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Rosetta
2019.07
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
|
Rosetta
2019.07
|
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) 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 | 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 | 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 < 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 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::shared_ptr < ResidueProperties > | ResiduePropertiesOP |
| typedef utility::pointer::shared_ptr < ResidueProperties const > | ResiduePropertiesCOP |
| 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::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 |
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 name, 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... | |
| ResidueTypeOP | apply_adducts_to_residue (ResidueType const &rsd, utility::vector1< bool > &add_mask) |
| Apply adducts to residue using a boolean mask. More... | |
| ResidueTypeOPs | 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") |
| 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 &output, AtomProperties const &object_to_output) |
| AtomProperty & | operator++ (AtomProperty &property) |
| 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 (ResidueType &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 (ResidueType &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 (ResidueType &res) |
| void | quick_ring_detection (ResidueType &res) |
| utility::vector1< VD > | get_connecting_atoms (ResidueType const &res, ED const &edge) |
| utility::vector1< VD > | get_connecting_atoms (ResidueGraph const &graph, ED const &edge) |
| ED | get_bond (ResidueType 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 (ResidueType 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, ResidueType 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") |
| void | reroot_restype (core::chemical::ResidueType &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 (ICoorAtomID const &stub, std::set< VD > const &assigned, core::chemical::ResidueType 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::ResidueType &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") |
| 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 (ResidueType 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, ResidueType const &rsd) |
| 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") |
| id::AtomID | atom_id_from_icoor_line (std::string const &name, ResidueType const &rsd) |
| helper fxn More... | |
| AtomIndices | define_mainchain_atoms (ResidueTypeOP rsd) |
| If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER. More... | |
| ResidueTypeOP | 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... | |
| ResidueTypeOP | 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... | |
| ResidueTypeOP | 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... | |
| ResidueTypeOP | 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... | |
| ResidueTypeOP | 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 | set_up_mapfile_reassignments_from_commandline (ResidueTypeOP 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... | |
| LightWeightResidueGraph | convert_residuetype_to_light_graph (ResidueType const &res) |
| void | rename_atoms (ResidueType &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 (ResidueType 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 (ResidueType 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 (ResidueType &res) |
| Apply molfile_to_params style partial charges to the ResidueType. More... | |
| ResidueTypeOP | make_centroid (ResidueType const &res) |
| Make a centroid version of the fullatom ResidueType passed in. 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) |
| 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()) |
| static basic::Tracer | tr ("core.chemical.ResidueType") |
| std::string | strip_whitespace (std::string const &name) |
| std::ostream & | operator<< (std::ostream &output, ResidueType const &object_to_output) |
| std::string | get_element_color (std::string const &element) |
| 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... | |
| void | print_chis (std::ostream &out, ResidueType 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 (ResidueType const &res1, ResidueType 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 (ResidueType const &res1, ResidueType const &res2) |
| Are these two residues patched in exactly the same way? More... | |
| bool | nonadduct_variants_match (ResidueType const &res1, ResidueType const &res2) |
| Similar to variants_match(), but allows different adduct-modified states. 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 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< 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 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.
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 name, return its enum type.
References core::sequence::end, and name2aa().
Referenced by core::chemical::ResidueType::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::ResidueType::backbone_aa(), core::chemical::ResidueType::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(), protocols::motifs::make_dna_mutations(), protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop(), core::chemical::ResidueType::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(), core::chemical::ResidueType::rotamer_aa(), 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::evolution::NucleotideMutation::apply(), protocols::task_operations::ThreadSequenceOperation::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_3_letter_codes_from_peptide_consensus_sequence(), 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::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().
| ResidueTypeOP 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::ResidueType::defined_adducts(), core::chemical::ResidueType::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().
| id::AtomID core::chemical::atom_id_from_icoor_line | ( | std::string const & | name, |
| ResidueType const & | rsd | ||
| ) |
helper fxn
References core::id::GLOBAL_BOGUS_ATOM_ID.
| 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 | ( | ResidueType 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::ResidueType::atom_iterators(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::graph(), core::chemical::ResidueType::name(), core::chemical::ResidueType::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.
|
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().
| std::string const core::chemical::COARSE_RNA | ( | "coarse_rna" | ) |
tag name for querying COARSE_RNA chemical type set.
| void core::chemical::complex_ring_detection | ( | ResidueType & | res | ) |
| LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph | ( | ResidueType const & | res | ) |
References protocols::forge::methods::add_vertex(), and core::chemical::ResidueType::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().
| ResidueTypeOPs 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::ResidueType::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 | ||
| ) |
| AtomIndices core::chemical::define_mainchain_atoms | ( | ResidueTypeOP | rsd | ) |
If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER.
References core::id::D, get_residue_path_distances(), protocols::sic_dock::scores::nbr, and tr().
Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), and read_topology_file().
| 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::ResidueType::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::ResidueType::defined_adducts().
Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().
| std::string core::chemical::expand_icoor_atom_name | ( | std::string | name, |
| ResidueType const & | rsd | ||
| ) |
References core::chemical::ResidueType::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::ResidueType & | restype, |
| core::chemical::ResidueGraph const & | graph | ||
| ) |
Contains logic originally from read_topology_file()
References core::pose::motif::a(), core::chemical::ResidueType::atom_name(), has_assigned_coords(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::set_ideal_xyz(), and TR().
Referenced by core::chemical::ResidueType::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 | ( | ResidueType & | res, |
| bool const | complex_ring | ||
| ) |
Determine which bonds are in rings, and set the BondRingness property of each.
References core::chemical::ResidueType::bond(), BondNotInRing, complex_ring_detection(), core::chemical::ResidueType::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(), and core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().
| utility::vector1< VDs > core::chemical::find_chi_bonds | ( | ResidueType 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::ResidueType::atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::atom_name(), protocols::match::upstream::b, core::chemical::ResidueType::bond(), core::chemical::ResidueType::bond_iterators(), BondInRing, core::chemical::element::C, core::pack::dunbrack::c, core::chemical::Atom::element_type(), core::chemical::ResidueType::graph(), core::chemical::element::H, core::chemical::Bond::order(), core::chemical::ResidueType::root_atom(), SingleBond, core::id::swap(), TR(), and TripleBondOrder.
Referenced by core::chemical::ResidueType::autodetermine_chi_bonds().
| core::Real core::chemical::find_nbr_dist | ( | ResidueType 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::ResidueType::atom(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_vertex(), core::chemical::ResidueType::bonded_neighbor_iterators(), calculate_rigid_matrix(), core::chemical::Atom::element_type(), core::sequence::end, core::chemical::element::H, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::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().
| 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, 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, TRIAZOLE_LINKER, TRIOSE, UPPER_TERMINUS, UPPERTERM_CAP, UPPERTERM_TRUNC, URONIC_ACID, VIRTUAL_RESIDUE, 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, 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, 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, TRIAZOLE_LINKER, TRIOSE, UPPER_TERMINUS, UPPERTERM_CAP, UPPERTERM_TRUNC, URONIC_ACID, VIRTUAL_RESIDUE, 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, 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, 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 | ( | ResidueType const & | res, |
| VD const & | source, | ||
| VD const & | target | ||
| ) |
References core::chemical::ResidueType::graph().
| utility::vector1< VD > core::chemical::get_connecting_atoms | ( | ResidueType const & | res, |
| ED const & | edge | ||
| ) |
References core::chemical::ResidueType::graph().
| utility::vector1< VD > core::chemical::get_connecting_atoms | ( | ResidueGraph const & | graph, |
| ED const & | edge | ||
| ) |
| 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::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 define_mainchain_atoms(), and core::chemical::ResidueType::update_derived_data().
|
inline |
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::ResidueType::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(), and protocols::sewing::data_storage::SmartAssembly::to_pose().
|
inline |
Does a ResidueGraph have a given edge descriptor?
| bool core::chemical::has_assigned_coords | ( | ICoorAtomID const & | stub, |
| std::set< VD > const & | assigned, | ||
| core::chemical::ResidueType const & | restype | ||
| ) |
Utility function for fill_ideal_xyz_from_icoor() – does this ICoorAtomID have all the dependancies filled?
References core::chemical::ICoorAtomID::atomno(), core::chemical::ICoorAtomID::CONNECT, core::chemical::ResidueType::has(), core::chemical::ResidueConnection::icoor(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::name(), core::chemical::ICoorAtomID::POLYMER_LOWER, core::chemical::ICoorAtomID::POLYMER_UPPER, core::chemical::ResidueType::residue_connection(), core::chemical::ICoorAtomID::type(), core::chemical::ResidueType::upper_connect(), and core::chemical::ICoorAtomID::vertex().
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().
| 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::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_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_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::pack::task::operation::DesignRestrictions::parse_tag(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), 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, |
| ResidueType 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::ResidueType::bond(), core::chemical::ResidueType::bond_iterators(), core::chemical::Bond::bond_name(), core::chemical::ResidueType::chi_atom_vds(), DoubleBond, and SingleBond.
Referenced by core::chemical::ResidueType::autodetermine_chi_bonds().
| ResidueTypeOP 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:
References core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_name(), core::chemical::Atom::atom_type_index(), core::chemical::ResidueType::atom_type_set(), CENTROID, CENTROID_t, core::chemical::ResidueType::clone(), FULL_ATOM_t, core::chemical::AtomTypeSet::has_atom(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::name(), and TR().
