 |
Rosetta Core
2014.16.56682
|
|
Rosetta Core
2014.16.56682
|
Namespaces | |
| carbohydrates | |
| gasteiger | |
| orbitals | |
| rna | |
| sdf | |
Classes | |
| class | AcceptorAtomFilter |
| The filter responsible for obtaining all acceptor atoms. More... | |
| class | AddAtom |
| add an atom to ResidueType More... | |
| class | AddBond |
| add a bond to 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 | 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 | AppendInterchangeabilityGroup_String |
| Append a string to the existing interchangeability_group string for a ResidueType. 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 |
| basic chemical atom More... | |
| class | AtomICoor |
| A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More... | |
| class | AtomType |
| basic atom type More... | |
| class | AtomTypeDatabaseIO |
| class | AtomTypeSet |
| a set of AtomTypes More... | |
| class | AutomorphismIterator |
| Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations. More... | |
| class | Bond |
| basic chemical Bond More... | |
| class | ChemicalManager |
| a class managing different sets of atom_type_set and residue_type_set More... | |
| class | DeleteAtom |
| delete an atom 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 | ElectronConfiguration |
| describes the electron configuration of atoms More... | |
| class | Element |
| stores element properties More... | |
| class | ElementSet |
| A set of Bcl Elements. 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 | MMAtomType |
| Basic MM atom type. More... | |
| class | MMAtomTypeSet |
| A set of MMAtomTypes. 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 | PrependMainchainAtom |
| add a mainchain atom before the first mainchain atom 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 | 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 | ResidueConnection |
| A simple class marking atoms at inter-residue connections. More... | |
| class | ResidueDatabaseIO |
| class | ResidueLoader |
| class | ResidueLoaderCreator |
| class | ResidueLoaderOptions |
| class | ResidueLoaderOptionsCreator |
| class | ResidueSelector |
| A class picking out a subset of ResidueType by multiple criteria. More... | |
| class | ResidueSelectorSingle |
| A base class for defining a ResidueSelector by a single criterion. More... | |
| class | ResidueType |
| A class for defining a type of residue. More... | |
| class | ResidueTypeKinWriter |
| class | ResidueTypeSet |
| A collection of ResidueType defined. More... | |
| struct | RingConformer |
| class | RingConformerSet |
| class | Selector_AA |
| Does the residue belong to ANY of these AAs? More... | |
| class | Selector_CMDFLAG |
| Is a certain string in the command-line option -chemical:allow_patch present ? this selector does actually not depend on the residuetype it is queried for. More... | |
| class | Selector_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 to 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_POSITION |
| 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 | 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 | SetICoor |
| set an atom's AtomICoord More... | |
| class | SetInterchangeabilityGroup_String |
| set the interchangeability_group string for a ResidueType More... | |
| class | SetIO_String |
| set atom's chemical type 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 | SetOrientAtom |
| Set orient atom selection mode. More... | |
| class | SetPolymerConnectAtom |
| set an atom as polymer connection More... | |
Enumerations | |
| enum | AA { aa_ala = 1, aa_cys, aa_asp, aa_glu, aa_phe, aa_gly, aa_his, aa_ile, aa_lys, aa_leu, aa_met, aa_asn, aa_pro, aa_gln, aa_arg, aa_ser, aa_thr, aa_val, aa_trp, aa_tyr, num_canonical_aas = aa_tyr, na_ade, first_DNA_aa = na_ade, na_cyt, na_gua, na_thy, last_DNA_aa = na_thy, na_rgu, na_rad, na_rcy, na_ura, aa_dal, first_D_aa = aa_dal, aa_dcs, aa_das, aa_dgu, aa_dph, aa_dhi, aa_dil, aa_dly, aa_dle, aa_dme, aa_dan, aa_dpr, aa_dgn, aa_dar, aa_dse, aa_dth, aa_dva, aa_dtr, aa_dty, last_D_aa = aa_dty, aa_b3a, first_beta3_aa = aa_b3a, aa_b3c, aa_b3d, aa_b3e, aa_b3f, aa_b3g, aa_b3h, aa_b3i, aa_b3k, aa_b3l, aa_b3m, aa_b3n, aa_b3p, aa_b3q, aa_b3r, aa_b3s, aa_b3t, aa_b3v, aa_b3w, aa_b3y, aa_b3cisACPrC, aa_b3cisACPC, aa_b3cisACHC, last_beta3_aa = aa_b3cisACHC, aa_h2o, aa_vrt, aa_unp, aa_unk, num_aa_types = aa_unk } |
| enumeration for amino acids and nucleotides types with the total number as num_aa_types More... | |
| enum | BondName { UnknownBond =0, SingleBond =1, DoubleBond =2, TripleBond =3, AromaticBond =4, OrbitalBond =5 } |
| enum | BondOrder { UnknownBondOrder =0, SingleBondOrder =1, DoubleBondOrder =2, TripleBondOrder =3, OrbitalBondOrder, PseudoBondOrder =99 } |
| enum | BondConjugability { UnknownConjugability, NotConjugableBond, ConjugableBond } |
| As with the BCL, bond conjugability is more about the atom types on either end of the bond than about the bond itself. A conjugatable bond is one where it is known that the atoms on both sides of the bond can participate in a conjugated system. Double, triple and aromatic bonds are always conjugatable, and single bonds are conjugatable if both atoms are in other triple, double, or aromatic systems. More... | |
| enum | BondRingness { UnknownRingness, BondNotInRing, BondInRing } |
| enum | BondAromaticity { UnknownAromaticity, NonaromaticBond, IsAromaticBond } |
| Proper aromaticity implies participation in a 4n+2 electron ring system. For simple single-double alternation, see conjugatable bond. More... | |
| enum | BondIsometry { UnknownIsometry, NoBondIsometry, EIsometry, ZIsometry } |
| enum | CPParameter { q = 1, PHI, THETA } |
| Enumerators for the three Cremer-Pople "ring-puckering" parameters used to describe 4-, 5-, and 6-membered ring conformers. More... | |
| enum | Hybridization { SP2_HYBRID = 1, SP3_HYBRID, RING_HYBRID, UNKNOWN_HYBRID, HYBRID_MAX = UNKNOWN_HYBRID } |
