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Rosetta 3.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta 3.5
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Namespaces | |
| carbohydrates | |
| orbitals | |
| rna | |
| sdf | |
Classes | |
| class | Adduct |
| Description of optional single-atom residue adducts. More... | |
| class | Atom |
| basic chemical atom More... | |
| class | ICoorAtomID |
| Atom 's ID in internal coordinates in a ResidueType. More... | |
| class | AtomICoor |
| A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More... | |
| class | 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 | ChemicalManager |
| a class managing different sets of atom_type_set and residue_type_set More... | |
| class | CSDAtomType |
| Basic "conformational" atom type derived from analysis of Cambridge Structure Database. More... | |
| class | CSDAtomTypeSet |
| A set of CSDAtomTypes. More... | |
| class | Element |
| class to describe Elements More... | |
| class | ElementSet |
| A set of Elements. More... | |
| class | IdealBondLengthSet |
| A set of Elements. More... | |
| class | MMAtomType |
| Basic MM atom type. More... | |
| class | MMAtomTypeSet |
| A set of MMAtomTypes. More... | |
| class | Orbital |
| basic chemical atom More... | |
| class | PatchCase |
| A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More... | |
| class | Patch |
| A class patching basic ResidueType to create variant types, containing multiple PatchCase. More... | |
| class | PatchOperation |
| A single operation that needs to be applied in a residue patch. More... | |
| class | DeleteAtom |
| delete an atom More... | |
| class | SetBackboneHeavyatom |
| set an atom as backbone heavy atom More... | |
| class | SetPolymerConnectAtom |
| set an atom as polymer connection More... | |
| class | AddConnect |
| class | AddProperty |
| add a property to ResidueType More... | |
| class | DeleteProperty |
| delete a property from ResidueType Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM's (e.g. methylation) More... | |
| class | AddChi |
| Add a chi angle to ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's, which often result in one or more extra chi angles. More... | |
| class | AddProtonChi |
| class | RedefineChi |
| Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTM's. More... | |
| class | AddChiRotamer |
| Add a rotamer sample to a chi angle of the ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's. More... | |
| class | AddAtom |
| add an atom to ResidueType More... | |
| class | AddBond |
| add a bond to ResidueType More... | |
| class | SetAtomicCharge |
| set an atom's charge More... | |
| class | SetAtomType |
| set atom's chemical type More... | |
| class | SetIO_String |
| set atom's chemical type More... | |
| class | SetMMAtomType |
| set atom's MM chemical type More... | |
| class | SetICoor |
| set an atom's AtomICoord More... | |
| class | PrependMainchainAtom |
| add a mainchain atom before the first mainchain atom More... | |
| class | AppendMainchainAtom |
| add a mainchain atom after the last mainchain atom More... | |
| class | SetNbrAtom |
| set the residue neighbor atom More... | |
| class | SetNbrRadius |
| set the residue neighbor radius More... | |
| class | SetOrientAtom |
| Set orient atom selection mode. More... | |
| class | NCAARotLibPath |
| set the path to a rotamer library for an NCAA that is not in dunbrack 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 | ResidueSelectorSingle |
| A base class for defining a ResidueSelector by a single criterion. More... | |
| class | Selector_AA |
| Does the residue belong to ANY of these AAs? More... | |
| class | Selector_CMDFLAG |
| Is a certain string in the command-line option -chemical:allow_patch present ? this selector does actually not depend on the residuetype it is queried for. More... | |
| class | Selector_NAME3 |
| Does the residue have to ANY of these three-letter codes? More... | |
| class | Selector_PROPERTY |
| Does the residue have ANY of these properties? More... | |
| class | Selector_VARIANT_TYPE |
| Does the residue have ANY of variant types? More... | |
| class | Selector_MATCH_VARIANTS |
| Does the residue have ALL of the variant types and no more. More... | |
| class | Selector_NO_VARIANTS |
| Does the residue have ANY of variant types? More... | |
| class | Selector_NAME1 |
| Does the residue belong to ANY of these AAs? More... | |
| class | ResidueSelector |
| A class picking out a subset of ResidueType by multiple criteria. More... | |
| class | ResidueType |
| silly demo class – what would the most familiar residue look like? More... | |
| class | ResidueTypeSet |