Referenced by core::chemical::GlobalResidueTypeSet::attempt_readin(), core::util::generate_replacement_restype(), and core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline().
| 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 | ) |
|
inline |
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::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), 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::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_3_letter_codes_from_peptide_consensus_sequence(), 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(), 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(), 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::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::membrane::FaMPEnvSmoothEnergy::representative_atom_name(), core::scoring::methods::EnvSmoothEnergy::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 | ( | ResidueType const & | res1, |
| ResidueType const & | res2 | ||
| ) |
Similar to variants_match(), but allows different adduct-modified states.
References ADDUCT_VARIANT, and variants_match_with_exceptions().
|
inline |
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(), 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_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::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().
|
inline |
References core::chemical::Element::write().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | out, |
| Atom const & | atom | ||
| ) |
References core::conformation::membrane::out, and core::chemical::Atom::show().
|
inline |
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 & | output, |
| ResidueType const & | object_to_output | ||
| ) |
References core::chemical::ResidueType::show().
| bool core::chemical::operator== | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
|
inline |
References core::chemical::Element::read().
|
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::task::ResidueLevelTask_::reset(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), 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_name(), core::chemical::AtomICoor::built_atom_vertex(), core::chemical::ICoorAtomID::CONNECT, core::chemical::AtomICoor::d(), core::chemical::ResidueType::has(), core::chemical::ResidueType::icoor(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::null_vertex, core::chemical::AtomICoor::phi(), core::chemical::ICoorAtomID::POLYMER_LOWER, core::chemical::ICoorAtomID::POLYMER_UPPER, core::chemical::AtomICoor::stub_atom(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::theta(), and core::chemical::ICoorAtomID::vertex().
Referenced by core::chemical::ResidueType::debug_dump_icoor(), core::conformation::Residue::fill_missing_atoms(), core::chemical::ResidueType::generate_atom_indices(), 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::ResidueType::name(), and core::chemical::ResidueType::nchi().
|
static |
| void core::chemical::quick_ring_detection | ( | ResidueType & | res | ) |
| ResidueTypeOP 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
References read_topology_file().
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(), and core::scoring::FACTSRsdTypeInfo::initialize_parameters().
| ResidueTypeOP 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().
| ResidueTypeOP 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().
| ResidueTypeOP 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().
| ResidueTypeOP 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.
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 be a child of the grandparent. E.g., "ICOOR_INTERNAL CB -122.000000 69.862976 1.516263 CA N C" from SER.params.
LOWER_CONNECT: For a polymer residue, declares which atom forms the "lower" inter-residue connection (chemical bond), i.e., the bond to residue i-1. E.g., "LOWER_CONNECT N" from SER.params.
LOWEST_RING_CONFORMER: For a cyclic residue, declares which ideal ring conformation is most stable by IUPAC name. There is no check in place for valid IUPAC conformer names; if the name is not found in the database, no lowest conformer will be set. E.g., "LOWEST_RING_CONFORMER 4C1" from to3-alpha-D-Glcp.params.
LOW_RING_CONFORMERS: For a cyclic residue, declares which ideal ring conformations are local minima/stable by IUPAC name. (If present, the LOWEST_RING_CONFORMER will automatically included to this subset within RingConformerSet.) There is no check in place for valid IUPAC conformer names; if the name is not found in the database, that conform- er will not be added to the subset. E.g., "LOW_RING_CONFORMERS O3B B14 3S1 5S1 2SO BO3 1S3 14B 1S5 B25 OS2 1C4" from to3-alpha-D-Glcp.params.
MAINCHAIN_ATOMS: This is a list of atom names that define the main chain. The main chain describes the linear connection of atoms from the lower-terminus to the upper-terminus in a residue. This is NOT synonymous with "backbone atoms". (Backbone atoms are any atoms NOT included in a side chain, as defined by FIRST_SIDECHAIN_ATOM. See above.) All main-chain atoms will necessarily be backbone atoms, but not all backbone atoms are main-chain atoms because some residues include rings and/or non-rotatable functional groups. For example, the carbonyl oxygen of an amino acid residue is a backbone atom but NOT a part of the main chain. If a topology file does not include a MAINCHAIN_ATOMS record, Rosetta will determine the main chain by finding the shortest path from lower terminus to upper terminus, which may be through any CUT_BONDs you have defined! Use of this tag is required for those residue types that ONLY come in LOWER_TERMINUS or UPPER_TERMINUS varieties, such as any residue type that serves exclusively as a "cap" for a larger polymer. E.g., "MAINCHAIN_ATOMS C1 C2 C3 C4 O4" from an aldohexopyranose topology file.
METAL_BINDING_ATOMS: For polymer residue types that can bind metals (METALBINDING property), this is a list of the atoms that can form a direct bond to the metal. For example, in ASP.params, it would read: "METAL_BINDING_ATOMS OD1 OD2" DISULFIDE_ATOM_NAME: For polymer residue types that can form disulfide bonds (SIDECHAIN_THIOL property), this is the atom it does so with. For example, in CYS.params, it would read: "DISULFIDE_ATOM_NAME SG"
NAME: Gives the name for this ResidueType. The name for each ResidueType must be unique within a ResidueTypeSet. It is not limited to three letters. E.g., "NAME SER" from SER.params.