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 > & | name2aa () |
| map that converts string name to AA enum More... | |
| std::map< char, AA > & | 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 > & | 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 > & | 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... | |
| bool | is_canonical_D_aa (AA 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... | |
| AA | get_L_equivalent (AA 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 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... | |
| void | error_check_requested_adducts (AdductMap const &add_map, ResidueTypeCOPs const &rsd_types) |
| Make sure requested adducts exist in some residue. More... | |
| std::ostream & | operator<< (std::ostream &out, Atom const &atom) |
| std::ostream & | operator<< (std::ostream &out, const AtomType &atom_type) |
| BondName | convert_to_BondName (std::string const &id) |
| std::ostream & | operator<< (std::ostream &out, Bond const &bond) |
| void | find_bonds_in_rings (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) |
| 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 centroid chemical type set. More... | |
| std::string const | CENTROID_ROT ("centroid_rot") |
| tag name for querying centroid_rot chemical type set. More... | |
| std::string const | COARSE_TWO_BEAD ("coarse_two_bead") |
| tag name for querying coarse-grained 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... | |
| 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) |
| std::ostream & | operator<< (std::ostream &out, const Orbital &orbital) |
| std::string const | patch_linker ("_p:") |
| the string used to generate new residue names 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... | |
| std::string | tag_from_line (std::string const &line) |
| handy function, return the first word from a line More... | |
| PatchCaseOP | case_from_lines (utility::vector1< std::string > const &lines) |
| create a PatchCase from input lines More... | |
| std::string | expand_icoor_atom_name (std::string name, ResidueType const &rsd) |
| PatchOperationOP | patch_operation_from_patch_file_line (std::string const &line) |
| 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) |
| 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::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types,chemical::ResidueTypeSetCAP rsd_type_set) |
| virtual constructor for ResidueType objects More... | |
| ResidueTypeOP | read_topology_file (utility::io::izstream &data, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types, chemical::ResidueTypeSetCAP rsd_type_set) |
| void | write_topology_file (ResidueType const &rsd) |
| writes a .params file from a given ResidueType object More... | |
| ResidueSelectorSingleOP | residue_selector_single_from_line (std::string const &line) |
| create a singe ResidueSelector from an input line. More... | |
| 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) |
| std::string | strip_whitespace (std::string const &name) |
| bool | retype_is_virtual (std::string const &element) |
| Should the element be considered to be a virtual atom? More... | |
| std::string | retype_get_element (VD const &vd, Atom const &a, ElementMap const &emap, AtomTypeSet const &atom_type_set) |
| bool | retype_is_aromatic (VD const &atom, ResidueGraph const &graph, ElementMap const &emap, AtomTypeSet const &atom_type_set) |
| An atom is aromatic if it has any aromatic bonds to a non-virtual atom. TODO: We need better aromatic ring detection. More... | |
| std::ostream & | operator<< (std::ostream &output, ResidueType const &object_to_output) |
| std::string | get_element_color (std::string const &element) |
| utility::vector1< std::string > | get_lines_from_file_data (std::string const &filename) |
| Local method that opens a file and returns its data as a list of lines after checking for errors. More... | |
| utility::vector1< RingConformer > | read_conformers_from_database_file_for_ring_size (std::string const &filename, core::Size ring_size) |
| Return a list of ring conformers, read from a database file. More... | |
| std::ostream & | operator<< (std::ostream &output, RingConformer const &object_to_output) |
| std::ostream & | operator<< (std::ostream &output, RingConformerSet const &object_to_output) |
| static std::string const | chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz") |
| core::chemical::ResidueTypeSetCAP | rsd_set_from_cmd_line () |
| 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. Called by ChemicalManager at time of AtomTypeSet creation. 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. Called by ChemicalManager at time of AtomTypeSet creation. More... | |
| VariantType const | UPPER_TERMINUS ("UPPER_TERMINUS") |
| C-terminus cap. More... | |
| VariantType const | LOWER_TERMINUS ("LOWER_TERMINUS") |
| N-terminus cap. More... | |
| VariantType const | UPPERTERM_TRUNC ("UPPERTERM_TRUNC") |
| C-terminus truncation. More... | |
| VariantType const | LOWERTERM_TRUNC ("LOWERTERM_TRUNC") |
| N-terminus truncation. More... | |
| VariantType const | CUTPOINT_LOWER ("CUTPOINT_LOWER") |
| for use during loop modeling, at positions before a cutpoint More... | |
| VariantType const | CUTPOINT_UPPER ("CUTPOINT_UPPER") |
| for use during loop modeling, at positions after a cutpoint More... | |
| VariantType const | DISULFIDE ("DISULFIDE") |
| VariantType const | BRANCH_POINT ("BRANCH_POINT") |
| Variant type used for branched polymers and glycosylations. More... | |
| VariantType const | BRANCH_LOWER_TERMINUS ("BRANCH_LOWER_TERMINUS") |
| Variant type used for branched polymers and glycosylations. More... | |
| VariantType const | ADDUCT ("ADDUCT") |
| VariantType const | METHYLATION ("METHYLATION") |
| VariantType const | CENTROID_HA ("CENTROID_WITH_HA") |
| VariantType const | PROTONATED ("PROTONATED") |
| VariantType const | DEPROTONATED ("DEPROTONATED") |
