|
Rosetta 3.4
|
|
Rosetta 3.4
|
Namespaces | |
| namespace | orbitals |
| namespace | rna |
| namespace | sdf |
Classes | |
| class | Adduct |
| Description of optional single-atom residue adducts. 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 | MMAtomType |
| Basic MM atom type. More... | |
| class | MMAtomTypeSet |
| A set of MMAtomTypes. 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 | 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 | 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 | 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... | |
Typedefs | |
| typedef utility::pointer::owning_ptr < Adduct > | AdductOP |
| typedef std::map< std::string, int > | AdductMap |
| typedef utility::pointer::owning_ptr < AtomTypeDatabaseIO > AtomTypeDatabaseIOOP typedef utility::pointer::owning_ptr < AtomTypeDatabaseIO const > | AtomTypeDatabaseIOCOP |
| typedef utility::pointer::access_ptr < AtomTypeSet > | AtomTypeSetAP |
| typedef utility::pointer::access_ptr < AtomTypeSet const > | AtomTypeSetCAP |
| typedef utility::pointer::owning_ptr < AtomTypeSet > | AtomTypeSetOP |
| typedef utility::pointer::owning_ptr < AutomorphismIterator > | AutomorphismIteratorOP |
| typedef utility::pointer::owning_ptr < AutomorphismIterator const > | AutomorphismIteratorCOP |
| typedef utility::pointer::access_ptr < CSDAtomTypeSet > | CSDAtomTypeSetAP |
| typedef utility::pointer::access_ptr < CSDAtomTypeSet const > | CSDAtomTypeSetCAP |
| typedef utility::pointer::owning_ptr < CSDAtomTypeSet > | CSDAtomTypeSetOP |
| typedef utility::pointer::owning_ptr < CSDAtomTypeSet const > | CSDAtomTypeSetCOP |
| typedef utility::pointer::access_ptr < ElementSet > | ElementSetAP |
| typedef utility::pointer::access_ptr < ElementSet const > | ElementSetCAP |
| typedef utility::pointer::owning_ptr < ElementSet > | ElementSetOP |
| typedef utility::pointer::access_ptr < MMAtomTypeSet > | MMAtomTypeSetAP |
| typedef utility::pointer::access_ptr < MMAtomTypeSet const > | MMAtomTypeSetCAP |
| typedef utility::pointer::owning_ptr < MMAtomTypeSet > | MMAtomTypeSetOP |
| typedef utility::pointer::owning_ptr < PatchCase > | PatchCaseOP |
| typedef utility::pointer::owning_ptr < Patch > | PatchOP |
| typedef utility::pointer::owning_ptr < PatchOperation > | PatchOperationOP |
| typedef utility::pointer::owning_ptr < ResidueSelectorSingle > | ResidueSelectorSingleOP |
| typedef utility::pointer::owning_ptr < ResidueSelector > | ResidueSelectorOP |
| typedef utility::pointer::access_ptr < ResidueType > | ResidueTypeAP |
| typedef utility::pointer::access_ptr < ResidueType const > | ResidueTypeCAP |
| typedef utility::pointer::owning_ptr < ResidueType > | ResidueTypeOP |
| typedef utility::pointer::owning_ptr < ResidueType const > | ResidueTypeCOP |
| typedef utility::vector1 < ResidueTypeOP > | ResidueTypeOPs |
| typedef utility::vector1 < ResidueTypeCAP > | ResidueTypeCAPs |
| typedef utility::vector1< Size > | AtomIndices |
| typedef utility::vector1< Size > | OrbitalIndices |
| typedef utility::keys::Key2Tuple< Size, Size > | two_atom_set |
| typedef utility::keys::Key3Tuple< Size, Size, Size > | three_atom_set |
| typedef utility::keys::Key3Tuple< Size, Size, Size > | bondangle_atom_set |
| typedef utility::keys::Key4Tuple< Size, Size, Size, Size > | dihedral_atom_set |
| typedef utility::pointer::owning_ptr < ResidueTypeSet > | ResidueTypeSetOP |
| typedef utility::pointer::access_ptr < ResidueTypeSet const > | ResidueTypeSetCAP |
| typedef std::string | VariantType |
| Notion of Residue variant, eg PHOSPHO, NTERM, TERMINUS, PROTONATION, GLYCOSO ?? | |
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 | |
| std::map< char, AA > | setup_oneletter2aa () |
| setup the map the converts one letter char to AA enum | |
| std::map< std::string, AA > & | name2aa () |
| map that converts string name to AA enum | |
| std::map< char, AA > & | oneletter2aa () |
| map that converts one letter char to AA enum | |
| utility::vector1< std::string > | setup_aa2name () |
| setup the vector that maps AA enum to string name | |
| utility::vector1< std::string > & | aa2name () |