NBR_ATOM: Declares the name of the atom which will be used to define the center of the residue for neighbor calculations. The coordinate of this atom is used along side the radius given in in the NBR_RADIUS tag. This atom should be chosen to not move during packing so that neighbor relationships can be discerned for an entire set of rotamers from the backbone coordinates from the existing residue. E.g., "NBR_ATOM CB" from SER.params.
NBR_RADIUS: Declares a radius that defines a sphere which, when centered on the NBR_ATOM, is guaranteed to contain all heavy atoms under all possible dihedral angle assignments (but where bond angles and lengths are considered ideal). This is used to determine which residues are close enough that they might interact. Only the interactions of those such residues are ever evaluated by the scoring machinery. E.g., "NBR_RADIUS 3.4473" from SER.params.
NCAA_ROTLIB_PATH: Gives the path to the rotamer library file to use for a non-canonical amino acid. E.g., "NCAA_ROTLIB_PATH E35.rotlib" from d-ncaa/d-5-fluoro-tryptophan.params See the ROTAMERS tag for a more general way of specifying how to build rotamers.
NCAA_ROTLIB_NUM_ROTAMER_BINS: Lists the number of rotamers and the number of bins for each rotamer. E.g., "NCAA_ROTLIB_NUM_ROTAMER_BINS 2 3 2" from d-ncaa/d-5-fluoro-tryptophan.params See the ROTAMERS tag for a more general way of specifying how to build rotamers.
NCAA_SEMIROTAMERIC: Indicates if a NCAA is semirotameric (this is hard coded for canonicals)
NCAA_ROTLIB_BB_TORSIONS: This is followed by a series of integers indicating which of the mainchain torsions are used for backbone-dependent rotamers in sampling and scoring. For example, in oliogureas, the line is "NCAA_ROTLIB_BB_TORSIONS 1 2 3", indicating that mainchain torsions 1, 2, and 3 (but not mainchain torsion 4 or the inter-residue torsion) are used for backbone-dependent rotamers. If not specified, all mainchain torsions except the final, inter-residue torsion are used. (For example, for alpha-amino acids, phi and psi, but not omega, are used, so "NCAA_ROTLIB_BB_TORSIONS 1 2" is implied and needs not be written out explicitly).
NET_FORMAL_CHARGE: The overall charge on this residue. This must be an integer, though it can be positive or negative.
NRCHI_START_ANGLE: The lower bound for non rotameric chi sampling (sometimes you don't want 0 or 180 to be minimum so you get both sides of these critical values; take this from the input file you used with MakeRotLib
NRCHI_SYMMETRIC: Indicates if the nonrotameric chi is symmetric (PHE); if absent it is assumed not (ASN)
NU: Declares an internal ring dihedral, its index, and the four atoms that define it. E.g., "NU 2 C1 C2 C3 C4 ".
NUMERIC_PROPERTY: Stores an arbitrary float value that goes along with an arbitrary string key in a ResidueType. No examples can be currently found in the database (10/13). E.g., "NUMERIC_PROPERTY twelve 12.0" would be a way to store the number "12.0" with the key "twelve".
ORIENT_ATOM: Describes how to orient rotamers onto an existing residue either by orienting onto the NBR_ATOM atom, or by using the more complicated (default) logic in ResidueType::select_orient_atoms. There are two options here: "ORIENT_ATOM NBR" (orient onto NBR_ATOM) and "ORIENT_ATOM DEFAULT". If this tag is not given in the topology file, then the default behavior is used. E.g., "SET_ORIENT_ATOM NBR" from SC_Fragment.txt
PDB_ROTAMERS: Gives the file name that describes entire-residue rotamers which can be used in the packer to consider alternate conformations for a residue. This is commonly used for small molecules. See the ROTAMERS tag for a more general way of specifying how to build rotamers.
PROPERTIES: Adds a given set of property strings to a residue type. E.g., "PROPERTIES PROTEIN AROMATIC SC_ORBITALS" from TYR.params.
PROTON_CHI: Declares a previously-declared chi angle to be a "proton chi" and describe how this dihedral should be sampled by code that takes discrete sampling of side-chain conformations. The structure of these samples is as follows: First the word "SAMPLES" is given. Next the number of samples should be given. Next a list of dihedral angles, in degrees, should be given. Next, the word "EXTRA" is given. Next the number of extra samples is given. Finally, a list of perturbations angles, in degrees, is given. In cases where extra rotamers are requested (e.g., with the -ex2 flag), then the listed samples are are perturbed +/- the listed perturbations. E.g., "PROTON_CHI 2 SAMPLES 18 0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 EXTRA 0" from SER.params.