| VariantType const | SPECIAL_ROT ("SPECIAL_ROT") |
| Generic variant type that allows for differential scoring of a set of residues/rotamers. More... | |
| VariantType const | VIRTUAL_PHOSPHATE ("VIRTUAL_PHOSPHATE") |
| VariantType const | VIRTUAL_RNA_RESIDUE ("VIRTUAL_RNA_RESIDUE") |
| VariantType const | VIRTUAL_O2PRIME_HYDROGEN ("VIRTUAL_O2PRIME_HYDROGEN") |
| VariantType const | PHOSPHORYLATION ("PHOSPHORYLATION") |
| VariantType const | ACETYLATION ("ACETYLATION") |
| VariantType const | SULFATION ("SULFATION") |
| VariantType const | CARBOXYLATION ("CARBOXYLATION") |
| VariantType const | HYDROXYLATION ("HYDROXYLATION") |
| VariantType const | DIMETHYLATION ("DIMETHYLATION") |
| VariantType const | TRIMETHYLATION ("TRIMETHYLATION") |
| VariantType const | DIIODINATION ("DIIODINATION") |
| VariantType const | ACETYLATED_NTERMINUS ("ACETYLATED_NTERMINUS") |
| Acetylated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More... | |
| VariantType const | METHYLATED_CTERMINUS ("METHYLATED_CTERMINUS") |
| Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More... | |
| VariantType const | SC_ORBITALS ("SC_ORBITALS") |
| VariantType const | N_ACETYLATION ("N_ACETYLATION") |
| Cap extensions at termini to include peptide bonds, written for stepwise assembly (SWA) code. More... | |
| VariantType const | C_METHYLAMIDATION ("C_METHYLAMIDATION") |
| VariantType const | REPLONLY ("REPLONLY") |
| @ brief only the repulsive energy will be considered during structure calculations More... | |
| VariantType const | OOP_PRE ("OOP_PRE") |
| @ brief oop_pre patch, used for oligooxopiperazines (OOPs) More... | |
| VariantType const | OOP_POST ("OOP_POST") |
| @ brief oop_post patch, used for oligooxopiperazines (OOPs) More... | |
| VariantType const | HBS_PRE ("HBS_PRE") |
| @ brief hbs_pre patch, used for hydrogen bond surrogates More... | |
| VariantType const | HBS_POST ("HBS_POST") |
| @ brief hbs_post patch, used for hydrogen bond surrogates More... | |
| VariantType const | C1_MODIFIED_SUGAR ("C1_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 1 position More... | |
| VariantType const | C2_MODIFIED_SUGAR ("C2_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 2 position More... | |
| VariantType const | C3_MODIFIED_SUGAR ("C3_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 3 position More... | |
| VariantType const | C4_MODIFIED_SUGAR ("C4_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 4 position More... | |
| VariantType const | C5_MODIFIED_SUGAR ("C5_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 5 position More... | |
| VariantType const | C6_MODIFIED_SUGAR ("C6_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 6 position More... | |
| VariantType const | C7_MODIFIED_SUGAR ("C7_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 7 position More... | |
| VariantType const | C8_MODIFIED_SUGAR ("C8_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 8 position More... | |
| VariantType const | C9_MODIFIED_SUGAR ("C9_MODIFIED_SUGAR") |
| @ brief variant for any saccharide residue modified at the 9 position More... | |
| VariantType const | SIDECHAIN_CONJUGATION ("SIDECHAIN_CONJUGATION") |
| This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination) More... | |
| 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::map< std::string, int > core::chemical::AdductMap |
| typedef boost::graph_traits<ResidueGraph>::adjacency_iterator core::chemical::AdjacentIter |
| 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 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 utility::pointer::owning_ptr< AtomTypeDatabaseIO > AtomTypeDatabaseIOOP typedef utility::pointer::owning_ptr< AtomTypeDatabaseIO const > core::chemical::AtomTypeDatabaseIOCOP |
| typedef utility::pointer::owning_ptr< AutomorphismIterator const > core::chemical::AutomorphismIteratorCOP |
| 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 std::map< VD, std::string > core::chemical::ElementMap |
| 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 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 utility::pointer::access_ptr< IdealBondLengthSet const > core::chemical::IdealBondLengthSetCAP |
| 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 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<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 boost::graph_traits<ResidueGraph>::out_edge_iterator core::chemical::OutEdgeIter |
| typedef std::pair<OutEdgeIter, OutEdgeIter> core::chemical::OutEdgeIterPair |
| 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 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 boost::undirected_graph< Atom, Bond > core::chemical::ResidueGraph |
| typedef utility::pointer::owning_ptr< ResidueSelectorSingle > core::chemical::ResidueSelectorSingleOP |
| typedef utility::pointer::owning_ptr< ResidueTypeKinWriter const > core::chemical::ResidueTypeKinWriterCOP |
| typedef std::string core::chemical::VariantType |
Notion of Residue variant, eg PHOSPHO, NTERM, TERMINUS, PROTONATION, GLYCOSO ??
| typedef ResidueGraph::vertex_descriptor core::chemical::VD |
| 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
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 | |
|
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, name2aa(), and utility_exit_with_message.
Referenced by core::chemical::ResidueType::aa(), core::pack::task::operation::RestrictYSDesign::apply(), core::chemical::ResidueType::backbone_aa(), core::pose::rna::correctly_position_cutpoint_phosphate_torsions(), core::pack::dunbrack::RotamerLibrary::create_centroid_rotamer_libraries_from_ASCII(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), core::scoring::P_AA::read_P_AA(), core::scoring::P_AA::read_P_AA_n(), core::scoring::P_AA::read_P_AA_pp(), and core::chemical::ResidueType::rotamer_aa().
| AA core::chemical::aa_from_oneletter_code | ( | char | onelettercode | ) |
give a 1 letter code and return the string name
References oneletter2aa().
