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Rosetta 3.5
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Rosetta 3.5
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#include <SingleResidueDunbrackLibrary.hh>
Public Types | |
| typedef chemical::AA | AA |
Public Member Functions | |
| SingleResidueDunbrackLibrary (AA const aa, Size const n_rotameric_chi, bool dun02) | |
| c-tor More... | |
| virtual | ~SingleResidueDunbrackLibrary () |
| void | read_options () |
| virtual void | write_to_binary (utility::io::ozstream &out) const |
| virtual void | read_from_binary (utility::io::izstream &in) |
| virtual utility::vector1 < DunbrackRotamerSampleData > | get_all_rotamer_samples (Real phi, Real psi) const =0 |
| Return all of the rotamer sample data given a particular phi/psi. For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes. More... | |
| virtual Real | get_probability_for_rotamer (Real phi, Real psi, Size rot_ind) const =0 |
| Return the probability for a particular rotamer where rotamers are indexed in order of decreasing probability (or something very close to decreasing probability). More... | |
| virtual DunbrackRotamerSampleData | get_rotamer (Real phi, Real psi, Size rot_ind) const =0 |
| virtual Real | get_phi_from_rsd (conformation::Residue const &rsd) const =0 |
| virtual Real | get_psi_from_rsd (conformation::Residue const &rsd) const =0 |
| virtual Size | memory_usage_in_bytes () const |
| Virtual functions the derived classes must implement. More... | |
| virtual Size | nchi () const =0 |
| The number of chi represented by the library. More... | |
| virtual Size | n_rotamer_bins () const =0 |
| void | set_n_chi_bins (utility::vector1< Size > const &) |
| Tell the base class the number of chi bins for each rotameric chi dimension. More... | |
| virtual void | get_rotamer_from_chi (ChiVector const &chi, RotVector &rot) const =0 |
| Convert a vector of chi angles (degrees) into a integer vector of rotamer wells. Derived class should be consistent, but may be arbitrary in how wells divide angle space. More... | |
| Size | rotwell_2_rotno (utility::vector1< Size > const &rotwell) const |
| Conversion functions. More... | |
| Size | rotwell_2_rotno (Size4 const &rotwell) const |
| Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number". More... | |
| Size | rotno_2_packed_rotno (Size const rotno) const |
| Convert from the rotamer number to the compacted "packed rotamer number". Returns 0 if rotno has no corresponding packed rotno. More... | |
| Size | rotwell_2_packed_rotno (utility::vector1< Size > const &rotwell) const |
| Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno. More... | |
| Size | rotwell_2_packed_rotno (Size4 const &rotwell) const |
| Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno. More... | |
| void | packed_rotno_2_rotwell (Size const packed_rotno, utility::vector1< Size > &rotwell) const |
| Convert from the packed rotamer number to the rotamer well. More... | |
| void | packed_rotno_2_rotwell (Size const packed_rotno, Size4 &rotwell) const |
| utility::vector1< Size > const & | packed_rotno_2_rotwell (Size const packed_rotno) const |
| void | rotno_2_rotwell (Size const rotno, utility::vector1< Size > &rotwell) const |
| Convert from the rotamer number to the rotamer well. More... | |
| Size | bin_rotameric_chi (Real chi, Size which_chi) const |
| , Turns out, when non-rotameric chi are taken out of the picture, all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries. More... | |
| void | bin_angle (Real const angle_start, Real const angle_step, Real const ASSERT_ONLY(angle_range), Size const nbins, Real const ang, Size &bin_lower, Size &bin_upper, Real &angle_alpha) const |
| This is not the right place for this code, but the numeric interpolation library uselessly indexes by 0 and the basic functions aren't inlined... More... | |
| AA | aa () const |
| The amino acid this library is representing. More... | |
| Real | probability_to_accumulate_while_building_rotamers (bool buried) const |
| When creating rotamer, what position in the CDF should one build until? Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful. More... | |
| void | prob_to_accumulate (Real, Real) |
| setters for accumulation probability cutoff (to support externally-controlled option dependence) More... | |
