN, TRIMETHYLATION, UPPER_CONNECTION_RNA, UPPER_TERMINUS_VARIANT, UPPERTERM_TRUNC_VARIANT, URONIC_ACID_VARIANT, VIRTUAL_BACKBONE_EXCEPT_C1PRIME, VIRTUAL_BASE, VIRTUAL_BASE_HEAVY_ATOM, VIRTUAL_BB, VIRTUAL_DNA_PHOSPHATE, VIRTUAL_METAL_CONJUGATION, VIRTUAL_NTERM, VIRTUAL_O2PRIME_HYDROGEN, VIRTUAL_PHOSPHATE, VIRTUAL_RESIDUE_VARIANT, VIRTUAL_RIBOSE, VIRTUAL_RNA_RESIDUE, VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, VIRTUAL_SIDE_CHAIN, YB3_COORDINATION, and ZN_CONNECT.
| utility::vector1< std::string > const* core::chemical::generate_variant_to_string_vector | ( | ) |
References A3B_HBS_POST, A3B_HBS_PRE, ACETYLATED_NTERMINUS_VARIANT, ACETYLATION, ADDUCT_VARIANT, ALDONIC_ACID_VARIANT, ALTERNATIVE_PROTONATION, BLOCK_STACK_ABOVE, BLOCK_STACK_BELOW, BULGE, C1_ACETYLAMINO_SUGAR, C1_AMINO_SUGAR, C1_BRANCH_POINT, C1_DEOXY_SUGAR, C1_METHYLATED_SUGAR, C1_PHOSPHATE, C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_SULFATED_SUGAR, C1_SULFOAMINO_SUGAR, C2_ACETYLAMINO_SUGAR, C2_AMINO_SUGAR, C2_BRANCH_POINT, C2_DEOXY_SUGAR, C2_KETOALDONIC_ACID, C2_METHYLATED_SUGAR, C2_PHOSPHATE, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_SULFATED_SUGAR, C2_SULFOAMINO_SUGAR, C3_ACETYLAMINO_SUGAR, C3_AMINO_SUGAR, C3_BRANCH_POINT, C3_DEOXY_SUGAR, C3_KETOALDONIC_ACID, C3_METHYLATED_SUGAR, C3_PHOSPHATE, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_SULFATED_SUGAR, C3_SULFOAMINO_SUGAR, C4_ACETYLAMINO_SUGAR, C4_AMINO_SUGAR, C4_BRANCH_POINT, C4_DEOXY_SUGAR, C4_KETOALDONIC_ACID, C4_METHYLATED_SUGAR, C4_PHOSPHATE, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C4_SULFATED_SUGAR, C4_SULFOAMINO_SUGAR, C5_ACETYLAMINO_SUGAR, C5_AMINO_SUGAR, C5_BRANCH_POINT, C5_DEOXY_SUGAR, C5_KETOALDONIC_ACID, C5_METHYLATED_SUGAR, C5_PHOSPHATE, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_SULFATED_SUGAR, C5_SULFOAMINO_SUGAR, C6_ACETYLAMINO_SUGAR, C6_AMINO_SUGAR, C6_BRANCH_POINT, C6_DEOXY_SUGAR, C6_KETOALDONIC_ACID, C6_METHYLATED_SUGAR, C6_PHOSPHATE, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_SULFATED_SUGAR, C6_SULFOAMINO_SUGAR, C7_ACETYLAMINO_SUGAR, C7_AMINO_SUGAR, C7_BRANCH_POINT, C7_DEOXY_SUGAR, C7_KETOALDONIC_ACID, C7_METHYLATED_SUGAR, C7_PHOSPHATE, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_SULFATED_SUGAR, C7_SULFOAMINO_SUGAR, C8_ACETYLAMINO_SUGAR, C8_AMINO_SUGAR, C8_BRANCH_POINT, C8_DEOXY_SUGAR, C8_KETOALDONIC_ACID, C8_METHYLATED_SUGAR, C8_PHOSPHATE, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C8_SULFATED_SUGAR, C8_SULFOAMINO_SUGAR, C9_ACETYLAMINO_SUGAR, C9_AMINO_SUGAR, C9_BRANCH_POINT, C9_DEOXY_SUGAR, C9_METHYLATED_SUGAR, C9_PHOSPHATE, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_SULFATED_SUGAR, C9_SULFOAMINO_SUGAR, C_METHYLAMIDATION, CA2_COORDINATION, CA_CONNECT, CA_CONNECT2, CA_CONNECT3, CA_CONNECT4, CA_CONNECT5, CA_CONNECT6, CA_CONNECT7, CARBOXYLATION, CENTROID_WITH_HA, CO2_COORDINATION, CTERM_AMIDATION, CTERM_CONNECT, CU2_COORDINATION, CUTPOINT_LOWER, CUTPOINT_UPPER, DEOXY_O2PRIME, DEPROTONATED, DIIODINATION, DIMETHYLATED_CTERMINUS_VARIANT, DIMETHYLATION, DISULFIDE, DY3_COORDINATION, FE2_COORDINATION, FE3_COORDINATION, FIVE_PRIME_END_OH, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