| A collection of ResidueType defined. 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_vrt, 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 | 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 a AA string name and return its enum type 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, const Atom &atom_type) |
| static basic::Tracer | tw ("core.chemical.AtomICoor", basic::t_warning) |
| std::ostream & | operator<< (std::ostream &out, const AtomType &atom_type) |
| static basic::Tracer | tr ("core.chemical") |
| static basic::Tracer | tr ("core.chemical.ChemicalManager") |
| std::string const | FA_STANDARD ("fa_standard") |
| tag name for querying fullatom chemical type set. More... | |
| std::string const | CENTROID ("centroid") |
| tag name for querying centroid 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... | |
| static basic::Tracer | tr ("core.chemical") |
| bool | CSDAtomTypeSetcontains_atom_type (std::string const &atom_type_name) const |
| static basic::Tracer | tr ("core.chemical") |
| static basic::Tracer | tr ("core.chemical") |
| static basic::Tracer | tr ("core.chemical") |
| std::ostream & | operator<< (std::ostream &out, const Orbital &orbital) |
| static basic::Tracer | tr ("core.chemical") |
| 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... | |
| static basic::Tracer | tr ("core.chemical") |
| std::string | expand_icoor_atom_name (std::string name, ResidueType const &rsd) |
| helper function More... | |
| PatchOperationOP | patch_operation_from_patch_file_line (std::string const &line) |
| Virtual constructor, returns 0 if no match. More... | |
| static basic::Tracer | TR_PatchOperations ("core.chemical.PatchOperations.hh") |
| bool | operator< (ResConnID const &lhs, ResConnID const &rhs) |
| bool | operator== (ResConnID const &lhs, ResConnID const &rhs) |
| bool | operator!= (ResConnID const &lhs, ResConnID const &rhs) |
| static basic::Tracer | tr ("core.chemical") |
| id::AtomID | atom_id_from_icoor_line (std::string const name, ResidueType const &rsd) |
| helper fxn More... | |
| 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) |
| function to write out a topology file given a residue type, can be used to 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... | |
| static basic::Tracer | tr ("core.chemical.ResidueType") |
| std::string | strip_whitespace (std::string const &name) |
| must be a better place for this, probably already exists! More... | |
| static basic::Tracer | tr ("core.chemical.ResidueTypeSet") |
| static basic::Tracer | TR ("core.chemical.util") |
| 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 | 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_O2STAR_HYDROGEN ("VIRTUAL_O2STAR_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 | SIDECHAIN_CONJUGATION ("SIDECHAIN_CONJUGATION") |
| This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination) More... | |
| typedef std::map< std::string, int > core::chemical::AdductMap |
Definition at line 38 of file adduct_util.hh.
Definition at line 33 of file Adduct.fwd.hh.
| typedef utility::pointer::owning_ptr< Atom const > core::chemical::AtomCOP |
Definition at line 26 of file Atom.fwd.hh.
| typedef utility::vector1< AtomCOP > core::chemical::AtomCOPs |
Definition at line 28 of file Atom.fwd.hh.
| typedef utility::vector1< Size > core::chemical::AtomIndices |
Definition at line 48 of file ResidueType.fwd.hh.
Definition at line 23 of file Atom.fwd.hh.
| typedef utility::vector1< AtomOP > core::chemical::AtomOPs |
Definition at line 27 of file Atom.fwd.hh.
| typedef utility::pointer::owning_ptr< AtomTypeDatabaseIO > AtomTypeDatabaseIOOP typedef utility::pointer::owning_ptr< AtomTypeDatabaseIO const > core::chemical::AtomTypeDatabaseIOCOP |
Definition at line 22 of file AtomTypeDatabaseIO.fwd.hh.
| typedef int core::chemical::AtomTypeIndex |
Definition at line 43 of file IdealBondLengthSet.hh.
Definition at line 23 of file AtomTypeSet.fwd.hh.
| typedef utility::pointer::access_ptr< AtomTypeSet const > core::chemical::AtomTypeSetCAP |
Definition at line 26 of file AtomTypeSet.fwd.hh.
Definition at line 27 of file AtomTypeSet.fwd.hh.
| typedef utility::pointer::owning_ptr< AutomorphismIterator const > core::chemical::AutomorphismIteratorCOP |
Definition at line 33 of file automorphism.hh.
Definition at line 31 of file automorphism.hh.
| typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::bondangle_atom_set |
Definition at line 112 of file ResidueType.hh.
| typedef Real core::chemical::BondLength |
Definition at line 44 of file IdealBondLengthSet.hh.
Definition at line 23 of file CSDAtomTypeSet.fwd.hh.
| typedef utility::pointer::access_ptr< CSDAtomTypeSet const > core::chemical::CSDAtomTypeSetCAP |
Definition at line 26 of file CSDAtomTypeSet.fwd.hh.
| typedef utility::pointer::owning_ptr< CSDAtomTypeSet const > core::chemical::CSDAtomTypeSetCOP |
Definition at line 28 of file CSDAtomTypeSet.fwd.hh.