Referenced by core::sequence::AnnotatedSequence::aa(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), core::pose::Pose::annotated_sequence(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::sequence::ProfSimScoringScheme::initialize_parameters(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), core::fragment::make_pose_from_sequence_(), core::scoring::nv::NVlookup::NVlookup(), core::fragment::picking_old::vall::VallResidue::order_vector(), 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(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), core::pack::task::TARGET::residue_action(), core::pose::residue_types_from_sequence(), core::sequence::MatrixScoringScheme::score(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), and core::sequence::MatrixScoringScheme::values_for_aa().
| VariantType const core::chemical::ACETYLATED_NTERMINUS | ( | "ACETYLATED_NTERMINUS" | ) |
Acetylated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries.
| VariantType const core::chemical::ACETYLATION | ( | "ACETYLATION" | ) |
| 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 basic::options::OptionKeys::chemical::add_atom_type_set_parameters, core::chemical::AtomTypeSet::add_parameters_from_file(), utility::file::file_exists(), filename(), basic::options::option, tag, TR, user, and utility_exit_with_message.
Referenced by core::chemical::ChemicalManager::create_atom_type_set().
| VariantType const core::chemical::ADDUCT | ( | "ADDUCT" | ) |
| 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, core::chemical::PatchCase::apply(), core::chemical::ResidueType::defined_adducts(), core::chemical::ResidueType::name(), numeric::conversions::radians(), radians(), and TR.
Referenced by core::chemical::ResidueTypeSet::create_adduct_combinations().
| id::AtomID core::chemical::atom_id_from_icoor_line | ( | std::string const | name, |
| ResidueType const & | rsd | ||
| ) |
helper fxn
References core::id::BOGUS_ATOM_ID, type, and utility_exit_with_message.
| VariantType const core::chemical::BRANCH_LOWER_TERMINUS | ( | "BRANCH_LOWER_TERMINUS" | ) |
Variant type used for branched polymers and glycosylations.
| VariantType const core::chemical::BRANCH_POINT | ( | "BRANCH_POINT" | ) |
Variant type used for branched polymers and glycosylations.
| VariantType const core::chemical::C1_MODIFIED_SUGAR | ( | "C1_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 1 position
| VariantType const core::chemical::C2_MODIFIED_SUGAR | ( | "C2_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 2 position
| VariantType const core::chemical::C3_MODIFIED_SUGAR | ( | "C3_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 3 position
| VariantType const core::chemical::C4_MODIFIED_SUGAR | ( | "C4_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 4 position
| VariantType const core::chemical::C5_MODIFIED_SUGAR | ( | "C5_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 5 position
| VariantType const core::chemical::C6_MODIFIED_SUGAR | ( | "C6_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 6 position
| VariantType const core::chemical::C7_MODIFIED_SUGAR | ( | "C7_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 7 position
| VariantType const core::chemical::C8_MODIFIED_SUGAR | ( | "C8_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 8 position
| VariantType const core::chemical::C9_MODIFIED_SUGAR | ( | "C9_MODIFIED_SUGAR" | ) |
@ brief variant for any saccharide residue modified at the 9 position
| VariantType const core::chemical::C_METHYLAMIDATION | ( | "C_METHYLAMIDATION" | ) |
| VariantType const core::chemical::CARBOXYLATION | ( | "CARBOXYLATION" | ) |
| PatchCaseOP core::chemical::case_from_lines | ( | utility::vector1< std::string > const & | lines | ) |
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(), tag, and tag_from_line().
Referenced by core::chemical::Patch::read_file().
| std::string const core::chemical::CENTROID | ( | "centroid" | ) |
tag name for querying centroid chemical type set.
| VariantType const core::chemical::CENTROID_HA | ( | "CENTROID_WITH_HA" | ) |
| std::string const core::chemical::CENTROID_ROT | ( | "centroid_rot" | ) |
tag name for querying centroid_rot chemical type set.
|
static |
| std::string const core::chemical::COARSE_RNA | ( | "coarse_rna" | ) |
tag name for querying COARSE_RNA chemical type set.
| std::string const core::chemical::COARSE_TWO_BEAD | ( | "coarse_two_bead" | ) |
tag name for querying coarse-grained chemical type set.
| LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph | ( | ResidueType const & | res | ) |
References core::chemical::ResidueType::graph(), and target.
Referenced by find_bonds_in_rings().
| BondName core::chemical::convert_to_BondName | ( | std::string const & | id | ) |
References utility::string2int(), UnknownBond, and utility_exit_with_message.
Referenced by read_topology_file().
| VariantType const core::chemical::CUTPOINT_LOWER | ( | "CUTPOINT_LOWER" | ) |
for use during loop modeling, at positions before a cutpoint
| VariantType const core::chemical::CUTPOINT_UPPER | ( | "CUTPOINT_UPPER" | ) |
for use during loop modeling, at positions after a cutpoint
| 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(), and tr.
Referenced by read_topology_file().
| VariantType const core::chemical::DEPROTONATED | ( | "DEPROTONATED" | ) |
| VariantType const core::chemical::DIIODINATION | ( | "DIIODINATION" | ) |
| VariantType const core::chemical::DIMETHYLATION | ( | "DIMETHYLATION" | ) |
| VariantType const core::chemical::DISULFIDE | ( | "DISULFIDE" | ) |
| 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(), and utility_exit_with_message.
Referenced by core::chemical::ResidueTypeSet::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(), and utility_exit_with_message.
Referenced by core::chemical::ResidueTypeSet::place_adducts().
| std::string core::chemical::expand_icoor_atom_name | ( | std::string | name, |
| ResidueType const & | rsd | ||
| ) |
References core::chemical::ResidueType::n_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::find_bonds_in_rings | ( | ResidueType & | res | ) |
| 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 | 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, and aa_val.
| 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 | 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, and aa_val.
Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::scoring::Ramachandran::get_l_equivalent(), core::scoring::P_AA::get_l_equivalent(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static(), and core::pack::dunbrack::RotamerLibrary::get_rsd_library().
| utility::vector1< std::string > core::chemical::get_lines_from_file_data | ( | std::string const & | filename | ) |
Local method that opens a file and returns its data as a list of lines after checking for errors.
