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Rosetta
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A class to handle caching the calculations for the lddt, to speed things. More...
Public Member Functions | |
| lDDT_Cache (PredicateCOP predicate, bool ignore_oxt) | |
| utility::vector1< core::Size > const & | atoms_matching_predicate (core::pose::Pose const &pose, core::Size resno) |
| Return (and cache) a list of the atom numbers for atoms matching the supplied predicate. More... | |
| core::Size | get_n_maps (core::chemical::ResidueType const &type) |
| Return the number of states which the particular ResidueType has (Will return 1 for Residues without multiple mappings.) More... | |
| utility::vector1< core::Size > const & | get_mapping_state (core::chemical::ResidueType const &type, core::Size state_no) |
| Return (and cache) a specific chemically equivalent mapping (the equivalent mappings being a vector of atom index -> atom index) If the state_no is zero, or otherwise outside the range, will return the identity map. More... | |
| utility::vector1< utility::vector1< core::Size > > const & | residue_mapping_states (core::chemical::ResidueType const &type) |
| Return (and cache) a list of chemically equivalent mappings (the equivalent mappings being a vector of atom index -> atom index) More... | |
Private Member Functions | |
| void | make_mapping_states (core::chemical::ResidueType const &type) |
| Generate the alternative mapping states for the particular ResidueType (TODO: Figure out how to auto-extract info about the predicate to inform state generation) More... | |
| bool | swap_indexes (utility::vector1< core::Size > &vec, core::chemical::ResidueType const &type, char const *const atm1, char const *const atm2) |
| Utility function for make_mapping_states – Flips the indexes for the specified atom on the passed vector Returns false on failure. More... | |
| void | add_states_from_automorphisms (utility::vector1< utility::vector1< core::Size > > &states, core::chemical::ResidueType const &type) |
| Utility function for make_mapping_states – changes states to be from the automorphism iterator. More... | |
Private Attributes | |
| friend | lDDT_Calculator |
| PredicateCOP | predicate_ |
| bool | ignore_oxt_ |
| std::map< core::conformation::Residue const *, utility::vector1< core::Size > > | predicate_atoms_ |
| std::map< core::chemical::ResidueType const *, utility::vector1< utility::vector1< core::Size > > > | mapping_states_ |
Static Private Attributes | |
| static utility::vector1< core::Size > const | identity_map_ |
A class to handle caching the calculations for the lddt, to speed things.
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Utility function for make_mapping_states – changes states to be from the automorphism iterator.
References core::chemical::ResidueTypeBase::name(), core::chemical::AutomorphismIterator::next(), and core::scoring::TR().
| utility::vector1< core::Size > const & core::scoring::lDDT_Calculator::lDDT_Cache::atoms_matching_predicate | ( | core::pose::Pose const & | pose, |
| core::Size | resno | ||
| ) |
Return (and cache) a list of the atom numbers for atoms matching the supplied predicate.
References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), ignore_oxt_, core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), predicate_, predicate_atoms_, and core::pose::Pose::residue().
Referenced by core::scoring::lDDT_Calculator::residue_pair_stats().
| utility::vector1< core::Size > const & core::scoring::lDDT_Calculator::lDDT_Cache::get_mapping_state | ( | core::chemical::ResidueType const & | type, |
| core::Size | state_no | ||
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Return (and cache) a specific chemically equivalent mapping (the equivalent mappings being a vector of atom index -> atom index) If the state_no is zero, or otherwise outside the range, will return the identity map.
Referenced by core::scoring::lDDT_Calculator::determine_alt_states(), and core::scoring::lDDT_Calculator::get_stats_for_state().
| core::Size core::scoring::lDDT_Calculator::lDDT_Cache::get_n_maps | ( | core::chemical::ResidueType const & | type | ) |
Return the number of states which the particular ResidueType has (Will return 1 for Residues without multiple mappings.)
Referenced by core::scoring::lDDT_Calculator::determine_alt_states().
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Generate the alternative mapping states for the particular ResidueType (TODO: Figure out how to auto-extract info about the predicate to inform state generation)
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_b3a, core::chemical::aa_b3c, core::chemical::aa_b3d, core::chemical::aa_b3e, core::chemical::aa_b3f, core::chemical::aa_b3g, core::chemical::aa_b3h, core::chemical::aa_b3i, core::chemical::aa_b3k, core::chemical::aa_b3l, core::chemical::aa_b3m, core::chemical::aa_b3n, core::chemical::aa_b3p, core::chemical::aa_b3q, core::chemical::aa_b3r, core::chemical::aa_b3s, core::chemical::aa_b3t, core::chemical::aa_b3v, core::chemical::aa_b3w, core::chemical::aa_b3y, core::chemical::aa_cys, core::chemical::aa_dal, core::chemical::aa_dan, core::chemical::aa_dar, core::chemical::aa_das, core::chemical::aa_dcs, core::chemical::aa_dgn, core::chemical::aa_dgu, core::chemical::aa_dhi, core::chemical::aa_dil, core::chemical::aa_dle, core::chemical::aa_dly, core::chemical::aa_dme, core::chemical::aa_dph, core::chemical::aa_dpr, core::chemical::aa_dse, core::chemical::aa_dth, core::chemical::aa_dtr, core::chemical::aa_dty, core::chemical::aa_dva, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_unk, core::chemical::aa_val, core::chemical::ResidueType::has(), core::scoring::lDDT_Calculator::ignore_oxt_, core::chemical::ResidueType::is_ligand(), core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_lra, core::chemical::na_lrc, core::chemical::na_lrg, core::chemical::na_lur, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, core::chemical::na_ura, core::chemical::ResidueType::nheavyatoms(), core::chemical::ou3_ala, core::chemical::ou3_arg, core::chemical::ou3_asn, core::chemical::ou3_asp, core::chemical::ou3_cys, core::chemical::ou3_gln, core::chemical::ou3_glu, core::chemical::ou3_gly, core::chemical::ou3_his, core::chemical::ou3_ile, core::chemical::ou3_leu, core::chemical::ou3_lys, core::chemical::ou3_met, core::chemical::ou3_phe, core::chemical::ou3_pro, core::chemical::ou3_ser, core::chemical::ou3_thr, core::chemical::ou3_trp, core::chemical::ou3_tyr, and core::chemical::ou3_val.
| utility::vector1< utility::vector1< core::Size > > const & core::scoring::lDDT_Calculator::lDDT_Cache::residue_mapping_states | ( | core::chemical::ResidueType const & | type | ) |
Return (and cache) a list of chemically equivalent mappings (the equivalent mappings being a vector of atom index -> atom index)
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Utility function for make_mapping_states – Flips the indexes for the specified atom on the passed vector Returns false on failure.
References core::chemical::ResidueType::atom_index(), and core::chemical::ResidueType::has().
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Referenced by core::scoring::lDDT_Calculator::get_stats_for_state().
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Referenced by atoms_matching_predicate().
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Referenced by atoms_matching_predicate().
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Referenced by atoms_matching_predicate().
1.9.1