| vector that maps AA enum to string name | |
| utility::vector1< char > | setup_aa2oneletter () |
| setup the vector that maps AA enum to one letter char | |
| utility::vector1< char > & | aa2oneletter () |
| vector that maps AA enum to one letter char | |
| AA | aa_from_name (std::string const &name) |
| give a AA string name and return its enum type | |
| std::istream & | operator>> (std::istream &is, AA &aa) |
| input operator for AA enum type | |
| std::ostream & | operator<< (std::ostream &os, AA const &aa) |
| output operator for AA enum type | |
| std::string | name_from_aa (AA aa) |
| give a enum type and return the string name | |
| char | oneletter_code_from_aa (AA aa) |
| give a enum type and return the string name | |
| AA | aa_from_oneletter_code (char onelettercode) |
| give a 1 letter code and return the string name | |
| 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. | |
| void | error_check_requested_adducts (std::map< std::string, int > const &add_map, ResidueTypeCAPs const &rsd_types) |
| Make sure any adducts requested actually exist. | |
| ResidueTypeOP | apply_adducts_to_residue (ResidueType const &rsd, utility::vector1< bool > &add_mask) |
| Apply adducts to residue using a boolean mask. | |
| void | error_check_requested_adducts (AdductMap const &add_map, ResidueTypeCAPs const &rsd_types) |
| Make sure requested adducts exist in some residue. | |
| 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. | |
| std::string const | CENTROID ("centroid") |
| tag name for querying centroid chemical type set. | |
| std::string const | COARSE_TWO_BEAD ("coarse_two_bead") |
| tag name for querying coarse-grained chemical type set. | |
| std::string const | HYBRID_FA_STANDARD_CENTROID ("hybrid_fa_standard_centroid") |
| tag name for querying hybrid fullatom+centroid chemical type set. | |
| std::string const | RNA ("rna") |
| tag name for querying RNA chemical type set. | |
| std::string const | COARSE_RNA ("coarse_rna") |
| tag name for querying COARSE_RNA chemical type set. | |
| bool | CSDAtomTypeSetcontains_atom_type (std::string const &atom_type_name) const |
| std::string const | patch_linker ("_p:") |
| the string used to generate new residue names | |
| std::string | residue_type_base_name (ResidueType const &rsd_type) |
| helper function, returns the base residue name prior to any patching | |
| std::string | residue_type_all_patches_name (ResidueType const &rsd_type) |
| helper function, returns the name of all added patches | |
| std::string | tag_from_line (std::string const &line) |
| handy function, return the first word from a line | |
| PatchCaseOP | case_from_lines (utility::vector1< std::string > const &lines) |
| create a PatchCase from input lines | |
| std::string | expand_icoor_atom_name (std::string name, ResidueType const &rsd) |
| helper function | |
| PatchOperationOP | patch_operation_from_patch_file_line (std::string const &line) |
| Virtual constructor, returns 0 if no match. | |
| 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) |
| id::AtomID | atom_id_from_icoor_line (std::string const name, ResidueType const &rsd) |
| 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 | |
| void | write_topology_file (ResidueType const &rsd) |
| function to write out a topology file given a residue type, can be used to | |
| ResidueSelectorSingleOP | residue_selector_single_from_line (std::string const &line) |
| create a singe ResidueSelector from an input line. | |
| ObjexxFCL::FArray2D_int | get_residue_path_distances (ResidueType const &res) |
| relies on class Graph to find all pairs shortest path information | |
| 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! | |
| static basic::Tracer | tr ("core.chemical.ResidueTypeSet") |
| core::chemical::ResidueTypeSetCAP | rsd_set_from_cmd_line () |
| VariantType const | UPPER_TERMINUS ("UPPER_TERMINUS") |
| C-terminus cap. | |
| VariantType const | LOWER_TERMINUS ("LOWER_TERMINUS") |
| N-terminus cap. | |
| VariantType const | CUTPOINT_LOWER ("CUTPOINT_LOWER") |
| for use during loop modeling, at positions before a cutpoint | |