Definition at line 27 of file CSDAtomTypeSet.fwd.hh.
| typedef utility::keys::Key4Tuple< Size, Size, Size, Size > core::chemical::dihedral_atom_set |
Definition at line 113 of file ResidueType.hh.
Definition at line 23 of file ElementSet.fwd.hh.
| typedef utility::pointer::access_ptr< ElementSet const > core::chemical::ElementSetCAP |
Definition at line 26 of file ElementSet.fwd.hh.
Definition at line 27 of file ElementSet.fwd.hh.
Definition at line 23 of file IdealBondLengthSet.fwd.hh.
| typedef utility::pointer::access_ptr< IdealBondLengthSet const > core::chemical::IdealBondLengthSetCAP |
Definition at line 26 of file IdealBondLengthSet.fwd.hh.
Definition at line 27 of file IdealBondLengthSet.fwd.hh.
Definition at line 23 of file MMAtomTypeSet.fwd.hh.
| typedef utility::pointer::access_ptr< MMAtomTypeSet const > core::chemical::MMAtomTypeSetCAP |
Definition at line 26 of file MMAtomTypeSet.fwd.hh.
Definition at line 27 of file MMAtomTypeSet.fwd.hh.
| typedef utility::pointer::owning_ptr< Orbital const > core::chemical::OrbitalCOP |
Definition at line 26 of file Orbital.fwd.hh.
Definition at line 28 of file Orbital.fwd.hh.
Definition at line 49 of file ResidueType.fwd.hh.
Definition at line 23 of file Orbital.fwd.hh.
| typedef utility::vector1< OrbitalOP > core::chemical::OrbitalOPs |
Definition at line 27 of file Orbital.fwd.hh.
Definition at line 23 of file Patch.fwd.hh.
Definition at line 26 of file Patch.fwd.hh.
Definition at line 38 of file PatchOperation.fwd.hh.
Definition at line 38 of file ResidueSelector.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidueSelectorSingle > core::chemical::ResidueSelectorSingleOP |
Definition at line 35 of file ResidueSelector.fwd.hh.
Definition at line 38 of file ResidueType.fwd.hh.
| typedef utility::pointer::access_ptr< ResidueType const > core::chemical::ResidueTypeCAP |
Definition at line 41 of file ResidueType.fwd.hh.
Definition at line 45 of file ResidueType.fwd.hh.
| typedef utility::pointer::owning_ptr< ResidueType const > core::chemical::ResidueTypeCOP |
Definition at line 43 of file ResidueType.fwd.hh.
Definition at line 46 of file ResidueType.fwd.hh.
Definition at line 42 of file ResidueType.fwd.hh.
Definition at line 44 of file ResidueType.fwd.hh.
| typedef utility::pointer::access_ptr< ResidueTypeSet const > core::chemical::ResidueTypeSetCAP |
Definition at line 27 of file ResidueTypeSet.fwd.hh.
Definition at line 23 of file ResidueTypeSet.fwd.hh.
| typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::three_atom_set |
Definition at line 111 of file ResidueType.hh.
| typedef utility::keys::Key2Tuple< Size, Size > core::chemical::two_atom_set |
Definition at line 110 of file ResidueType.hh.
| typedef std::string core::chemical::VariantType |
Notion of Residue variant, eg PHOSPHO, NTERM, TERMINUS, PROTONATION, GLYCOSO ??
Definition at line 37 of file VariantType.fwd.hh.
| enum core::chemical::AA |
enumeration for amino acids and nucleotides types with the total number as num_aa_types
| Enumerator | |
|---|---|
| UnknownBond | |
| SingleBond | |
| DoubleBond | |
| TripleBond | |
| AromaticBond | |
| OrbitalBond | |
Definition at line 51 of file ResidueType.fwd.hh.
|
inline |
vector that maps AA enum to string name
Definition at line 159 of file AA.cc.
References setup_aa2name().
Referenced by name_from_aa().
|
inline |
vector that maps AA enum to one letter char
Definition at line 182 of file AA.cc.
References setup_aa2oneletter().
Referenced by oneletter_code_from_aa().
| AA core::chemical::aa_from_name | ( | std::string const & | name) |
give a AA string name and return its enum type
Definition at line 193 of file AA.cc.
References core::sequence::end, and name2aa().