Blank and commented lines are not returned and the file is closed before returning the lines.
References utility::io::izstream::close(), file_exists(), getline(), utility::io::izstream::good(), trim(), and utility_exit_with_message.
Referenced by read_conformers_from_database_file_for_ring_size().
| 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().
| VariantType const core::chemical::HBS_POST | ( | "HBS_POST" | ) |
@ brief hbs_post patch, used for hydrogen bond surrogates
| VariantType const core::chemical::HBS_PRE | ( | "HBS_PRE" | ) |
@ brief hbs_pre patch, used for hydrogen bond surrogates
| std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID | ( | "hybrid_fa_standard_centroid" | ) |
tag name for querying hybrid fullatom+centroid chemical type set.
| VariantType const core::chemical::HYDROXYLATION | ( | "HYDROXYLATION" | ) |
| bool core::chemical::is_canonical_D_aa | ( | AA | 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::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), 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_residue_pair_derivatives(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsion_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsions_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbind(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), core::scoring::Ramachandran::is_canonical_d_aminoacid(), core::scoring::P_AA::is_canonical_d_aminoacid(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep().
| VariantType const core::chemical::LOWER_TERMINUS | ( | "LOWER_TERMINUS" | ) |
N-terminus cap.
| VariantType const core::chemical::LOWERTERM_TRUNC | ( | "LOWERTERM_TRUNC" | ) |
N-terminus truncation.
| VariantType const core::chemical::METHYLATED_CTERMINUS | ( | "METHYLATED_CTERMINUS" | ) |
Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries.
| VariantType const core::chemical::METHYLATION | ( | "METHYLATION" | ) |
| 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(), mod(), basic::options::option, basic::options::OptionKeys::chemical::set_atom_properties, TR, user, and utility_exit_with_message.
Referenced by core::chemical::ChemicalManager::create_atom_type_set().
| VariantType const core::chemical::N_ACETYLATION | ( | "N_ACETYLATION" | ) |
Cap extensions at termini to include peptide bonds, written for stepwise assembly (SWA) code.
|
inline |
map that converts string name to AA enum
References setup_name2aa().
Referenced by aa_from_name(), operator>>(), and setup_aa2name().
| std::string core::chemical::name_from_aa | ( | AA | aa | ) |
give a enum type and return the string name
References aa2name(), and num_aa_types.
Referenced by core::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), core::pose::Pose::annotated_sequence(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), 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(), core::scoring::methods::get_restag(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), operator<<(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::chemical::ResidueDatabaseIO::read_residue_type(), read_topology_file(), core::scoring::methods::EnvSmoothEnergy::representative_atom_name(), core::scoring::methods::MembraneEnvSmoothEnergy::representative_atom_name(), and core::pack::task::ResidueLevelTask_::restrict_absent_nas().
|
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 aa2oneletter(), and num_canonical_aas.
Referenced by core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), and core::fragment::SingleResidueFragData::steal().
| bool core::chemical::oneletter_code_specifies_aa | ( | char | onelettercode | ) |
References oneletter2aa().
Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pose::Pose::annotated_sequence(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), core::sequence::MatrixScoringScheme::read_data(), core::pack::task::TARGET::residue_action(), and core::sequence::MatrixScoringScheme::values_for_aa().
| VariantType const core::chemical::OOP_POST | ( | "OOP_POST" | ) |
@ brief oop_post patch, used for oligooxopiperazines (OOPs)
| VariantType const core::chemical::OOP_PRE | ( | "OOP_PRE" | ) |
@ brief oop_pre patch, used for oligooxopiperazines (OOPs)
| bool core::chemical::operator!= | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
| 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::chemical::Orbital::print().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const AtomType & | atom_type | ||
| ) |
References core::chemical::AtomType::print().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| Bond const & | bond | ||
| ) |
References core::chemical::Bond::print().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| Atom const & | atom | ||
| ) |
References core::chemical::Atom::print().
|
inline |
References core::chemical::Element::write().
|
inline |
References core::chemical::ElectronConfiguration::write().
| std::ostream & core::chemical::operator<< | ( | std::ostream & | output, |
| RingConformer const & | object_to_output | ||
| ) |
| 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, |
| RingConformerSet const & | object_to_output | ||
| ) |
References core::chemical::RingConformerSet::show().
| 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 | ||
| ) |
References core::chemical::ResConnID::conn_id_, and core::chemical::ResConnID::res_id_.
|
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.
References utility::options::StringVectorOption::size().
Referenced by core::chemical::ResidueTypeSet::place_adducts().
| std::string const core::chemical::patch_linker | ( | "_p:" | ) |
the string used to generate new residue names
| PatchOperationOP core::chemical::patch_operation_from_patch_file_line | ( | std::string const & | line | ) |
Virtual constructor, returns 0 if no match.
References l, mean, path, numeric::conversions::radians(), radians(), radius, runtime_assert, tag, tr, and utility_exit_with_message.
Referenced by case_from_lines().
| VariantType const core::chemical::PHOSPHORYLATION | ( | "PHOSPHORYLATION" | ) |
| VariantType const core::chemical::PROTONATED | ( | "PROTONATED" | ) |
| utility::vector1< RingConformer > core::chemical::read_conformers_from_database_file_for_ring_size | ( | std::string const & | filename, |
| core::Size | ring_size | ||
| ) |
Return a list of ring conformers, read from a database file.
References core::chemical::RingConformer::CP_parameters, core::chemical::RingConformer::degeneracy, core::chemical::RingConformer::general_name, get_lines_from_file_data(), core::chemical::RingConformer::nu_angles, core::chemical::RingConformer::specific_name, core::chemical::RingConformer::tau_angles, TR, and utility_exit_with_message.
Referenced by core::chemical::RingConformerSet::conformers_for_ring_size().
| 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, | ||
| chemical::ResidueTypeSetCAP | rsd_type_set | ||
| ) |
virtual constructor for ResidueType objects
References utility::file::file_exists(), read_topology_file(), and utility_exit_with_message.