| VariantType const | CUTPOINT_UPPER ("CUTPOINT_UPPER") |
| for use during loop modeling, at positions after a cutpoint | |
| VariantType const | DISULFIDE ("DISULFIDE") |
| 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. | |
| 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 | ACTYLATED_NTERMINUS ("ACTYLATED_NTERMINUS") |
| Actyleated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. | |
| VariantType const | METHYLATED_CTERMINUS ("METHYLATED_CTERMINUS") |
| Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. | |
| 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. | |
| VariantType const | C_METHYLAMIDATION ("C_METHYLAMIDATION") |
| VariantType const | REPLONLY ("REPLONLY") |
Variables | |
| Real const | MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 } |
| Maximum distance between a heavy atom and a hydrogen atom to which it is chemically bound Set in .cc file. | |
| std::string const | FA_STANDARD |
| std::string const | CENTROID |
| std::string const | COARSE_TWO_BEAD |
| std::string const | HYBRID_FA_STANDARD_CENTROID |
| std::string const | RNA |
| std::string const | COARSE_RNA |
| std::string const | patch_linker |
| the string used to create new residue names after patching | |
| VariantType const | UPPER_TERMINUS |
| VariantType const | LOWER_TERMINUS |
| VariantType const | CUTPOINT_UPPER |
| VariantType const | CUTPOINT_LOWER |
| VariantType const | DISULFIDE |
| VariantType const | METHYLATION |
| VariantType const | ADDUCT |
| VariantType const | CENTROID_HA |
| VariantType const | PROTONATED |
| VariantType const | DEPROTONATED |
| VariantType const | SPECIAL_ROT |
| VariantType const | VIRTUAL_PHOSPHATE |
| VariantType const | VIRTUAL_RNA_RESIDUE |
| VariantType const | VIRTUAL_O2STAR_HYDROGEN |
| VariantType const | PHOSPHORYLATION |
| VariantType const | ACETYLATION |
| VariantType const | SULFATION |
| VariantType const | CARBOXYLATION |
| VariantType const | HYDROXYLATION |
| VariantType const | DIMETHYLATION |
| VariantType const | TRIMETHYLATION |
| VariantType const | DIIODINATION |
| VariantType const | ACTYLATED_NTERMINUS |
| VariantType const | METHYLATED_CTERMINUS |
| VariantType const | N_ACETYLATION |
| VariantType const | C_METHYLAMIDATION |
| VariantType const | SC_ORBITALS |
| VariantType const | REPLONLY |
| typedef std::map< std::string, int > core::chemical::AdductMap |
| typedef utility::vector1< Size > core::chemical::AtomIndices |
| typedef utility::pointer::owning_ptr< AtomTypeDatabaseIO > AtomTypeDatabaseIOOP typedef utility::pointer::owning_ptr< AtomTypeDatabaseIO const > core::chemical::AtomTypeDatabaseIOCOP |
| typedef utility::pointer::access_ptr< AtomTypeSet const > core::chemical::AtomTypeSetCAP |
| typedef utility::pointer::owning_ptr< AutomorphismIterator const > core::chemical::AutomorphismIteratorCOP |
| typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::bondangle_atom_set |
| typedef utility::pointer::access_ptr< CSDAtomTypeSet const > core::chemical::CSDAtomTypeSetCAP |
| typedef utility::pointer::owning_ptr< CSDAtomTypeSet const > core::chemical::CSDAtomTypeSetCOP |
| typedef utility::keys::Key4Tuple< Size, Size, Size, Size > core::chemical::dihedral_atom_set |
| typedef utility::pointer::access_ptr< ElementSet const > core::chemical::ElementSetCAP |
| typedef utility::pointer::access_ptr< MMAtomTypeSet const > core::chemical::MMAtomTypeSetCAP |
| typedef utility::pointer::owning_ptr< ResidueSelectorSingle > core::chemical::ResidueSelectorSingleOP |
| typedef utility::pointer::access_ptr< ResidueType const > core::chemical::ResidueTypeCAP |
| typedef utility::pointer::owning_ptr< ResidueType const > core::chemical::ResidueTypeCOP |
| typedef utility::pointer::access_ptr< ResidueTypeSet const > core::chemical::ResidueTypeSetCAP |
| typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::three_atom_set |
| typedef utility::keys::Key2Tuple< Size, Size > core::chemical::two_atom_set |
| typedef std::string core::chemical::VariantType |
Notion of Residue variant, eg PHOSPHO, NTERM, TERMINUS, PROTONATION, GLYCOSO ??