Referenced by core::chemical::ResidueType::aa(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), core::pack::task::operation::RestrictYSDesign::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::motifs::Motif::build_rotamers(), protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::motifs::MotifDnaPacker::expand_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::match::Matcher::initialize_from_file(), protocols::motifs::make_dna_mutations(), protocols::simple_filters::RotamerBoltzmannWeight::parse_def(), protocols::simple_filters::NeighborTypeFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::P_AA::read_P_AA(), core::scoring::P_AA::read_P_AA_n(), core::scoring::P_AA::read_P_AA_pp(), core::chemical::ResidueType::rotamer_aa(), and protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters().
| AA core::chemical::aa_from_oneletter_code | ( | char | onelettercode) |
give a 1 letter code and return the string name
Definition at line 264 of file AA.cc.
References oneletter2aa().
Referenced by core::sequence::AnnotatedSequence::aa(), protocols::noesy_assign::ResonanceList::aa_from_resid(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), protocols::forge::components::BDR::allowed_surface_aa(), protocols::forge::remodel::RemodelMover::allowed_surface_aa(), core::pose::Pose::annotated_sequence(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::monte_carlo::RNA_AddMover::apply(), protocols::toolbox::task_operations::ThreadSequenceOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::rna::RNA_HelixAssembler::build_on_base_pair(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::flxbb::LayerDesignOperation::get_restrictions(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), 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(), protocols::sasa_scores::load_avge_polynomial_coefficients(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::optimize_weights::IterativeOptEDriver::load_pssm_data(), protocols::sasa_scores::load_sasapack_polynomial_coefficients(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::pmut_scan::PointMutScanDriver::make_mutant_structure(), core::fragment::make_pose_from_sequence_(), protocols::analysis::InterfaceAnalyzerMover::mut_to_gly(), core::scoring::nv::NVlookup::NVlookup(), core::fragment::picking_old::vall::VallResidue::order_vector(), protocols::frag_picker::VallResidue::order_vector(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter(), protocols::multistate_design::PosType::PosType(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::forge::components::BDR::process_continuous_design_string(), protocols::forge::remodel::RemodelMover::process_continuous_design_string(), protocols::forge::components::BDR::process_insert_design_string(), protocols::forge::remodel::RemodelMover::process_insert_design_string(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), protocols::dna::DnaInterfacePacker::protein_scan(), core::sequence::MatrixScoringScheme::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::read_in_mutations(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), core::pose::residue_types_from_sequence(), core::sequence::MatrixScoringScheme::score(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), 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.
Definition at line 56 of file util.cc.
References core::chemical::AtomTypeSet::add_parameters_from_file(), protocols::swa::rna::file_exists(), protocols::abinitio::filename(), and TR().
Referenced by core::chemical::ChemicalManager::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.
Definition at line 117 of file adduct_util.cc.
References core::chemical::PatchCase::add_operation(), ADDUCT, core::chemical::PatchCase::apply(), core::chemical::ResidueType::defined_adducts(), core::chemical::ResidueType::name(), 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
Definition at line 105 of file residue_io.cc.
References core::id::BOGUS_ATOM_ID, and protocols::swa::monte_carlo::INTERNAL.
| 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::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
Definition at line 220 of file Patch.cc.
References patch_operation_from_patch_file_line(), 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::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.
| bool core::chemical::CSDAtomTypeSetcontains_atom_type | ( | std::string const & | atom_type_name) | const |
Definition at line 47 of file CSDAtomTypeSet.cc.
| 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
| 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.
Definition at line 85 of file adduct_util.cc.
References core::chemical::ResidueType::defined_adducts().
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.
Definition at line 85 of file adduct_util.cc.
References core::chemical::ResidueType::defined_adducts().
Referenced by core::chemical::ResidueTypeSet::place_adducts().
| std::string core::chemical::expand_icoor_atom_name | ( | std::string | name, |
| ResidueType const & | rsd | ||
| ) |
helper function
Definition at line 59 of file PatchOperation.cc.
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.
| ObjexxFCL::FArray2D_int core::chemical::get_residue_path_distances | ( | ResidueType const & | res) |
relies on class Graph to find all pairs shortest path information
Definition at line 36 of file ResidueSupport.cc.
References core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::natoms(), and core::graph::Graph::set_num_nodes().
Referenced by read_topology_file(), 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" | ) |
| VariantType const core::chemical::LOWER_TERMINUS | ( | "LOWER_TERMINUS" | ) |
N-terminus cap.
| 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.
Definition at line 89 of file util.cc.
References core::chemical::AtomTypeSet::atom_type_index(), core::chemical::AtomTypeSet::has_atom(), and TR().