RAMA_PREPRO_FILENAME: Specify mainchain torsion potential to be used for this ResidueType when scoring with the rama_prepro score term. Two strings follow. The first is the filename for general scoring, and the second is the filename for scoring in the special case of this residue occurring before a proline residue.
RAMA_PREPRO_RESNAME: The name of the amino acid as listed in the rama_prepro scoring table file in the database. If not specified, the amino acid name is used.
REMAP_PDB_ATOM_NAMES: When reading in a PDB, attempt to match the input atoms for this residue based on elements and estimated connectivity, rather than atom names. (Connectivity by CONECT lines is ignored.) This only applies to input poses, and not to individually loaded residues, e.g. from the PDB_ROTAMERS line.
ROTAMER_AA: Sets the "rotamer_aa" for a particular residue, which can be used to describe to the RotamerLibrary what amino acid to mimic for the sake of building rotamers. E.g., "ROTAMER_AA SER" See the ROTAMERS tag for a more general way of specifying how to build rotamers.
ROTAMERS: Sets the rotamer generation to a given type. The line should be formatted as "ROTAMERS <TAG> <optional data>", where <TAG> specifies what sort of rotamer library to build for this residue, and <optional data>=""> is type-specific data describing how to build. E.g. "ROTAMERS DUNBRACK SER" will cause Serine-like Dunbrack rotamers to be used for this residue type, and "ROTAMERS PDB /path/to/ligand.conf.pdb" will cause the rotamer library to be read from the PDB file "/path/to/ligand.conf.pdb" Currently the following types are known (more may be added):
STRING_PROPERTY: Stores an arbitrary string value with a given string key. No example can be currently found in the database (10/13). A valid case would be "STRING_PROPERTY count twelve" which could store the string "twelve" for the key "count".
TYPE: States whether this is a polymeric or ligand residue type. E.g., "TYPE POLYMER" or "TYPE LIGAND" which adds either "POLYMER" or "LIGAND" properties to this residue type.
UPPER_CONNECT: For a polymer residue, declares which atom forms the "upper" inter-residue connection (chemical bond), i.e., the bond to residue i+1. E.g., "UPPER_CONNECT C" from SER.params.
VARIANT: Declares this residue type to have a particular variant type. Variant types are used by the packer to determine which ResidueTypes are compatible with a given starting residue. Variants are similar to properties, except that the packer does not restrict itself to residue types that have the same set of properties. Variant information is also used by the residue-type-patching system to avoid applying patches to certain residue types. E.g., "VARIANT DISULFIDE". from CYD.params.
VIRTUAL_SHADOW: Declares the first atom as a shadower of the second atom, implying that the atoms ought to be restrained to lie directly on top of each other. E.g. "VIRTUAL_SHADOW NV N" from PRO.params. Currently, the cart_bonded and ring_close energy terms are the only energy terms that enforce this.
References aa_gly, aa_ser, aa_thr, apply_symm_gly_corrections(), convert_to_BondName(), define_mainchain_atoms(), detect_ld_chirality_from_polymer_residue(), FULL_ATOM_t, core::simple_metrics::metrics::mean, name_from_aa(), protocols::hybridization::path, protocols::cluster::calibur::rotate(), set_up_mapfile_reassignments_from_commandline(), setup_atom_type_reassignments_from_commandline(), setup_atomic_charge_reassignments_from_commandline(), setup_icoor_reassignments_from_commandline(), core::kinematics::Stub::spherical(), core::chemical::orbitals::strip_whitespace(), and tr().
Referenced by read_topology_file().
| void core::chemical::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.
References core::sequence::end.
Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), and core::chemical::ResidueType::finalize().
| void core::chemical::rename_atoms | ( | ResidueType & | 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.)
References core::chemical::ResidueType::atom(), core::chemical::Atom::element_type(), core::chemical::ResidueType::graph(), core::chemical::Atom::name(), core::chemical::ResidueType::remap_pdb_atom_names(), core::id::to_string(), and TR().
Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().
| void core::chemical::reroot_restype | ( | core::chemical::ResidueType & | 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.
Doing a depth first search here because that's what molfile_to_params.py does: "Protein residues appear to go depth first, so that all chi angles ride on each other." RM: Doing a breadth first search would likely result in a shallower tree, but with possibly different behavior on how ring atom trees are built.
Note that updating the ICOOR records will also update the atom_base values. ... Which has the knock-on effect of possibly invalidating the chi values. The validity of the chis will be checked, and if the new icoord tree has invalidated them, they will be re-assigned.
Assumes:
References core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::autodetermine_chi_bonds(), core::chemical::ResidueType::chi_atom_vds(), core::id::D, core::chemical::ResidueType::has(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), core::id::PHI, core::chemical::ResidueType::set_icoor(), core::id::THETA, and TR().