| enum core::chemical::AA |
enumeration for amino acids and nucleotides types with the total number as num_aa_types
| utility::vector1< std::string >& core::chemical::aa2name | ( | ) | [inline] |
| utility::vector1< char >& core::chemical::aa2oneletter | ( | ) | [inline] |
vector that maps AA enum to one letter char
References setup_aa2oneletter().
Referenced by oneletter_code_from_aa().
| AA core::chemical::aa_from_name | ( | std::string const & | name | ) |
give a AA string name and return its enum type
References core::sequence::end, and name2aa().
Referenced by core::chemical::ResidueType::aa(), protocols::flxbb::LayerDesignOperation::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::operation::RestrictYSDesign::apply(), protocols::motifs::Motif::build_rotamers(), protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::Matcher::initialize_from_file(), protocols::motifs::make_dna_mutations(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_filters::NeighborTypeFilter::parse_my_tag(), protocols::protein_interface_design::NeighborTypeFilter::parse_my_tag(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), and protocols::noesy_assign::ResonanceList::read_from_stream().
| AA core::chemical::aa_from_oneletter_code | ( | char | onelettercode | ) |
give a 1 letter code and return the string name
References oneletter2aa().
Referenced by core::sequence::AnnotatedSequence::aa(), protocols::noesy_assign::ResonanceList::aa_from_resid(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pose::Pose::annotated_sequence(), protocols::toolbox::task_operations::ThreadSequenceOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::scoring::methods::get_restag(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::PIKAA::initialize_from_tokens(), core::sequence::ProfSimScoringScheme::initialize_parameters(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), core::fragment::make_pose_from_sequence_(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter(), protocols::multistate_design::PosType::PosType(), 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(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), core::pose::residue_types_from_sequence(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), core::sequence::MatrixScoringScheme::score(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(), and core::sequence::MatrixScoringScheme::values_for_aa().
| VariantType const core::chemical::ACETYLATION | ( | "ACETYLATION" | ) |
| VariantType const core::chemical::ACTYLATED_NTERMINUS | ( | "ACTYLATED_NTERMINUS" | ) |
Actyleated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries.
| VariantType const core::chemical::ADDUCT | ( | "ADDUCT" | ) |
| ResidueTypeOP core::chemical::apply_adducts_to_residue | ( | ResidueType const & | rsd, |
| utility::vector1< bool > & | add_mask | ||
| ) |
Apply adducts to residue using a boolean mask.
References core::chemical::PatchCase::add_operation(), ADDUCT, core::chemical::PatchCase::apply(), core::chemical::ResidueType::defined_adducts(), core::chemical::ResidueType::name(), and core::TR().
Referenced by core::chemical::ResidueTypeSet::create_adduct_combinations().
| id::AtomID core::chemical::atom_id_from_icoor_line | ( | std::string const | name, |
| ResidueType const & | rsd | ||
| ) |
helper fxn
References core::id::BOGUS_ATOM_ID.
| VariantType const core::chemical::C_METHYLAMIDATION | ( | "C_METHYLAMIDATION" | ) |
| VariantType const core::chemical::CARBOXYLATION | ( | "CARBOXYLATION" | ) |
| PatchCaseOP core::chemical::case_from_lines | ( | utility::vector1< std::string > const & | lines | ) |
create a PatchCase from input lines
add selector_ from lines enclosed by "BEGIN_SELECTOR" and "END_SELECTOR".
add operations_ from each input line containing a single operation
References patch_operation_from_patch_file_line(), 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 |
| 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, |
| ResidueTypeCAPs const & | rsd_types | ||
| ) |
Make sure any adducts requested actually exist.
References core::chemical::ResidueType::defined_adducts().
Referenced by core::chemical::ResidueTypeSet::place_adducts().
| void core::chemical::error_check_requested_adducts | ( | AdductMap const & | add_map, |
| ResidueTypeCAPs const & | rsd_types | ||
| ) |
Make sure requested adducts exist in some residue.
| std::string core::chemical::expand_icoor_atom_name | ( | std::string | name, |
| ResidueType const & | rsd | ||
| ) |
helper function
References core::chemical::ResidueType::n_residue_connections(), and make_table_of_pilot_apps::name.