Referenced by core::chemical::ChemicalManager::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.
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inline |
map that converts string name to AA enum
Definition at line 127 of file AA.cc.
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
Definition at line 250 of file AA.cc.
References aa2name(), and num_aa_types.
Referenced by protocols::noesy_assign::MethylNames::aa_name(), core::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), core::pose::Pose::annotated_sequence(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::rna::base_atoms_square_deviation(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::dna::dna_base_partner(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::swa::rna::Get_num_side_chain_atom_from_res_name(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::swa::rna::Is_virtual_base(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::toolbox::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), operator<<(), protocols::noesy_assign::MethylNameLibrary::operator[](), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), 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::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::chemical::ResidueDatabaseIO::read_residue_type(), read_topology_file(), core::scoring::methods::EnvSmoothEnergy::representative_atom_name(), core::scoring::methods::MembraneEnvSmoothEnergy::representative_atom_name(), core::pack::task::ResidueLevelTask_::restrict_absent_nas(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::swa::rna::suite_square_deviation(), protocols::swa::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), and protocols::noesy_assign::Resonance::write_to_stream().
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inline |
map that converts one letter char to AA enum
Definition at line 136 of file AA.cc.
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
Definition at line 257 of file AA.cc.
References aa2oneletter(), and num_canonical_aas.
Referenced by protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::optimize_weights::IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpus(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::design_opt::insert_point_mut_filter_vals(), protocols::ddg::ddGMover::mutation_label(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::loops::set_secstruct_from_dssp(), core::fragment::SingleResidueFragData::steal(), protocols::multistate_design::PosType::to_string(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile(), protocols::noesy_assign::ResonanceList::write_talos_format(), and protocols::noesy_assign::Resonance::write_to_stream().
| bool core::chemical::oneletter_code_specifies_aa | ( | char | onelettercode) |
Definition at line 271 of file AA.cc.
References oneletter2aa().
Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pose::Pose::annotated_sequence(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), 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(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), core::sequence::MatrixScoringScheme::read_data(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), 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 | ||
| ) |
Definition at line 46 of file ResConnID.cc.
| bool core::chemical::operator< | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
Definition at line 35 of file ResConnID.cc.
References core::chemical::ResConnID::conn_id_, and core::chemical::ResConnID::res_id_.
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const Orbital & | orbital | ||
| ) |
Definition at line 60 of file Orbital.cc.
References core::chemical::Orbital::print().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const Atom & | atom_type | ||
| ) |
Definition at line 63 of file Atom.cc.
References core::chemical::Atom::print().
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const AtomType & | atom_type | ||
| ) |
Definition at line 91 of file AtomType.cc.
References core::chemical::AtomType::print().
| 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;
Definition at line 239 of file AA.cc.
References name_from_aa().
| bool core::chemical::operator== | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
Definition at line 41 of file ResConnID.cc.
References core::chemical::ResConnID::conn_id_, and core::chemical::ResConnID::res_id_.
| 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.
Definition at line 213 of file AA.cc.
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.
Definition at line 49 of file adduct_util.cc.
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.
Definition at line 90 of file PatchOperation.cc.
References protocols::swa::phi(), and tr().
Referenced by case_from_lines().
| VariantType const core::chemical::PHOSPHORYLATION | ( | "PHOSPHORYLATION" | ) |
| VariantType const core::chemical::PROTONATED | ( | "PROTONATED" | ) |
| 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
Definition at line 130 of file residue_io.cc.
References protocols::swa::rna::file_exists().
Referenced by core::chemical::ResidueLoader::create_resource(), 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 rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/???.params These files contain information about each basic ResidueType which can be patched to created various variant types.
Definition at line 157 of file residue_io.cc.
References core::id::D, protocols::abinitio::filename(), get_residue_path_distances(), name_from_aa(), protocols::swa::phi(), protocols::swa::rotate(), core::kinematics::Stub::spherical(), strip_whitespace(), and tr().
| 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.
Definition at line 57 of file ResidueSelector.cc.
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
Definition at line 197 of file Patch.cc.
References core::chemical::ResidueType::name(), and patch_linker.
Referenced by protocols::simple_moves::chiral::get_chiral_residue_type(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper().
| std::string core::chemical::residue_type_base_name | ( | ResidueType const & | rsd_type) |
helper function, returns the base residue name prior to any patching
Definition at line 191 of file Patch.cc.
References core::chemical::ResidueType::name(), and patch_linker.