Referenced by core::chemical::ResidueType::assign_internal_coordinates().
| ResidueTypeSelectorSingleOP core::chemical::residue_selector_single_from_line | ( | std::string const & | line | ) |
create a singe ResidueTypeSelector from an input line.
References protocols::cluster::calibur::aa, and update_ResidueType_enum_files::properties.
Referenced by core::chemical::ResidueTypeSelector::add_line().
| std::string core::chemical::residue_type_all_patches_name | ( | ResidueType const & | rsd_type | ) |
helper function, returns the name of all added patches
References core::chemical::ResidueType::name(), and PATCH_LINKER.
Referenced by core::util::add_covalent_linkage_helper(), core::chemical::ResidueTypeFinder::filter_all_patch_names(), get_patch_names(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper().
| std::string core::chemical::residue_type_base_name | ( | ResidueType const & | rsd_type | ) |
helper function, returns the base residue name prior to any patching
References protocols::vip::base_name(), core::chemical::ResidueType::name(), and PATCH_LINKER.
Referenced by core::util::add_covalent_linkage_helper(), core::chemical::ResidueTypeFinder::append_relevant_pdb_components(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), core::chemical::ResidueTypeFinder::filter_by_residue_type_base_name(), core::chemical::ResidueTypeFinder::fixes_interchangeability_group(), core::chemical::ResidueTypeFinder::fixes_name3(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeFinder::get_possible_base_unpatchable_residue_types(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), and core::pose::Pose::virtual_to_real().
| bool core::chemical::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.
References AromaticBond, core::chemical::Atom::element_type(), and protocols::hybridization::t.
Referenced by rosetta_retype_fullatom().
| void core::chemical::rosetta_recharge_fullatom | ( | ResidueType & | res | ) |
Apply molfile_to_params style partial charges to the ResidueType.
These partial charges are based off of the Rosetta atom type, adjusted such that the net partial charge is equal to the net formal charge.
These charges are almost certainly dodgy. If you have any other source of partial charges that are at all reasonable, you probably want to consider those instead.
Assumes:
References core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_type_set(), core::chemical::Atom::charge(), core::chemical::Atom::formal_charge(), core::chemical::ResidueType::graph(), core::chemical::ResidueType::name(), and TR().
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(), and core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().
| void core::chemical::rosetta_retype_fullatom | ( | ResidueType & | restype, |
| bool | preserve | ||
| ) |
Reassign Rosetta atom types based on the current fullatom heuristics.
If preserve is true, only retype those atoms which have an atom_type_index of zero.
The logic here comes from molfile_to_params.py Which is itself based on Rosetta++ ligand_ns.cc set_rosetta_atom_types(), and has been validated against the Meiler and Baker 2006 cross docking test set assignments.
I'm not saying the logic is good, but it's the logic we're using.
This function assumes that:
If preserve is true, only retype those atoms which have an atom_type_index of zero.
References core::pose::motif::a(), AromaticBond, core::chemical::Atom::atom_type_index(), core::chemical::ResidueType::atom_type_set(), core::chemical::element::B, core::chemical::element::Br, core::chemical::element::C, core::chemical::element::Ca, core::chemical::element::Cl, core::chemical::element::Co, core::chemical::element::Cu, DoubleBond, core::chemical::Atom::element_type(), core::chemical::element::F, core::chemical::element::Fe, core::chemical::ResidueType::graph(), core::chemical::element::H, core::chemical::AtomTypeSet::has_atom(), core::chemical::element::I, core::chemical::element::K, core::chemical::element::Mg, core::chemical::element::N, core::chemical::element::Na, core::chemical::element::name_from_elements(), core::chemical::element::O, core::chemical::element::P, retype_is_aromatic(), core::chemical::element::S, core::chemical::ResidueType::set_atom_type(), SingleBond, core::chemical::ResidueType::smallest_ring_size(), protocols::hybridization::t, TripleBond, and core::chemical::element::Zn.
Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().
| core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line | ( | ) |
Return a constant access pointer to the ResidueTypeSet specified by the command-line options.
Referenced by protocols::simple_filters::StructureSimilarityEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::boinc::boincOutputFilter(), protocols::denovo_design::construct_dummy_pose(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::hotspot_hashing::StubGenerator::getStubByName(), protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line(), and protocols::comparative_modeling::poses_from_cmd_line().
| void core::chemical::set_up_mapfile_reassignments_from_commandline | ( | ResidueTypeOP | rsd | ) |
Certain commandline flags override the default RamaPrePro maps used by the 20 canonical amino acids. This function applies those overrides.
References is_canonical_L_aa_or_gly().
Referenced by read_topology_file().
| utility::vector1< std::string > core::chemical::setup_aa2name | ( | ) |
setup the vector that maps AA enum to string name
References name2aa(), and num_aa_types.
Referenced by aa2name().
| utility::vector1< char > core::chemical::setup_aa2oneletter | ( | ) |
setup the vector that maps AA enum to one letter char
References num_aa_types, and oneletter2aa().