Referenced by core::chemical::ResidueTypeSet::add_residue_type(), core::chemical::ResidueLoader::create_resource(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::chemical::ResidueTypeSet::read_files(), and core::chemical::ResidueTypeSet::ResidueTypeSet().
| ResidueTypeOP core::chemical::read_topology_file | ( | utility::io::izstream & | data, |
| chemical::AtomTypeSetCAP | atom_types, | ||
| chemical::ElementSetCAP | elements, | ||
| chemical::MMAtomTypeSetCAP | mm_atom_types, | ||
| chemical::orbitals::OrbitalTypeSetCAP | orbital_atom_types, | ||
| chemical::ResidueTypeSetCAP | rsd_type_set | ||
| ) |
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.
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, "ROTAMER_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.
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. See the "BondName" enumeration for acceptable bond types.
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.
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"
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
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
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 also the CHI_ROTAMERS and NCAA_ROTLIB_PATH tags for alternate ways to provide 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.
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" No examples currently found in the database (10/13).
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.
References aa_ser, aa_thr, utility::io::izstream::close(), convert_to_BondName(), define_mainchain_atoms(), numeric::conversions::degrees(), basic::options::OptionKeys::corrections::chemical::expand_st_chi2sampling, FA_STANDARD, utility::io::izstream::filename(), filename(), getline(), j, l, mean, name_from_aa(), basic::options::option, basic::options::OptionKeys::corrections::chemical::parse_charge, parse_charge, utility::file::FileName::path(), path, numeric::conversions::radians(), radians(), radius, core::kinematics::Stub::spherical(), strip_whitespace(), tag, tr, utility_exit_with_message, and utility::file::FileName::vol().
Referenced by read_topology_file().
| VariantType const core::chemical::REPLONLY | ( | "REPLONLY" | ) |
@ brief only the repulsive energy will be considered during structure calculations
| ResidueSelectorSingleOP core::chemical::residue_selector_single_from_line | ( | std::string const & | line | ) |
create a singe ResidueSelector from an input line.
Referenced by core::chemical::ResidueSelector::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(), and core::io::pdb::build_pose_as_is1().
| std::string core::chemical::residue_type_base_name | ( | ResidueType const & | rsd_type | ) |
helper function, returns the base residue name prior to any patching
References core::chemical::ResidueType::name(), and patch_linker.
Referenced by core::util::add_covalent_linkage(), core::util::add_covalent_linkage_helper(), core::io::pdb::FileData::append_residue(), core::io::pdb::build_pose_as_is1(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), and core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed().
| std::string core::chemical::retype_get_element | ( | VD const & | vd, |
| Atom const & | a, | ||
| ElementMap const & | emap, | ||
| AtomTypeSet const & | atom_type_set | ||
| ) |
References core::chemical::Atom::atom_type_index(), and utility_exit_with_message.
Referenced by core::chemical::ResidueType::retype_atoms(), and retype_is_aromatic().
| bool core::chemical::retype_is_aromatic | ( | VD const & | atom, |
| ResidueGraph const & | graph, | ||
| ElementMap const & | emap, | ||
| AtomTypeSet const & | atom_type_set | ||
| ) |
An atom is aromatic if it has any aromatic bonds to a non-virtual atom. TODO: We need better aromatic ring detection.
References AromaticBond, retype_get_element(), retype_is_virtual(), and core::scoring::hbonds::t.
Referenced by core::chemical::ResidueType::retype_atoms().
| bool core::chemical::retype_is_virtual | ( | std::string const & | element | ) |
Should the element be considered to be a virtual atom?
Referenced by core::chemical::ResidueType::retype_atoms(), and retype_is_aromatic().
| core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line | ( | ) |
| VariantType const core::chemical::SC_ORBITALS | ( | "SC_ORBITALS" | ) |
| utility::vector1< std::string > core::chemical::setup_aa2name | ( | ) |
setup the vector that maps AA enum to string name
References begin, core::sequence::end, 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 begin, core::sequence::end, num_aa_types, and oneletter2aa().
Referenced by aa2oneletter().
| 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_b3cisACPrC, aa_b3d, aa_b3e, aa_b3f, aa_b3g, aa_b3h, aa_b3i, aa_b3k, aa_b3l, aa_b3m, aa_b3n, aa_b3p, aa_b3q, aa_b3r, aa_b3s, aa_b3t, aa_b3v, aa_b3w, aa_b3y, aa_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, and na_ura.
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_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().
| VariantType const core::chemical::SIDECHAIN_CONJUGATION | ( | "SIDECHAIN_CONJUGATION" | ) |
This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination)
| VariantType const core::chemical::SPECIAL_ROT | ( | "SPECIAL_ROT" | ) |
Generic variant type that allows for differential scoring of a set of residues/rotamers.
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| VariantType const core::chemical::SULFATION | ( | "SULFATION" | ) |
| 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(), and core::chemical::Patch::read_file().
| VariantType const core::chemical::TRIMETHYLATION | ( | "TRIMETHYLATION" | ) |
| VariantType const core::chemical::UPPER_TERMINUS | ( | "UPPER_TERMINUS" | ) |
C-terminus cap.
| VariantType const core::chemical::UPPERTERM_TRUNC | ( | "UPPERTERM_TRUNC" | ) |
C-terminus truncation.