PACKABLE_TRIPHOSPHATE, FIVE_PRIME_PHOSPHATE, FIVE_PRIME_RME_PHOSPHATE, FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE, FIVEPRIME_CAP, HBS_POST, HBS_PRE, HYDROXYLATION, HYDROXYLATION1, HYDROXYLATION2, LA3_COORDINATION, LOWER_TERMINUS_VARIANT, LOWERTERM_TRUNC_VARIANT, LU3_COORDINATION, METHYL_GLYCOSIDE, METHYLATED_CTERMINUS_VARIANT, METHYLATED_NTERM_VARIANT, METHYLATION, MG2_COORDINATION, MN2_COORDINATION, N_ACETYLATION, N_FORMYLATION, N_METHYLATION, N_VARIANTS, NE2_CONNECT, NTERM_CONNECT, 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, O_CONNECT, OD1_CONNECT, OD2_CONNECT, OE1_CONNECT, OE2_CONNECT, OG1_CONNECT, OG_CONNECT, OOP_POST, OOP_PRE, PHOSPHONATE_UPPER_VARIANT, PHOSPHORYLATION, PROTONATED, PROTONATED_N1, PROTONATED_N3, REPL_PHOSPHATE, REPLONLY, REPLS_BB, SC_BRANCH_POINT, SC_FRAGMENT, SG_CONNECT, SHOVE_BB, SIDECHAIN_CONJUGATION, SPECIAL_ROT, SULFATION, TB3_COORDINATION, THREE_PRIME_AZIDE, THREE_PRIME_DEOXY, THREE_PRIME_END_OH, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, THREE_PRIME_PACKABLE_PHOSPHATE, THREE_PRIME_PHOSPHATE, THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE, TM3_COORDINATION, TRIAZOLAMERC, TRIAZOLAMERN, TRIMETHYLATION, UPPER_CONNECTION_RNA, UPPER_TERMINUS_VARIANT, UPPERTERM_TRUNC_VARIANT, URONIC_ACID_VARIANT, VIRTUAL_BACKBONE_EXCEPT_C1PRIME, VIRTUAL_BASE, VIRTUAL_BASE_HEAVY_ATOM, VIRTUAL_BB, VIRTUAL_DNA_PHOSPHATE, VIRTUAL_METAL_CONJUGATION, VIRTUAL_NTERM, VIRTUAL_O2PRIME_HYDROGEN, VIRTUAL_PHOSPHATE, VIRTUAL_RESIDUE_VARIANT, VIRTUAL_RIBOSE, VIRTUAL_RNA_RESIDUE, VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, VIRTUAL_SIDE_CHAIN, YB3_COORDINATION, and ZN_CONNECT.
| ED core::chemical::get_bond | ( | MutableResidueType const & | res, |
| VD const & | source, | ||
| VD const & | target | ||
| ) |
References core::chemical::MutableResidueType::graph().
| utility::vector1< VD > core::chemical::get_connecting_atoms | ( | MutableResidueType const & | res, |
| ED const & | edge | ||
| ) |
References core::chemical::MutableResidueType::graph().
| utility::vector1< VD > core::chemical::get_connecting_atoms | ( | ResidueGraph const & | graph, |
| ED const & | edge | ||
| ) |
| Size core::chemical::get_connection_number | ( | std::string const & | name | ) |
Get the connection number from a string representing an CONNECT type (e.g. 4 from CONN4)
Referenced by core::chemical::MutableICoorRecord::build_xyz(), core::chemical::MutableICoorRecord::buildable(), correct_conn(), has_assigned_coords(), core::chemical::ICoorAtomID::ICoorAtomID(), core::chemical::MutableResidueType::set_icoor(), core::chemical::MutableResidueType::update_icoors_after_connection_deletion(), and core::chemical::MutableICoorRecord::xyz().
| AA core::chemical::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).
References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_dal, aa_dan, aa_dar, aa_das, aa_dcs, aa_dgn, aa_dgu, aa_dhi, aa_dil, aa_dle, aa_dly, aa_dme, aa_dph, aa_dpr, aa_dse, aa_dth, aa_dtr, aa_dty, aa_dva, aa_gln, aa_glu, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_val, na_lra, na_lrc, na_lrg, na_lur, na_rad, na_rcy, na_rgu, and na_ura.