Referenced by protocols::toolbox::match_enzdes_util::add_relevant_restypes_to_subset(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), core::io::pdb::build_pose_as_is1(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), protocols::simple_moves::chiral::is_d_chiral(), protocols::simple_moves::chiral::is_l_chiral(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), and protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose().
| core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line | ( | ) |
Definition at line 39 of file util.cc.
References core::chemical::ChemicalManager::get_instance(), and core::chemical::ChemicalManager::residue_type_set().
Referenced by protocols::simple_filters::StructureSimilarityEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::hotspot_hashing::StubGenerator::getStubByName(), protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line(), and protocols::comparative_modeling::poses_from_cmd_line().
| 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
Definition at line 144 of file AA.cc.
References 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
Definition at line 167 of file AA.cc.
References 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
Definition at line 39 of file AA.cc.
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_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
Definition at line 83 of file AA.cc.
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_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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inline |
must be a better place for this, probably already exists!
Definition at line 107 of file ResidueType.cc.
Referenced by core::chemical::ResidueType::add_atom(), core::chemical::ResidueType::add_orbital(), and core::chemical::ResidueType::reorder_primary_data().
| 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
Definition at line 207 of file Patch.cc.
Referenced by case_from_lines(), and core::chemical::Patch::read_file().
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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::scoring::hbonds::assign_abase_derivs(), core::chemical::ResidueType::atom_index(), core::scoring::automorphic_rmsd(), core::scoring::CA_gdtmm(), core::scoring::CA_maxsub(), core::scoring::CA_rmsd(), core::scoring::CA_rmsd_symmetric(), core::chemical::ResidueType::calculate_icoor(), protocols::noesy_assign::CrossPeakList::calibrate(), protocols::canonical_sampling::canonical_sampling_main(), core::chemical::ResidueType::debug_dump_icoor(), core::chemical::ResidueType::delete_property(), core::scoring::gdtha(), core::scoring::gdtsc(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbond_compute_energy(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), OPT_1GRP_KEY(), 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::CSDAtomTypeSet::read_file(), core::chemical::MMAtomTypeSet::read_file(), core::chemical::ElementSet::read_file(), core::chemical::Patch::read_file(), core::chemical::AtomTypeSet::read_file(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), read_topology_file(), core::chemical::ResidueType::report_adducts(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::ResidueType::set_lower_connect_atom(), core::chemical::ResidueType::set_upper_connect_atom(), core::chemical::ResidueType::setup_atom_ordering(), core::fragment::SecstructSRFD::steal(), protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score(), protocols::vip::VIP_Mover::VIP_Mover(), core::scoring::xyz_gdtmm(), and core::chemical::ResidueType::~ResidueType().
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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::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 | ( | "TRIMETHYLATION" | ) |
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Referenced by core::chemical::ICoorAtomID::xyz().
| VariantType const core::chemical::UPPER_TERMINUS | ( | "UPPER_TERMINUS" | ) |
C-terminus cap.
| VariantType const core::chemical::VIRTUAL_O2STAR_HYDROGEN | ( | "VIRTUAL_O2STAR_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) |
function to write out a topology file given a residue type, can be used to
writes a .params file from a given ResidueType object
debug on the fly generated residue types. Note: not perfect yet, the enums for the connection types are given in numbers instead of names
Definition at line 776 of file residue_io.cc.
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(), protocols::abinitio::filename(), core::chemical::ResidueType::force_nbr_atom_orient(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lower_terminus(), 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(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::mm_atom_type(), 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::AtomICoor::phi(), core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), 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 |
Referenced by apply_adducts_to_residue(), protocols::dna::make_sequence_combinations(), protocols::dna::make_single_mutants(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), core::chemical::ResidueType::nonadduct_variants_match(), and core::pack::task::ResidueLevelTask_::or_adducts().