Referenced by aa2oneletter().
| void core::chemical::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 | ||
| ) |
References tr(), and type_set_mode_from_string().
Referenced by read_topology_file().
| void core::chemical::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 | ||
| ) |
References tr(), and type_set_mode_from_string().
Referenced by read_topology_file().
| void core::chemical::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 | ||
| ) |
References tr(), and type_set_mode_from_string().
Referenced by read_topology_file().
| std::map< std::string, AA > core::chemical::setup_name2aa | ( | ) |
setup the map that converts string name to AA enum
References aa_ala, aa_arg, aa_asn, aa_asp, aa_b3a, aa_b3c, aa_b3cisACHC, aa_b3cisACPC, aa_b3d, aa_b3e, aa_b3f, aa_b3g, aa_b3h, aa_b3i, aa_b3k, aa_b3l, aa_b3m, aa_b3n, aa_b3p, aa_b3q, aa_b3r, aa_b3s, aa_b3t, aa_b3transACPC, aa_b3v, aa_b3w, aa_b3y, 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_gly, aa_h2o, 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_unp, aa_val, aa_vrt, na_ade, na_cyt, na_gua, na_rad, na_rcy, na_rgu, na_thy, na_ura, ou3_aib, ou3_ala, ou3_arg, ou3_asn, ou3_asp, ou3_cys, ou3_gln, ou3_glu, ou3_gly, ou3_his, ou3_ile, ou3_leu, ou3_lys, ou3_met, ou3_phe, ou3_pro, ou3_ser, ou3_thr, ou3_trp, ou3_tyr, and ou3_val.
Referenced by name2aa().
| std::map< char, AA > core::chemical::setup_oneletter2aa | ( | ) |
setup the map the converts one letter char to AA enum
References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_gln, aa_glu, aa_gly, aa_h2o, 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_unp, aa_val, aa_vrt, na_ade, na_cyt, na_gua, na_rad, na_rcy, na_rgu, na_thy, and na_ura.
Referenced by oneletter2aa().
| void core::chemical::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
References core::chemical::ResidueType::aa(), aa_from_name(), core::chemical::ResidueType::add_property(), get_L_equivalent(), is_canonical_D_aa(), is_canonical_L_aa_or_gly(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::name3(), oneletter_code_from_aa(), tr(), and type_set_mode_from_string().
Referenced by case_from_lines().
| bool core::chemical::sort_patchop_by_name | ( | PatchOP | p, |
| PatchOP | q | ||
| ) |
| std::string core::chemical::string_from_type_set_mode | ( | TypeSetMode | mode | ) |
References CENTROID, CENTROID_ROT, CENTROID_ROT_t, CENTROID_t, COARSE_RNA, COARSE_RNA_t, DEFAULT_t, FA_STANDARD, FULL_ATOM_t, HYBRID_FA_STANDARD_CENTROID, HYBRID_FA_STANDARD_CENTROID_t, INVALID_t, and TR().
Referenced by operator<<(), protocols::features::ResidueTypesFeatures::report_features(), core::chemical::ChemicalManager::residue_type_set(), core::util::switch_to_centroid_rot_set(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and core::io::serialization::write_binary().
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Referenced by core::chemical::ResidueType::add_atom(), core::chemical::ResidueType::add_atom_alias(), core::chemical::ResidueType::add_orbital(), core::chemical::ResidueType::delete_atom(), core::chemical::ResidueType::delete_atom_alias(), core::chemical::ResidueType::generate_atom_indices(), and core::chemical::ResidueType::operator=().
| std::string core::chemical::tag_from_line | ( | std::string const & | line | ) |
handy function, return the first word from a line
Referenced by case_from_lines(), core::chemical::Metapatch::read_file(), and core::chemical::Patch::read_file().