Referenced by core::chemical::ChiralFlipNaming::apply(), and core::conformation::get_residue_from_name1().
| std::string core::chemical::get_element_color | ( | std::string const & | element | ) |
Referenced by core::chemical::ResidueTypeKinWriter::write_restype().
| AA core::chemical::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).
References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_dal, aa_dan, aa_dar, aa_das, aa_dcs, aa_dgn, aa_dgu, aa_dhi, aa_dil, aa_dle, aa_dly, aa_dme, aa_dph, aa_dpr, aa_dse, aa_dth, aa_dtr, aa_dty, aa_dva, aa_gln, aa_glu, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_val, na_lra, na_lrc, na_lrg, na_lur, na_rad, na_rcy, na_rgu, and na_ura.
Referenced by core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::scoring::P_AA::get_l_equivalent(), core::scoring::Ramachandran::get_l_equivalent(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::scoring::RamaPrePro::random_mainchain_torsions(), and setup_patch_atomic_charge_reassignments_from_commandline().
| utility::vector1< std::string > core::chemical::get_patch_names | ( | ResidueType const & | rsd_type | ) |
| ObjexxFCL::FArray2D_int core::chemical::get_residue_path_distances | ( | ResidueType const & | res | ) |
relies on class Graph to find all pairs shortest path information
References core::chemical::ResidueType::natoms(), and core::chemical::ResidueType::nbrs().
Referenced by core::chemical::ResidueType::define_mainchain_atoms(), and core::chemical::ResidueType::initialize_derived_data().
| utility::vector1< VariantType > core::chemical::get_terminal_varianttypes | ( | ) |
Get a list of those VariantTypes that affect termini.
References A3B_HBS_POST, A3B_HBS_PRE, ACETYLATED_NTERMINUS_VARIANT, C_METHYLAMIDATION, CTERM_CONNECT, CUTPOINT_LOWER, CUTPOINT_UPPER, FIVE_PRIME_END_OH, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PHOSPHATE, HBS_POST, HBS_PRE, LOWER_TERMINUS_VARIANT, LOWERTERM_TRUNC_VARIANT, METHYLATED_CTERMINUS_VARIANT, METHYLATED_NTERM_VARIANT, N_ACETYLATION, NTERM_CONNECT, OOP_POST, OOP_PRE, PHOSPHONATE_UPPER_VARIANT, THREE_PRIME_END_OH, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, THREE_PRIME_PACKABLE_PHOSPHATE, THREE_PRIME_PHOSPHATE, TRIAZOLAMERC, TRIAZOLAMERN, UPPER_TERMINUS_VARIANT, UPPERTERM_TRUNC_VARIANT, VIRTUAL_NTERM, and VIRTUAL_PHOSPHATE.
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Does a ResidueGraph have a given vertex descriptor?
Referenced by protocols::multistage_rosetta_scripts::NoFailDataMap::add(), protocols::abinitio::StructureStore::add(), protocols::rna::movers::RNAIdealizeMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::rna::movers::RNAIdealizeMover::add_bond_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::match::downstream::ClassicMatchAlgorithm::add_external_geom_sampler(), core::pose::datacache::ObserverCache::attach(), core::pose::datacache::ObserverCache::detach(), core::chemical::MutableResidueType::has(), protocols::mean_field::jagged_array< AAProb >::has_value(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::pose::datacache::ObserverCache::is_attached(), core::conformation::Conformation::jump_atom_id(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::reindex_AtomIDs(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::denovo_design::components::Segment::set_template_pose(), shortest_path(), and protocols::sewing::data_storage::SmartAssembly::to_pose().
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Does a ResidueGraph have a given edge descriptor?
| bool core::chemical::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?
References core::chemical::MutableResidueType::atom_vertex(), CONNECT, get_connection_number(), core::chemical::MutableResidueType::has(), core::chemical::MutableResidueConnection::icoor(), INTERNAL, core::chemical::MutableResidueType::lower_connect(), core::chemical::ResidueTypeBase::name(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::MutableResidueType::residue_connection(), string_to_icoord_type(), and core::chemical::MutableResidueType::upper_connect().
Referenced by fill_ideal_xyz_from_icoor().
| bool core::chemical::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.
References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::nheavyatoms(), core::chemical::orbitals::strip_whitespace(), and TR().
| std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID | ( | "hybrid_fa_standard_centroid" | ) |
tag name for querying hybrid fullatom+centroid chemical type set.
| bool core::chemical::is_aa_name_unknown | ( | std::string const & | name | ) |
Given aa three letter string, return true if it is an unknown aa.