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
References core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::natoms(), and core::graph::Graph::set_num_nodes().
Referenced by read_topology_file().
| 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" | ) |
| VariantType const core::chemical::N_ACETYLATION | ( | "N_ACETYLATION" | ) |
Cap extensions at termini to include peptide bonds, written for stepwise assembly (SWA) code.
| std::map< std::string, AA >& core::chemical::name2aa | ( | ) | [inline] |
map that converts string name to AA enum
References setup_name2aa().
Referenced by aa_from_name(), operator>>(), and setup_aa2name().
| std::string core::chemical::name_from_aa | ( | AA | aa | ) |
give a enum type and return the string name
References aa2name(), and num_aa_types.
Referenced by core::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), core::pose::Pose::annotated_sequence(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::rna::base_atoms_square_deviation(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::dna::dna_base_partner(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::swa::rna::Get_num_side_chain_atom_from_res_name(), core::scoring::methods::get_restag(), 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::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), read_topology_file(), core::pack::task::ResidueLevelTask_::restrict_absent_nas(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::swa::rna::suite_square_deviation(), and protocols::noesy_assign::ResonanceList::write_to_stream().
| std::map< char, AA >& core::chemical::oneletter2aa | ( | ) | [inline] |
map that converts one letter char to AA enum
References setup_oneletter2aa().
Referenced by aa_from_oneletter_code(), oneletter_code_specifies_aa(), and setup_aa2oneletter().
| char core::chemical::oneletter_code_from_aa | ( | AA | aa | ) |
give a enum type and return the string name
References aa2oneletter(), and num_canonical_aas.
Referenced by protocols::simple_filters::ConservedPosMutationFilter::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), 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_xpk::write_assignment(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::ResonanceList::write_talos_format(), and protocols::noesy_assign::ResonanceList::write_to_stream().
| bool core::chemical::oneletter_code_specifies_aa | ( | char | onelettercode | ) |
References oneletter2aa().
Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pose::Pose::annotated_sequence(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::scoring::methods::get_restag(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), 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().
| bool core::chemical::operator!= | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
| bool core::chemical::operator< | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
| std::ostream& core::chemical::operator<< | ( | std::ostream & | out, |
| const AtomType & | atom_type | ||
| ) |
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;
References name_from_aa().
| bool core::chemical::operator== | ( | ResConnID const & | lhs, |
| ResConnID const & | rhs | ||
| ) |
| std::istream & core::chemical::operator>> | ( | std::istream & | is, |
| AA & | aa | ||
| ) |
input operator for AA enum type
read in a string name from a file or std::cin and directly convert it to an AA enum type, for example, std::cin >> AA. This will first check if the lookup map has been set up already. If the string name cannot be converted properly, it will flag the input stream as failure (e.g., istream.fail() is true) and set AA enum type to aa_unk.
References aa_unk, core::sequence::end, make_table_of_pilot_apps::name, and name2aa().
| AdductMap core::chemical::parse_adduct_string | ( | utility::options::StringVectorOption & | add_vec | ) |
Convert input string to map of adducts->max usage.
Referenced by core::chemical::ResidueTypeSet::place_adducts().
| std::string const core::chemical::patch_linker | ( | "_p:" | ) |
the string used to generate new residue names
| PatchOperationOP core::chemical::patch_operation_from_patch_file_line | ( | std::string const & | line | ) |
Virtual constructor, returns 0 if no match.
References make_table_of_pilot_apps::d, 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
construct a ResidueType from a file. Example files are currently in minirosetta_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.
References core::id::D, make_table_of_pilot_apps::d, protocols::swa::rna::file_exists(), get_residue_path_distances(), make_table_of_pilot_apps::name, name_from_aa(), protocols::swa::phi(), protocols::swa::rotate(), core::kinematics::Stub::spherical(), strip_whitespace(), and tr().
Referenced by core::chemical::ResidueTypeSet::read_files(), and core::chemical::ResidueTypeSet::ResidueTypeSet().
| VariantType const core::chemical::REPLONLY | ( | "REPLONLY" | ) |
| ResidueSelectorSingleOP core::chemical::residue_selector_single_from_line | ( | std::string const & | line | ) |
create a singe ResidueSelector from an input line.