| VariantType const core::chemical::VIRTUAL_O2PRIME_HYDROGEN | ( | "VIRTUAL_O2PRIME_HYDROGEN" | ) |
| VariantType const core::chemical::VIRTUAL_PHOSPHATE | ( | "VIRTUAL_PHOSPHATE" | ) |
| VariantType const core::chemical::VIRTUAL_RNA_RESIDUE | ( | "VIRTUAL_RNA_RESIDUE" | ) |
| void core::chemical::write_topology_file | ( | ResidueType const & | rsd | ) |
writes a .params file from a given ResidueType object
function to write out a topology file given a residue type, can be used to debug on the fly generated residue types. Note: not perfect yet, the enums for the connection types are given in numbers instead of names
References core::chemical::ResidueType::aa(), core::chemical::ResidueType::actcoord_atoms(), core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ICoorAtomID::atomno(), core::chemical::ResidueConnection::atomno(), core::chemical::Atom::charge(), core::chemical::ResidueType::chi_atoms(), core::chemical::AtomICoor::d(), numeric::conversions::degrees(), degrees(), filename(), core::chemical::ResidueType::force_nbr_atom_orient(), core::chemical::Atom::formal_charge(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_d_aa(), core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_l_aa(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_metalbinding(), core::chemical::ResidueType::is_polar(), core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueType::is_RNA(), core::chemical::ResidueType::is_surface(), core::chemical::ResidueType::is_terminus(), core::chemical::ResidueType::is_upper_terminus(), j, core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::mm_atom_type(), core::chemical::ResidueType::n_nus(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueType::nbrs(), core::chemical::ResidueType::nchi(), core::chemical::ResidueType::nu_atoms(), out, core::chemical::AtomICoor::phi(), core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), numeric::conversions::radians(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::chemical::AtomICoor::theta(), core::chemical::ICoorAtomID::type(), and core::chemical::ResidueType::upper_connect().
| VariantType const core::chemical::ACETYLATED_NTERMINUS |
| VariantType const core::chemical::ACETYLATION |
| VariantType const core::chemical::ADDUCT |
| VariantType const core::chemical::BRANCH_LOWER_TERMINUS |
Referenced by core::io::pdb::build_pose_as_is1(), and core::import_pose::set_reasonable_fold_tree().
| VariantType const core::chemical::BRANCH_POINT |
Referenced by core::io::pdb::build_pose_as_is1(), and core::import_pose::set_reasonable_fold_tree().
| VariantType const core::chemical::C1_MODIFIED_SUGAR |
| VariantType const core::chemical::C2_MODIFIED_SUGAR |
| VariantType const core::chemical::C3_MODIFIED_SUGAR |
| VariantType const core::chemical::C4_MODIFIED_SUGAR |
| VariantType const core::chemical::C5_MODIFIED_SUGAR |
| VariantType const core::chemical::C6_MODIFIED_SUGAR |
| VariantType const core::chemical::C7_MODIFIED_SUGAR |
| VariantType const core::chemical::C8_MODIFIED_SUGAR |
| VariantType const core::chemical::C9_MODIFIED_SUGAR |
| VariantType const core::chemical::C_METHYLAMIDATION |
| VariantType const core::chemical::CARBOXYLATION |
| std::string const core::chemical::CENTROID |
Referenced by core::membrane::geometry::MembraneResidueFactory::add_embedding_residue(), core::membrane::geometry::MembraneResidueFactory::add_membrane_residue(), core::pose::addVirtualResAsRoot(), core::scoring::AtomVDW::AtomVDW(), core::import_pose::centroid_pose_from_pdb(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::chemical::ChemicalManager::create_residue_type_set(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_centroid(), core::import_pose::pose_from_pdb(), core::import_pose::poseOPs_from_pdbs(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), and core::util::switch_to_residue_type_set().
| VariantType const core::chemical::CENTROID_HA |
| std::string const core::chemical::CENTROID_ROT |
Referenced by core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), and core::util::switch_to_residue_type_set().
| std::string const core::chemical::COARSE_RNA |
| std::string const core::chemical::COARSE_TWO_BEAD |
| VariantType const core::chemical::CUTPOINT_LOWER |
Referenced by core::util::add_cutpoint_variants(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), core::pose::rna::correctly_add_cutpoint_variants(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::scoring::rna::RNA_TorsionPotential::is_cutpoint_closed_torsion(), core::pose::rna::is_cutpoint_open(), core::scoring::methods::is_lower_cutpoint(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::util::remove_cutpoint_variants(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::conformation::setup_links(), and core::pose::rna::virtualize_5prime_phosphates().
| VariantType const core::chemical::CUTPOINT_UPPER |
Referenced by core::util::add_cutpoint_variants(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), core::pose::rna::correctly_add_cutpoint_variants(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::scoring::rna::RNA_TorsionPotential::is_cutpoint_closed_torsion(), core::pose::rna::is_cutpoint_open(), core::scoring::methods::is_upper_cutpoint(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::util::remove_cutpoint_variants(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::conformation::setup_links(), and core::pose::rna::virtualize_5prime_phosphates().
| VariantType const core::chemical::DEPROTONATED |
| VariantType const core::chemical::DIIODINATION |
| VariantType const core::chemical::DIMETHYLATION |
| VariantType const core::chemical::DISULFIDE |
Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::OptCysHG::apply(), core::io::pdb::build_pose_as_is1(), core::conformation::change_cys_state(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::conformation::disulfide_bonds(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), and core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy().
| std::string const core::chemical::FA_STANDARD |
Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::membrane::geometry::MembraneResidueFactory::add_embedding_residue(), core::membrane::geometry::MembraneResidueFactory::add_membrane_residue(), core::pose::addVirtualResAsRoot(), core::import_pose::build_pose_as_is2(), core::io::pdb::build_pose_from_pdb_as_is(), core::scoring::geometric_solvation::compute_exact_geosol(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::ChemicalManager::create_residue_type_set(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::ScoringManager::etable(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::io::silent::SilentStruct::fill_pose(), core::import_pose::PDBSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::conformation::form_disulfide(), core::chemical::IdealBondLengthSet::get_bond_length(), core::scoring::ScoringManager::get_MMBondAngleLibrary(), core::scoring::ScoringManager::get_MMBondLengthLibrary(), core::scoring::ScoringManager::get_MMLJLibrary(), core::scoring::ScoringManager::get_MMTorsionLibrary(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_fullatom(), core::scoring::ScoringManager::memb_etable(), core::conformation::orient_residue_for_ideal_bond(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdbstring(), core::io::pdb::pose_from_pose(), core::import_pose::poseOPs_from_pdbs(), core::import_pose::poses_from_pdbs(), read_topology_file(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::pack::task::operation::util::select_coord_for_residue(), and core::util::switch_to_residue_type_set().