References core::sequence::end, and name2aa().
Referenced by core::io::mmtf::make_current_group().
| bool core::chemical::is_canonical_beta3_aa | ( | AA const | aa | ) |
Given an enum type, return true if and only if it is a canonical beta-amino acid.
References first_beta3_aa, and last_beta3_aa.
| bool core::chemical::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.
References first_D_aa, and last_D_aa.
Referenced by core::chemical::rotamers::DunbrackRotamerLibrarySpecification::aa(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::scoring::P_AA::is_canonical_d_aminoacid(), core::scoring::Ramachandran::is_canonical_d_aminoacid(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), and setup_patch_atomic_charge_reassignments_from_commandline().
| bool core::chemical::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.
Given an enum type, return true if and only if it is a canonical L-amino acid.
References first_l_aa, and num_canonical_aas.
Referenced by protocols::nmr::pre::PREMover::apply(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), core::io::mmtf::make_current_group(), core::pack::task::operation::DesignRestrictions::parse_tag(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(), set_up_mapfile_reassignments_from_commandline(), and setup_patch_atomic_charge_reassignments_from_commandline().
| bool core::chemical::is_mainchain_torsion_also_ring_torsion | ( | ResidueType const & | res_type, |
| uint | torsion_index | ||
| ) |
Are these main-chain torsions also ring torsions?
References core::chemical::ResidueType::is_cyclic(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueType::n_nus(), and core::chemical::ResidueType::nu_atoms().
Referenced by protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), and core::pose::setup_dof_mask_from_move_map().
| bool core::chemical::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?
The use case is to see if the proton chi should flat or staggered with rotamers
References AromaticBond, core::chemical::MutableResidueType::bond(), core::chemical::MutableResidueType::bond_iterators(), core::chemical::Bond::bond_name(), core::chemical::MutableResidueType::chi_atom_vds(), DoubleBond, and SingleBond.
Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().
| utility::vector1< VD > core::chemical::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.
References core::chemical::MutableResidueType::lower_connect_atom(), core::chemical::MutableResidueType::lower_connect_id(), shortest_path(), core::chemical::MutableResidueType::upper_connect_atom(), and core::chemical::MutableResidueType::upper_connect_id().
Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
| MutableResidueTypeOP core::chemical::make_centroid | ( | ResidueType const & | res | ) |
Make a centroid version of the fullatom ResidueType passed in.
May return a nullptr if the conversion is not possible
This uses the same crude heuristics as in molfile_to_params That is, all heavy atoms and polar hydrogens are transfered over 1:1, and non-polar hydrogens are deleted.
Of particular note is that it makes no attempt to transfer things over into "Superatoms"
Current limitation: it cannot convert a ResidueType which has connections, if any of the ICOORs depend on deleted hydrogens.
Assumes:
Referenced by core::chemical::GlobalResidueTypeSet::attempt_readin(), core::util::generate_replacement_restype(), and core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline().
| MutableResidueTypeOP core::chemical::make_centroid | ( | MutableResidueType const & | res | ) |
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::ResidueTypeBase::atom_type_set(), CENTROID, CENTROID_t, FULL_ATOM_t, core::chemical::AtomTypeSet::has_atom(), INTERNAL, core::chemical::MutableResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name(), and TR().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().
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Convenience constructor.
References core::chemical::MutableResidueType::graph().
| void core::chemical::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.
Called by ChemicalManager at time of AtomTypeSet creation.
References core::chemical::AtomTypeSet::atom_type_index(), core::chemical::AtomTypeSet::has_atom(), and TR().
Referenced by core::chemical::ChemicalManager::create_atom_type_set().
| merge_residue_behavior core::chemical::mrb_from_name | ( | std::string const & | mrb | ) |
References mrb_do_not_merge, mrb_merge_w_next, and mrb_merge_w_prev.
Referenced by core::chemical::MergeBehaviorManager::read_merge_behaviors_from_database_file().
| MergeBehaviorManager::AtomRenamingMap core::chemical::mrb_map_from_correspondence | ( | std::string const & | correspondence | ) |
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map that converts string name to AA enum
References setup_name2aa().
Referenced by aa_from_name(), is_aa_name_unknown(), operator>>(), and setup_aa2name().
| std::string core::chemical::name_from_aa | ( | AA | aa | ) |
give a enum type and return the string name
References protocols::cluster::calibur::aa, aa2name(), and num_aa_types.