Referenced by core::chemical::ResidueSelector::add_line().
| std::string core::chemical::residue_type_all_patches_name | ( | ResidueType const & | rsd_type | ) |
helper function, returns the name of all added patches
References core::chemical::ResidueType::name(), and patch_linker.
| std::string core::chemical::residue_type_base_name | ( | ResidueType const & | rsd_type | ) |
helper function, returns the base residue name prior to any patching
References core::chemical::ResidueType::name(), and patch_linker.
Referenced by protocols::toolbox::match_enzdes_util::add_relevant_restypes_to_subset(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), and protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose().
| std::string const core::chemical::RNA | ( | "rna" | ) |
tag name for querying RNA chemical type set.
| core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line | ( | ) |
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(), 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
References make_table_of_pilot_apps::begin, core::sequence::end, name2aa(), and num_aa_types.
Referenced by aa2name().
| utility::vector1< char > core::chemical::setup_aa2oneletter | ( | ) |
setup the vector that maps AA enum to one letter char
References make_table_of_pilot_apps::begin, core::sequence::end, num_aa_types, and oneletter2aa().
Referenced by aa2oneletter().
| std::map< std::string, AA > core::chemical::setup_name2aa | ( | ) |
setup the map that converts string name to AA enum
References aa_ala, aa_arg, aa_asn, aa_asp, aa_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
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::SPECIAL_ROT | ( | "SPECIAL_ROT" | ) |
Generic variant type that allows for differential scoring of a set of residues/rotamers.
| std::string core::chemical::strip_whitespace | ( | std::string const & | name | ) | [inline] |
must be a better place for this, probably already exists!
Referenced by core::chemical::ResidueType::add_atom(), and core::chemical::ResidueType::add_orbital().
| VariantType const core::chemical::SULFATION | ( | "SULFATION" | ) |
| std::string core::chemical::tag_from_line | ( | std::string const & | line | ) |
handy function, return the first word from a line
Referenced by case_from_lines(), and core::chemical::Patch::read_file().
| static basic::Tracer core::chemical::tr | ( | "core.chemical.ResidueTypeSet" | ) | [static] |
| static basic::Tracer core::chemical::tr | ( | "core.chemical" | ) | [static] |
Referenced by core::chemical::ResidueType::add_actcoord_atom(), core::chemical::ResidueType::add_atom(), 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::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::MMAtomTypeSet::read_file(), core::chemical::ElementSet::read_file(), core::chemical::CSDAtomTypeSet::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(), protocols::rna::RNA_StructureParameters::setup_base_pair_constraints(), 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().
| static basic::Tracer core::chemical::tr | ( | "core.chemical.ResidueType" | ) | [static] |
| static basic::Tracer core::chemical::tr | ( | "core.chemical.ChemicalManager" | ) | [static] |
| static basic::Tracer core::chemical::TR_PatchOperations | ( | "core.chemical.PatchOperations.hh" | ) | [static] |
Referenced by core::chemical::RedefineChi::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::DeleteAtom::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomType::apply(), core::chemical::AddChi::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetMMAtomType::apply(), and core::chemical::PrependMainchainAtom::apply().
| VariantType const core::chemical::TRIMETHYLATION | ( | "TRIMETHYLATION" | ) |
| static basic::Tracer core::chemical::tw | ( | "core.chemical.AtomICoor" | , |
| basic::t_warning | |||
| ) | [static] |
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
References core::chemical::ResidueType::aa(), core::chemical::ResidueType::actcoord_atoms(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::atomic_charge(), core::chemical::ResidueConnection::atomno(), core::chemical::ICoorAtomID::atomno(), core::chemical::ResidueType::chi_atoms(), core::chemical::AtomICoor::d(), 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::AtomType::name(), core::chemical::ResidueType::name(), core::chemical::MMAtomType::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().