| VariantType const core::chemical::HBS_POST |
Referenced by core::pose::ncbb::initialize_hbs(), and core::pose::ncbb::initialize_ncbbs().
| VariantType const core::chemical::HBS_PRE |
Referenced by core::pose::ncbb::initialize_hbs(), and core::pose::ncbb::initialize_ncbbs().
| std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID |
| VariantType const core::chemical::HYDROXYLATION |
| VariantType const core::chemical::LOWER_TERMINUS |
Referenced by core::conformation::add_lower_terminus_type_to_conformation_residue(), core::pose::add_lower_terminus_type_to_pose_residue(), core::scoring::GenBornPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pose::rna::correctly_add_cutpoint_variants(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), core::pose::remove_lower_terminus_type_from_pose_residue(), and core::pose::residue_types_from_sequence().
| VariantType const core::chemical::LOWERTERM_TRUNC |
Referenced by core::io::pdb::build_pose_as_is1().
| Real const core::chemical::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.
S-H bond length in CYS.
Referenced by core::scoring::rna::RNA_FullAtomStackingEnergy::atomic_interaction_cutoff(), core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff(), and core::scoring::elec::FA_ElecEnergy::hydrogen_interaction_cutoff().
| VariantType const core::chemical::METHYLATED_CTERMINUS |
| VariantType const core::chemical::METHYLATION |
| VariantType const core::chemical::N_ACETYLATION |
Referenced by core::pose::make_pose_from_sequence().
| VariantType const core::chemical::OOP_POST |
Referenced by core::pose::ncbb::initialize_ncbbs().
| VariantType const core::chemical::OOP_PRE |
| std::string const core::chemical::patch_linker |
the string used to create new residue names after patching
Referenced by core::chemical::Patch::apply(), residue_type_all_patches_name(), and residue_type_base_name().
| VariantType const core::chemical::PHOSPHORYLATION |
| VariantType const core::chemical::PROTONATED |
| VariantType const core::chemical::REPLONLY |
Referenced by core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::scoring::methods::OmegaTetherEnergy::old_eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::methods::CenRotEnvEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), and core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair().
| std::string const core::chemical::RNA = "rna" |
tag name for querying RNA chemical type set.
Referenced by core::import_pose::build_pose(), core::pose::rna::correctly_position_cutpoint_phosphate_torsions(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::pdb::fixup_rinfo_based_on_residue_type_set(), core::pose::rna::RNA_IdealCoord::init(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdbstring(), core::import_pose::poses_from_pdbs(), and core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs().
| VariantType const core::chemical::SC_ORBITALS |
| VariantType const core::chemical::SIDECHAIN_CONJUGATION |
| VariantType const core::chemical::SPECIAL_ROT |
| VariantType const core::chemical::SULFATION |
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Referenced by core::chemical::ResidueType::add_actcoord_atom(), core::chemical::ResidueType::add_atom(), core::chemical::AtomTypeSet::add_parameters_from_file(), core::chemical::ResidueType::add_property(), core::chemical::Patch::apply(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::calculate_icoor(), core::chemical::ResidueType::debug_dump_icoor(), core::chemical::ResidueType::delete_property(), 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::ElementSet::read_file(), core::chemical::Patch::read_file(), core::chemical::MMAtomTypeSet::read_file(), core::chemical::AtomTypeSet::read_file(), core::chemical::ResidueType::report_adducts(), core::chemical::ResidueTypeSet::ResidueTypeSet(), core::chemical::ResidueType::set_lower_connect_atom(), core::chemical::ResidueType::set_upper_connect_atom(), core::chemical::ResidueType::vd_from_name(), and core::chemical::ResidueType::~ResidueType().
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Referenced by add_atom_type_set_parameters_from_command_line(), apply_adducts_to_residue(), core::chemical::ChemicalManager::create_residue_type_set(), core::chemical::RingConformerSet::get_ideal_conformer_by_CP_parameters(), core::chemical::Bond::GetMaximumElectrons(), core::chemical::Bond::GetMinimumElectrons(), core::chemical::Bond::GetNumberOfElectrons(), core::chemical::Bond::GetSDAltFileID(), core::chemical::Bond::GetSDFileID(), core::chemical::Atom::is_fake(), modify_atom_properties_from_command_line(), core::chemical::carbohydrates::read_codes_and_roots_from_database_file(), read_conformers_from_database_file_for_ring_size(), core::chemical::carbohydrates::read_properties_from_database_file(), and core::chemical::Bond::SetSDFType().
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Referenced by define_mainchain_atoms(), and read_topology_file().
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Referenced by core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::AddAtom::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), and core::chemical::SetNbrAtom::apply().
| VariantType const core::chemical::TRIMETHYLATION |
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Referenced by core::chemical::ICoorAtomID::ICoorAtomID(), and core::chemical::ICoorAtomID::xyz().
| VariantType const core::chemical::UPPER_TERMINUS |
Referenced by core::conformation::add_upper_terminus_type_to_conformation_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::scoring::GenBornPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pose::rna::correctly_add_cutpoint_variants(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), and core::pose::residue_types_from_sequence().
| VariantType const core::chemical::UPPERTERM_TRUNC |
Referenced by core::io::pdb::build_pose_as_is1().
| VariantType const core::chemical::VIRTUAL_O2PRIME_HYDROGEN |
| VariantType const core::chemical::VIRTUAL_PHOSPHATE |
Referenced by core::pose::rna::correctly_add_cutpoint_variants().
| VariantType const core::chemical::VIRTUAL_RNA_RESIDUE |
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