Referenced by protocols::noesy_assign::MethylNames::aa_name(), core::conformation::Residue::annotated_name(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::matdes::ClashCheckFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::scoring::ResidueExclParams::create_excl_info(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa(), protocols::dna::dna_base_partner(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::enzymes::get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), protocols::recon_design::get_candidate_AAs(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::noesy_assign::CrossPeakInfo::label_atom_name(), protocols::noesy_assign::label_atom_name(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::simple_filters::ResidueDepthFilter::make_context(), protocols::membrane::MPMutateRelaxMover::make_mutations(), protocols::tcr::match_template_and_target_sequence(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), operator<<(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SingleResidueDunbrackLibrary::operator==(), protocols::noesy_assign::MethylNameLibrary::operator[](), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), core::scoring::motif::Xfres::place_sidechain_in_pose(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::scoring::PointWaterPotential::read_pointwater_tables(), core::chemical::ResidueDatabaseIO::read_residue_type(), read_topology_file(), core::scoring::methods::MembraneEnvSmoothEnergy::representative_atom_name(), core::scoring::methods::EnvSmoothEnergy::representative_atom_name(), core::scoring::membrane::FaMPEnvSmoothEnergy::representative_atom_name(), core::pack::task::ResidueLevelTask_::restrict_absent_nas(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), protocols::simple_moves::MutateResidue::set_res_name(), core::scoring::fiber_diffraction::setup_centroid_scatter(), protocols::mean_field::RotProb::show(), protocols::mean_field::AAProb::show(), core::pose::rna::update_edge_hbond_numbers(), core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), and protocols::noesy_assign::Resonance::write_to_stream().
| bool core::chemical::nonadduct_variants_match | ( | ResidueTypeBase const & | res1, |
| ResidueTypeBase const & | res2 | ||
| ) |
Similar to variants_match(), but allows different adduct-modified states.
References ADDUCT_VARIANT, and variants_match_with_exceptions().
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map that converts one letter char to AA enum
References setup_oneletter2aa().
Referenced by aa_from_oneletter_code(), oneletter_code_specifies_aa(), and setup_aa2oneletter().
| char core::chemical::oneletter_code_from_aa | ( | AA | aa | ) |
give a enum type and return the string name
References protocols::cluster::calibur::aa, aa2oneletter(), and num_canonical_aas.
Referenced by protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::splice::Splice::apply(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), core::scoring::membrane::MPSpanInsertionEnergy::calc_span_score(), protocols::optimize_weights::IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpus(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::mean_field::AAMatrix::dump_transfac(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_oneletter_codes(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::design_opt::insert_point_mut_filter_vals(), protocols::matdes::insert_point_mut_filter_vals(), core::io::mmtf::make_current_group(), protocols::ddg::ddGMover::mutation_label(), core::scoring::methods::ProQ_Energy::profile_index_to_aa(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), protocols::loops::set_secstruct_from_dssp(), setup_patch_atomic_charge_reassignments_from_commandline(), core::fragment::SingleResidueFragData::steal(), protocols::multistate_design::PosType::to_string(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile(), protocols::noesy_assign::ResonanceList::write_talos_format(), and protocols::noesy_assign::Resonance::write_to_stream().
| bool core::chemical::oneletter_code_specifies_aa | ( | char | onelettercode | ) |
References oneletter2aa().
Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT::aas_to_keep(), core::conformation::Residue::annotated_name(), protocols::task_operations::JointSequenceOperation::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), protocols::protein_interface_design::movers::LoopLengthChange::parse_my_tag(), core::pack::task::operation::DesignRestrictions::parse_tag(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), core::sequence::MatrixScoringScheme::read_data(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), protocols::task_operations::ConservativeDesignOperation::skip_resid(), and core::sequence::MatrixScoringScheme::values_for_aa().
| bool core::chemical::operator!= | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
| AtomProperty & core::chemical::operator++ | ( | AtomProperty & | property | ) |
| ResidueProperty & core::chemical::operator++ | ( | ResidueProperty & | property | ) |
| VariantType & core::chemical::operator++ | ( | VariantType & | variant | ) |
| bool core::chemical::operator< | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
References core::chemical::ResConnID::conn_id_, and core::chemical::ResConnID::res_id_.
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const Orbital & | orbital | ||
| ) |
References core::conformation::membrane::out, and core::chemical::Orbital::print().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const AtomType & | atom_type | ||
| ) |
References core::conformation::membrane::out, and core::chemical::AtomType::print().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | output, |
| AtomProperties const & | object_to_output | ||
| ) |
References core::chemical::AtomProperties::show().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| Bond const & | bond | ||
| ) |
References core::conformation::membrane::out, and core::chemical::Bond::print().