| 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::C_METHYLAMIDATION |
| VariantType const core::chemical::CARBOXYLATION |
| std::string const core::chemical::CENTROID |
Referenced by protocols::abinitio::StructureStore::add(), protocols::topology_broker::add_cmdline_claims(), protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::medal::MedalMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::FastGapMover::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::antibody::CloseOneMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), core::scoring::AtomVDW::AtomVDW(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), core::import_pose::centroid_pose_from_pdb(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::simple_moves::GunnCost::compute_gunn(), protocols::swa::StepWiseScreener::convert_to_centroid(), protocols::swa::protein::StepWiseProteinScreener::convert_to_centroid(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), protocols::seeded_abinitio::GrowPeptides::grow_from_verteces(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::swa::StepWiseScreener::initialize_ghost_pose(), protocols::swa::protein::StepWiseProteinScreener::initialize_ghost_pose(), core::conformation::Conformation::is_centroid(), protocols::docking::DockingEnsemble::load_ensemble(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::pose_from_pdb(), core::import_pose::poseOPs_from_pdbs(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), protocols::topology_broker::CoordConstraintClaimer::read_cst_pose(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::toolbox::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute(), protocols::checkpoint::CheckPointer::recover_checkpoint(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::chemical::ChemicalManager::residue_type_set(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::flexpep_docking::FlexPepDockingAbInitio::restorePSER(), protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::abinitio::run_boinc_debug(), protocols::symmetric_docking::SymDockProtocol::score_only(), protocols::abinitio::AbrelaxApplication::setup(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::docking::TemperedDocking::setup_objects(), protocols::docking::DockingProtocol::setup_objects(), protocols::abinitio::ResolutionSwitcher::start_pose(), protocols::star::to_centroid(), protocols::flexpep_docking::FlexPepDockingLowRes::to_centroid(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_centroid(), protocols::medal::to_centroid(), and protocols::jobdist::universal_main().
| VariantType const core::chemical::CENTROID_HA |
| std::string const core::chemical::COARSE_RNA |
| std::string const core::chemical::COARSE_TWO_BEAD |
| VariantType const core::chemical::CUTPOINT_LOWER |
Referenced by protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::ligand_docking::MinimizeBackbone::add_cut_points(), core::util::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::loops::add_single_cutpoint_variant(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::antibody2::LHSnugFitLegacy::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::swa::StepWisePoseSetup::apply_cutpoint_variants(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::rna::RNA_LoopCloser::check_closure(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::abinitio::copy_side_chains(), protocols::forge::methods::cyclize_pose(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), protocols::swa::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::swa::rna::get_default_allowed_bulge_res(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_torsion(), core::scoring::rna::is_cutpoint_open(), core::scoring::methods::is_lower_cutpoint(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::methods::make_star_foldtree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::swa::rna::remove_chain_break_jump_point(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::rna::remove_cutpoint_closed(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::rna::RNA_LoopCloser::remove_variants_at_extra_cutpoints(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::swa::rna::setup_chain_break_jump_point(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::jumping::MembraneJump::setup_fold_tree(), core::conformation::setup_links(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::rna::RNA_LoopCloser::setup_variants_at_extra_cutpoints(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), and protocols::rna::virtualize_5prime_phosphates().
| VariantType const core::chemical::CUTPOINT_UPPER |
Referenced by protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::ligand_docking::MinimizeBackbone::add_cut_points(), core::util::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::loops::add_single_cutpoint_variant(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::antibody2::LHSnugFitLegacy::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::swa::StepWisePoseSetup::apply_cutpoint_variants(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::rna::RNA_LoopCloser::check_closure(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::abinitio::copy_side_chains(), protocols::forge::methods::cyclize_pose(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), protocols::swa::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::swa::rna::get_default_allowed_bulge_res(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_torsion(), core::scoring::rna::is_cutpoint_open(), core::scoring::methods::is_upper_cutpoint(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::methods::make_star_foldtree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::swa::rna::remove_chain_break_jump_point(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::rna::remove_cutpoint_closed(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::rna::RNA_LoopCloser::remove_variants_at_extra_cutpoints(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::swa::rna::setup_chain_break_jump_point(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::jumping::MembraneJump::setup_fold_tree(), core::conformation::setup_links(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::rna::RNA_LoopCloser::setup_variants_at_extra_cutpoints(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), and protocols::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(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), core::io::pdb::build_pose_as_is1(), core::conformation::change_cys_state(), protocols::sasa_scores::compute_avge_scores(), protocols::sasa_scores::compute_sasapack_scores(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), 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::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), protocols::protein_interface_design::movers::Splice::fold_tree(), core::conformation::form_disulfide(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), and protocols::swa::StepWisePoseSetup::setup_disulfides().