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().
| std::string const core::chemical::CENTROID |
Referenced by protocols::abinitio::StructureStore::add(), protocols::topology_broker::add_cmdline_claims(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::medal::MedalMover::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::FastGapMover::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply(), protocols::antibody2::CDRH3Modeler2::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::antibody::CloseOneMover::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::abinitio::DomainAssembly::apply(), core::scoring::AtomVDW::AtomVDW(), core::import_pose::centroid_pose_from_pdb(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::protein_interface_design::EnergyPerResidueFilter::compute(), protocols::protein_interface_design::ScoreTypeFilter::compute(), protocols::simple_moves::GunnCost::compute_gunn(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::noesy_assign::CrossPeakList::generate_constraints(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), 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::toolbox::pose_manipulation::insert_pose_into_pose(), core::conformation::Conformation::is_centroid(), protocols::features::PoseConformationFeatures::load_sequence(), 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::RBSegmentRelax_main(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute(), protocols::toolbox::pose_metric_calculators::ClashCountCalculator::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::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::abinitio::ResolutionSwitcher::start_pose(), protocols::star::to_centroid(), protocols::medal::to_centroid(), and protocols::jobdist::universal_main().
| std::string const core::chemical::COARSE_RNA |
| std::string const core::chemical::COARSE_TWO_BEAD |
Referenced by protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::loops::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), core::util::add_cutpoint_variants(), protocols::loops::add_single_cutpoint_variant(), protocols::rna::RNA_LoopCloser::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::idealize::basic_idealize(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), 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(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::methods::is_lower_cutpoint(), core::scoring::methods::BondAngleDatabase::lookup(), protocols::antibody2::CDRH3Modeler2::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_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::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(), protocols::loops::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), core::util::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), 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::jumping::MembraneJump::setup_fold_tree(), core::conformation::setup_links(), protocols::antibody2::Ab_RelaxCDRs_Mover::setup_objects(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), and protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom().
Referenced by protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::loops::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), core::util::add_cutpoint_variants(), protocols::loops::add_single_cutpoint_variant(), protocols::rna::RNA_LoopCloser::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::idealize::basic_idealize(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), 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(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::methods::is_upper_cutpoint(), core::scoring::methods::BondAngleDatabase::lookup(), core::scoring::methods::TorsionDatabase::lookup(), protocols::antibody2::CDRH3Modeler2::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_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::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(), protocols::loops::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), core::util::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), 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::jumping::MembraneJump::setup_fold_tree(), core::conformation::setup_links(), protocols::antibody2::Ab_RelaxCDRs_Mover::setup_objects(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), and protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom().
Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), core::pack::task::operation::OptCysHG::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::io::pdb::build_pose_as_is1(), core::conformation::change_cys_state(), 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::Conformation::detect_disulfides(), core::conformation::disulfide_bonds(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), and protocols::enzdes::EnzdesFlexBBProtocol::modified_task().
| std::string const core::chemical::FA_STANDARD |
Referenced by core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::relax::MiniRelax::apply(), protocols::relax::FastRelax::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::match::MatcherMover::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::antibody2::CDRH3Modeler2::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::antibody::CloseOneMover::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::abinitio::DomainAssembly::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::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::protein_interface_design::EnergyPerResidueFilter::compute(), protocols::protein_interface_design::ScoreTypeFilter::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::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), 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::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::import_pose::PDBSilentStruct::fill_pose(), core::conformation::form_disulfide(), protocols::motifs::Motif::generate_atom_ints(), protocols::swa::protein::generate_beta_database_test(), protocols::ligand_docking::generate_unique_name(), 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(), core::conformation::Conformation::is_fullatom(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::features::PoseConformationFeatures::load_sequence(), core::scoring::ScoringManager::memb_etable(), protocols::MakeRotLib::min_rotamers(), protocols::motifs::Motif::Motif(), 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::RigidChunkClaimer::read_tag(), protocols::topology_broker::MetalloClaimer::read_tag(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::checkpoint::CheckPointer::recover_checkpoint(), 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::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::pack_daemon::DaemonSet::set_entity_resfile(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::motifs::single_residue_from_stream(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().
| std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID |
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::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pose::symmetry::extract_asymmetric_unit(), protocols::swa::protein::generate_beta_database_test(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), core::scoring::methods::TorsionDatabase::lookup(), 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.
Referenced by core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff(), and core::scoring::hackelec::HackElecEnergy::hydrogen_interaction_cutoff().
Referenced by protocols::swa::Figure_out_moving_residues(), and core::pose::make_pose_from_sequence().
| 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().
| std::string const core::chemical::RNA |
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::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pose::symmetry::extract_asymmetric_unit(), protocols::swa::protein::generate_beta_database_test(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::toolbox::pose_manipulation::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().
1.7.4