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| std::ostream & core::chemical::operator<< | ( | std::ostream & | out, |
| Atom const & | atom | ||
| ) |
References core::conformation::membrane::out, and core::chemical::Atom::show().
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References core::chemical::Element::write().
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References core::chemical::ElectronConfiguration::write().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | output, |
| ResidueProperties const & | object_to_output | ||
| ) |
References core::chemical::ResidueProperties::show().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | output, |
| ResidueProperty const & | object_to_output | ||
| ) |
| std::ostream & core::chemical::operator<< | ( | std::ostream & | out, |
| TypeSetMode | mode | ||
| ) |
References core::conformation::membrane::out, and string_from_type_set_mode().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | os, |
| AA const & | aa | ||
| ) |
output operator for AA enum type
example usage: std::cout << aa_gly << std::endl;
References name_from_aa().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | out, |
| ICoordAtomIDType | type | ||
| ) |
References CONNECT, INTERNAL, core::conformation::membrane::out, POLYMER_LOWER, and POLYMER_UPPER.
| std::ostream & core::chemical::operator<< | ( | std::ostream & | output, |
| ResidueType const & | object_to_output | ||
| ) |
References core::chemical::ResidueType::show().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | output, |
| MutableResidueType const & | object_to_output | ||
| ) |
References core::chemical::MutableResidueType::show().
| bool core::chemical::operator== | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
|
inline |
References core::chemical::Element::read().
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inline |
References core::chemical::ElectronConfiguration::read().
| std::istream & core::chemical::operator>> | ( | std::istream & | is, |
| AA & | aa | ||
| ) |
input operator for AA enum type
read in a string name from a file or std::cin and directly convert it to an AA enum type, for example, std::cin >> AA. This will first check if the lookup map has been set up already. If the string name cannot be converted properly, it will flag the input stream as failure (e.g., istream.fail() is true) and set AA enum type to aa_unk.
References aa_unk, core::sequence::end, and name2aa().
| AdductMap core::chemical::parse_adduct_string | ( | utility::options::StringVectorOption & | add_vec | ) |
Convert input string to map of adducts->max usage.
Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().
| 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.
References protocols::cluster::calibur::aa, anc_grandparent, anc_greatgrandparent, anc_parent, core::simple_metrics::metrics::mean, protocols::hybridization::path, and tr().
Referenced by case_from_lines().
| utility::vector1< VariantType > core::chemical::pH_mode_exceptions | ( | ) |
check if user has set -pH_mode.
used to determine exceptions to PROTONATION/DEPROTONAT in variants_match.
References DEPROTONATED, and PROTONATED.
Referenced by core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), and variants_match().
| void core::chemical::pretty_print_atomicoor | ( | std::ostream & | out, |
| AtomICoor const & | start, | ||
| ResidueType const & | rsd_type, | ||
| core::Size | indent, | ||
| AtomMemoOP | memo | ||
| ) |
References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::atomno(), core::chemical::AtomICoor::built_atom(), CONNECT, core::chemical::AtomICoor::d(), core::chemical::ResidueType::has(), core::chemical::ResidueType::icoor(), INTERNAL, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), core::chemical::AtomICoor::phi(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::AtomICoor::stub_atom(), core::chemical::AtomICoor::stub_atom1(), and core::chemical::AtomICoor::theta().
Referenced by core::chemical::ResidueType::debug_dump_icoor(), core::conformation::Residue::fill_missing_atoms(), and pretty_print_atomicoor().
| void core::chemical::pretty_print_atomicoor | ( | std::ostream & | out, |
| ResidueType const & | rsd_type | ||
| ) |
| void core::chemical::pretty_print_atomicoor | ( | std::ostream & | out, |
| AtomICoor const & | start, | ||
| ResidueType const & | rsd_type, | ||
| core::Size | indent | ||
| ) |
References pretty_print_atomicoor().
| void core::chemical::print_chis | ( | std::ostream & | out, |
| ResidueType const & | res | ||
| ) |
Utility to examine chi output.
References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::chi_atoms(), formatted_icoord_tree(), core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueTypeBase::name(), and core::chemical::ResidueType::nchi().
| void core::chemical::print_chis | ( | std::ostream & | out, |
| MutableResidueType const & | res | ||
| ) |
Utility to examine chi output.
References core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::chi_atom_vds(), formatted_icoord_tree(), core::chemical::MutableResidueType::is_proton_chi(), core::chemical::ResidueTypeBase::name(), and core::chemical::MutableResidueType::nchi().