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Referenced by add_atom_type_set_parameters_from_command_line(), core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSetCache::add_residue_type(), core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), apply_adducts_to_residue(), core::chemical::ResidueTypeFinder::apply_basic_filters(), core::chemical::ResidueTypeFinder::apply_filters_after_patches(), core::chemical::ResidueTypeFinder::apply_patches_recursively(), core::chemical::ResidueTypeFinder::apply_preferences_and_discouragements(), core::chemical::ICoorAtomID::atom_id(), core::chemical::ResidueTypeSet::atom_type_set(), core::chemical::PoseResidueTypeSet::atom_type_set(), core::chemical::GlobalResidueTypeSet::attempt_readin(), calculate_rigid_matrix(), core::chemical::ChemicalManager::create_residue_type_set(), core::chemical::PoseResidueTypeSet::element_set(), core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline(), fill_ideal_xyz_from_icoor(), core::chemical::ResidueTypeFinder::filter_all_patch_names(), core::chemical::ResidueTypeFinder::filter_all_properties(), core::chemical::ResidueTypeFinder::filter_all_variants_matched(), core::chemical::ResidueTypeFinder::filter_by_aa(), core::chemical::ResidueTypeFinder::filter_by_base_property(), core::chemical::ResidueTypeFinder::filter_by_interchangeability_group(), core::chemical::ResidueTypeFinder::filter_by_name1(), core::chemical::ResidueTypeFinder::filter_by_name3(), core::chemical::ResidueTypeFinder::filter_by_residue_type_base_name(), core::chemical::ResidueTypeFinder::filter_disallow_properties(), core::chemical::ResidueTypeFinder::filter_disallow_variants(), core::chemical::ResidueTypeFinder::filter_special_cases(), find_chi_bonds(), find_nbr_dist(), core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names(), core::chemical::rings::RingConformerSet::get_ideal_conformer_by_CP_parameters(), core::chemical::rings::RingConformerSet::get_ideal_conformer_from_nus(), core::chemical::Bond::GetMaximumElectrons(), core::chemical::Bond::GetMinimumElectrons(), core::chemical::Bond::GetNumberOfElectrons(), core::chemical::Bond::GetSDAltFileID(), core::chemical::Bond::GetSDFileID(), core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet(), core::chemical::ResidueProperties::has_property(), heavy_atom_names_match(), core::chemical::ICoorAtomID::ICoorAtomID(), core::chemical::GlobalResidueTypeSet::init_patches_from_database(), core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline(), core::chemical::GlobalResidueTypeSet::init_restypes_from_database(), core::chemical::rings::is_atom_axial_or_equatorial_to_ring(), core::chemical::Atom::is_fake(), core::chemical::ResidueProperties::is_variant_type(), core::chemical::GlobalResidueTypeSet::lazy_load_base_type(), core::chemical::GlobalResidueTypeSet::load_exclude_pdb_component_ids(), core::chemical::GlobalResidueTypeSet::load_pdb_component(), core::chemical::GlobalResidueTypeSet::load_residue_types_from_sql_database(), make_centroid(), core::chemical::PoseResidueTypeSet::mm_atom_type_set(), modify_atom_properties_from_command_line(), core::chemical::PoseResidueTypeSet::orbital_type_set(), core::chemical::GlobalResidueTypeSet::params_files_from_commandline(), protocols::recces::pose_setup_from_file(), core::chemical::carbohydrates::read_codes_and_roots_from_database_file(), core::chemical::rings::read_conformers_from_database_file_for_ring_size(), core::chemical::carbohydrates::read_linkage_conformers_from_database_file(), core::chemical::MergeBehaviorManager::read_merge_behaviors_from_database_file(), core::chemical::carbohydrates::read_nomenclature_table_from_database_file(), core::chemical::carbohydrates::read_ring_sizes_and_morphemes_from_database_file(), core::chemical::carbohydrates::read_short_names_to_iupac_format_string(), protocols::recces::recces_pose_setup(), rename_atoms(), reroot_restype(), rosetta_recharge_fullatom(), core::chemical::ResidueProperties::set_variant_type(), core::chemical::Bond::SetSDFType(), core::chemical::RerootRestypeVisitor::start_vertex(), and string_from_type_set_mode().
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Referenced by core::chemical::ResidueType::add_actcoord_atom(), core::chemical::ResidueType::add_cut_bond(), core::chemical::AtomTypeSet::add_parameters_from_file(), core::chemical::PatchCase::apply(), core::chemical::Patch::apply(), core::chemical::NCAARotLibPath::apply(), core::chemical::NCAARotLibBBTorsions::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::ResidueType::assign_internal_coordinates(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_vertex(), core::chemical::ResidueType::autodetermine_chi_bonds(), core::chemical::AtomTypeSet::clone_atom_types_from_commandline(), core::chemical::ResidueType::debug_dump_icoor(), core::chemical::ResidueType::delete_child_proton(), core::chemical::ResidueType::dump_vd_info(), core::chemical::ResidueType::generate_atom_indices(), patch_operation_from_patch_file_line(), core::chemical::ResidueType::print_bondangles(), core::chemical::ResidueType::print_dihedrals(), core::chemical::ResidueType::print_pretty_path_distances(), core::chemical::Metapatch::read_file(), core::chemical::ElementSet::read_file(), core::chemical::MMAtomTypeSet::read_file(), core::chemical::Patch::read_file(), core::chemical::AtomTypeSet::read_file(), core::chemical::ResidueType::report_adducts(), core::chemical::ResidueType::set_atom_base(), core::chemical::ResidueType::set_atom_type(), core::chemical::ResidueType::set_icoor_private(), core::chemical::ResidueType::set_lower_connect_atom(), core::chemical::ResidueType::set_upper_connect_atom(), setup_patch_atomic_charge_reassignments_from_commandline(), and protocols::vip::VIP_Mover::VIP_Mover().
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