| std::string const core::chemical::FA_STANDARD |
Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::relax::MiniRelax::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::match::MatcherMover::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::antibody::CloseOneMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::relax::FastRelax::batch_apply(), core::import_pose::build_pose_as_is2(), core::io::pdb::build_pose_from_pdb_as_is(), protocols::MakeRotLib::calc_std_dev(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::chemical::IdealBondLengthSet::contains_bond_length(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), core::scoring::ScoringManager::etable(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), 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::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), core::conformation::form_disulfide(), protocols::swa::protein::generate_beta_database_test(), protocols::ligand_docking::generate_unique_name(), core::chemical::IdealBondLengthSet::get_bond_length(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::enzdes::AddOrRemoveMatchCsts::get_EnzConstraintIO_for_cstfile(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_instance(), 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(), protocols::simple_moves::AddCavitiesMover::get_suck_res(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::match::MatcherTask::initialize_enzdes_input_data_from_command_line(), core::conformation::Conformation::is_fullatom(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), core::scoring::ScoringManager::memb_etable(), protocols::MakeRotLib::min_rotamers(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::motifs::Motif::Motif(), core::conformation::orient_residue_for_ideal_bond(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::fldsgn::BluePrintBDR::parse_my_tag(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::checkpoint::pose_from_binary_silent_file(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), 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(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::jumping::ResiduePairJumpSetup::read_file(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::topology_broker::MetalloClaimer::read_tag(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::features::RotamerFeatures::report_features(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), core::chemical::ChemicalManager::residue_type_set(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::pack::task::operation::util::select_coord_for_residue(), protocols::forge::constraints::InvrotTreeRCG::set_cstfile(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::pack_daemon::DaemonSet::set_entity_resfile(), protocols::ligand_docking::LigandDesign::set_fragments(), protocols::ligand_docking::GrowLigand::set_fragments(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::docking::DockingProtocol::setup_objects(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::motifs::single_residue_from_stream(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::flexpep_docking::FlexPepDockingLowRes::to_allatom().
| VariantType const core::chemical::HBS_POST |
Referenced by protocols::simple_moves::hbs::HbsPatcher::apply().
| VariantType const core::chemical::HBS_PRE |
Referenced by protocols::simple_moves::hbs::HbsPatcher::apply().
| std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID |
| VariantType const core::chemical::HYDROXYLATION |
| VariantType const core::chemical::LOWER_TERMINUS |
Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), core::conformation::add_lower_terminus_type_to_conformation_residue(), core::pose::add_lower_terminus_type_to_pose_residue(), protocols::simple_moves::MissingDensityToJumpMover::apply(), core::scoring::GenBornPotential::build_placeholders(), core::scoring::FACTSPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::simple_moves::HelicalPeptideLengthMover::create_residue_from_resname_(), core::pose::symmetry::extract_asymmetric_unit(), protocols::swa::protein::generate_beta_database_test(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::insert_pose_into_pose(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::make_pose_from_sequence(), 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().
| 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.
Definition at line 53 of file AtomType.cc.
Referenced by core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff(), and core::scoring::hackelec::HackElecEnergy::hydrogen_interaction_cutoff().
| VariantType const core::chemical::METHYLATED_CTERMINUS |
| VariantType const core::chemical::METHYLATION |
| VariantType const core::chemical::N_ACETYLATION |
Referenced by protocols::swa::Figure_out_moving_residues(), and core::pose::make_pose_from_sequence().
| VariantType const core::chemical::OOP_POST |
| 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 protocols::simple_moves::RepulsiveOnlyMover::apply(), 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::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::SmoothEnvEnergy::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::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::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::OmegaTetherEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::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_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.
Definition at line 425 of file ChemicalManager.cc.
Referenced by protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::create_VDW_rep_screen_pose(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), protocols::swa::rna::get_binary_rna_silent_struct_safe(), protocols::swa::rna::import_pose_from_silent_file(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), protocols::swa::rna::StepWiseRNA_Clusterer::initialize_parameters_and_input(), protocols::rna::RNA_ChunkLibrary::process_input_file(), core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs(), and protocols::rna::RNA_HelixAssembler::use_phenix_geo().
| VariantType const core::chemical::SC_ORBITALS |
| VariantType const core::chemical::SIDECHAIN_CONJUGATION |
| VariantType const core::chemical::SPECIAL_ROT |
| VariantType const core::chemical::SULFATION |
| VariantType const core::chemical::TRIMETHYLATION |
| VariantType const core::chemical::UPPER_TERMINUS |
Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), core::conformation::add_upper_terminus_type_to_conformation_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), protocols::simple_moves::MissingDensityToJumpMover::apply(), core::scoring::GenBornPotential::build_placeholders(), core::scoring::FACTSPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::simple_moves::HelicalPeptideLengthMover::create_residue_from_resname_(), core::pose::symmetry::extract_asymmetric_unit(), protocols::swa::protein::generate_beta_database_test(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::insert_pose_into_pose(), core::pose::make_pose_from_sequence(), 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::VIRTUAL_O2STAR_HYDROGEN |
| VariantType const core::chemical::VIRTUAL_PHOSPHATE |
| VariantType const core::chemical::VIRTUAL_RNA_RESIDUE |
1.8.4