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static |
| void core::chemical::quick_ring_detection | ( | MutableResidueType & | res | ) |
| MutableResidueTypeOP core::chemical::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
Referenced by core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline(), core::chemical::GlobalResidueTypeSet::init_restypes_from_database(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), and read_topology_file().
| MutableResidueTypeOP core::chemical::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
References read_topology_file().
| MutableResidueTypeOP core::chemical::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
References read_topology_file().
| MutableResidueTypeOP core::chemical::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)
References protocols::abinitio::filename(), and read_topology_file().
| MutableResidueTypeOP core::chemical::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
Construct a ResidueType from a file. Example files are currently in main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ directory These files contain information about each basic ResidueType which can be patched to created various variant types.
The topology file (.params file) is formatted as follows:
The file may contain any number of lines. Blank lines and lines beginning with "#" are ignored. Each non-ignored line must begin with a string, a "tag", which describes a piece of data for the ResidueType. The tags may be given in any order, though they will be processed so that ATOM tag lines are read first.
Valid tags are: AA: Gives the element of the AA enumeration (src/core/chemical/AA.hh) that is appropriate for this residue type. This information is used by the knowledge-based potentials which already encode information specifically for proteins or nucleic acids, and is also used by the RotamerLibrary to retrieve the appropriate rotamer library. Provide "aa_unk" here for "unknown" if not dealing with a canonical amino or nucleic acid. E.g., "AA SER" from SER.params
ACT_COORD_ATOMS: Lists the atoms that define the "action coordinate" which is used by the fa_pair potential followed by the "END" token. E.g., "ACT_COORD_ATOMS OG END" from SER.params.
ADD_RING: Declares a ring within the residue, its index, its saturation type (optional) and the atoms that define it. E.g., " ADD_RING 1 AROMATIC CG CD1 CE1 CZ CE2 CD2" from TYR.params.
ADDUCT: Defines an adduct as part of this residue type giving: a) the name, b) the adduct atom name, c) the adduct atom type, d) the adduct mm type, e) the adduct partial charge, and the f) the distance, g) improper bond angle, and h) dihedral that describe how to build the adduct from the i) parent, i) grandparent, and j) great grandparent atoms. E.g., "ADDUCT DNA_MAJOR_GROOVE_WATER WN6 HOH H 0.0 -6.000000 44.000000 2.990000 N6 C6 C5" from ADE.params.
ATOM: Declare a new atom by name and list several of its properties. This line is column formatted. The atom's name must be in columns 6-9 so that "ATOM CA ..." declares a different atom from "ATOM CA ...". This is for PDB formatting. All atom names must be distinct, and all atom names must be distinct when ignoring whitespace ("CA " and " CA " could not coexist). After the atom name is read, the rest of the line is simply whitespace delimited. Next, the (Rosetta) atom type name is given (which must have been defined in the input AtomTypeSet), and then the mm atom type name is given (which must have been defined in the input MMAtomTypeSet). Finally, the charge for this atom is given, either as the next input or (ignoring the next input) the one after, if the "parse_charge" flag is on (whatever that is). E.g., "ATOM CB CH3 CT3 -0.27 0.000" from ALA.params.
ATOM_ALIAS: Add alternative name(s) for a given atom, for example to be used when loading a PDB file. This line is column formatted. The canonical Rosetta atom name should be in columns 12-15, with the alternative names coming in columns 17-20, 22-25, etc: "ATOM_ALIAS RRRR 1111 2222 3333 ..." As with the ATOM line, whitespace matters. and aliases must be unique with respect to each other and with canonical names, even when whitespace is ignored
BACKBONE_AA: Sets the "backbone_aa" for a particular residue, which can be used to template the backbone scoring (rama and p_aa_pp terms). For example, "BACKBONE_AA ILE" in the non-canonical 4,5-dihydroxyisoleucine params file tells Rosetta to use isoleucine's ramachandran map and p_aa_pp scoring for this noncanonical.
BASE_ANALOGUE: Sets the "base_analogue" for a particular residue, which can be used for sidechain/base specific features. For example, peptide nucleic acid versions of RGU have a sidechain that works JUST LIKE RGU's.
NA_ANALOGUE: Sets the "na_analogue" for a particular residue, which can be used in fragment assembly. For example, it is a REALLY good first approximation that 5-methyl-uridine (i.e., thymine-but-on-ribose) can work with fragments identified by na_ura.
BOND: Declares a bond between two atoms giving their names. This line is whitespace delimited. E.g., "BOND N CA" from ALA.params.
BOND_TYPE: Declares a bond between two atoms, giving their names, and also describing the chemical nature of the bond. (The BOND_TYPE line takes the place of a BOND line - do not specify both.) Standard SDF-style numeric descriptors are accepted. (1, 2, 3 for single, double, triple), along with text version SINGLE, DOUBLE, TRIPLE, UNK (unknown), PSEUDO (pseudo bond), ORBITAL, ARO, AMIDE, CARBOXY (for delocalized carboxylate) and DELOCALIZED. Currently UNK/PSEUDO are treated identically, as are ARO/AMIDE/CARBOXY/DELOCALIZED. See convert_to_BondName() in src/core/chemical/Bond.cc for details on parsing.
CHARGE: Declares a charge for a particular atom. Format CHARGE atom type value Currently valid types are FORMAL. (Partial charges are handled above.) E.g. "CHARGE OG2 FORMAL -1"
CHI: A misnomer for non-amino acids, declares a side-chain dihedral, its index, and the four atoms that define it. E.g., "CHI 2 CA CB CG CD1" from PHE.params.
CHI_ROTAMERS: Lists the chi mean/standard-deviation pairs that define how to build rotamer samples. This is useful for residue types which do not come with their own rotamer libraries. E.g., "CHI_ROTAMERS 2 180 15" from carbohydrates/to5-beta-D-Psip.params.
CONNECT: Declares that an inter-residue chemical bond exists from a given atom. E.g. "CONNECT SG" from CYD.params. NOTE: Connection order is assumed to be preserved between residue types: connection #2 on one residue type is assumed to be "the same" as connection #2 on another residue type, if the two residue types are going to be exchanged in the packer (as ALA might be swapped out for ARG). CONNECT tags are processed in the order they are listed in the input file. For polymeric residue types (e.g., proteins, DNA, RNA, saccharides) "LOWER_CONNECT" and "UPPER_CONNECT" should be listed before any additional CONNECT records. CONNECTs are assigned an index beginning after the LOWER_CONNECT and UPPER_CONNECT, if present. That is, if a topology file lists both a LOWER_CONNECT and an UPPER_CONNECT, the 1st CONNECT will we given the index 3.
CUT_BOND: Declares a previously-declared bond to be off-limits to the basic atom-tree construction logic (user-defined atom trees can be created which defy this declaration, if desired). This is useful in cases where the chemical graph contains cycles. E.g. "CUT_BOND O4' C1'" from URA.params.
FIRST_SIDECHAIN_ATOM: Gives the name of the first side-chain atom. All heavy atoms that were declared before the first side-chain atom in the topology file are considered backbone atoms (but not necessarily main-chain atoms). All heavy atoms after the first side-chain atom are considered side-chain atoms. Hydrogen atoms are either side-chain or backbone depending on the heavy atom to which they are bound. E.g., "FIRST_SIDECHAIN_ATOM CB" from SER.params.
IO_STRING: Gives the three-letter and one-letter codes that are used to read and write this residue type from and to PDB files, and to FASTA files. This tag is column formatted. Columns 11-13 are for the three-letter code. Column 15 is for the 1-letter code. E.g., "IO_STRING Glc Z".
INTERCHANGEABILITY_GROUP: Gives the name for the group of ResidueType objects that are functionally Interchangeable (but which may have different variant types). This information is used by the packer to discern what ResidueType to put at a particular position. If this tag is not given in the topology file, the three-letter code given by the IO_STRING tag is used instead.
ICOOR_INTERNAL: Describes the geometry of the residue type from internal coordinates giving a) the atom, b) the torsion, phi, in degrees c) the improper bond angle that is (180-bond angle) in degrees, theta, d) the bond length, d, in Angstroms e) the parent atom, f) the grand-parent, and g) the great-grandparent. The first three atoms in the file have a peculiar structure where: 1) at1 lists itself as its own parent, at2 as its grand parent, and at3 as its great-grandparent, 2) at2 lists at1 as its parent, itself as its grand parent, and at3 as its great-grandparent, and 3) at3 list at2 as its parent, at1 as its grand parent, and itself as its great-grandparent. The atoms "LOWER" and "UPPER" are given for polymeric residues to describe the ideal coordinate of the previous and next residues. For non-polymeric inter-residue connections, atoms "CONN#" should be given (e.g., CONN3 for the disulfide connection in CYD). The number for an inter-residue connection comes from the order in which the connection is declared in the file, and includes the LOWER_CONNECT and UPPER_CONNECT connections in this count (e.g., for CYD, there is a LOWER_CONNECT, and UPPER_CONNECT, and only a single CONNECT declaration, so the disulfide connection is the third connection). The order in which internal coordinate data for atoms are given, excepting the first three, must define a "tree" in that atom geometry must only be specified in terms of atoms whose geometry has already been specified. Improper dihedrals may be specified, where the great grandparent is not the parent atom of the grandparent but in these cases, the great grandparent does need to