| void | prob_to_accumulate_buried (Real) |
| void | prob_to_accumulate_nonburied (Real) |
 Public Member Functions inherited from core::pack::dunbrack::SingleResidueRotamerLibrary | |
| virtual | ~SingleResidueRotamerLibrary () |
| virtual Real | rotamer_energy_deriv (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const =0 |
| virtual Real | rotamer_energy (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch) const =0 |
| virtual Real | best_rotamer_energy (conformation::Residue const &rsd, bool curr_rotamer_only, RotamerLibraryScratchSpace &scratch) const =0 |
| Returns the energy of the lowest-energy rotamer accessible to the given residue (based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum). More... | |
| virtual void | assign_random_rotamer_with_bias (conformation::Residue const &rsd, RotamerLibraryScratchSpace &scratch, numeric::random::RandomGenerator &RG, ChiVector &new_chi_angles, bool perturb_from_rotamer_center) const =0 |
| Pick a rotamer for the input residue according to the rotamer probability distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center is true, then push the rotamer off from the center; for chi angles with a normal distribution, the perturbation is taken from a Gaussian random number with a standard deviation matching the chi angle's standard deviation. For chi angles that are not normally distributed, the behavior is open to the derived classe's interpretation. More... | |
| virtual void | fill_rotamer_vector (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, pack::task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, utility::vector1< utility::vector1< Real > > const &extra_chi_steps, bool buried, RotamerVector &rotamers) const =0 |
| virtual void | write_to_file (utility::io::ozstream &out) const =0 |
Static Public Member Functions | |
| static void | n_rotamer_bins_for_aa (chemical::AA const aa, RotVector &rot) |
| Hard coded specifics about the amino acids. More... | |
| static void | n_rotameric_bins_for_aa (chemical::AA const aa, RotVector &rot, bool dun02) |
| Reports information about the rotameric chi only; no details about the non rotameric chi. More... | |
| static void | n_rotamer_bins_for_aa_02 (chemical::AA const aa, RotVector &rot) |
| Hard coded rotamer well info for the 2002 library. More... | |
Static Public Attributes | |
| static Real const | NEUTRAL_PHI = -90 |
| constants More... | |
| static Real const | NEUTRAL_PSI = 130 |
| A good "psi" value to use for C-term residues. More... | |
Protected Member Functions | |
| bool | dun02 () const |
| Read access for the derived class. More... | |
| virtual Size | memory_usage_static () const =0 |
| Worker functions available to the derived classes. More... | |
| virtual Size | memory_usage_dynamic () const |
| utility::vector1< Size > const & | n_chi_bins () const |
| Read access to the n_chi_bins_ vector. More... | |
| void | mark_rotwell_exists (utility::vector1< Size > const &rotwell) |
| The base class needs to be informed about which rotamer wells exist in order to create the rotwell to packed rot conversion data. set_chi_nbins must be called first. More... | |
| void | declare_all_existing_rotwells_encountered () |
| After the derived class has marked all the rotwells that do exist, the base class will create the rotwell to packerot conversion data. More... | |
| Size | n_packed_rots () const |
| The number of existing rotamers. More... | |
| Size | n_possible_rots () const |
| The number of possible rotamers – product of the chi_nbins_ array. More... | |
Private Member Functions | |
| void | hokey_template_workaround () |
| This function forces the instantiation of virtual templated methods in the derived classes. Functions like this one are necessary when combining polymorphism and templates. Though these functions must be compiled, they need never be called. Do not call this function. More... | |
Definition at line 45 of file SingleResidueDunbrackLibrary.hh.
Definition at line 47 of file SingleResidueDunbrackLibrary.hh.
| core::pack::dunbrack::SingleResidueDunbrackLibrary::SingleResidueDunbrackLibrary | ( | AA const | aa, |
| Size const | n_rotameric_chi, | ||
| bool | dun02 | ||
| ) |
c-tor
Definition at line 70 of file SingleResidueDunbrackLibrary.cc.
References aa_, core::chemical::aa_unk, n_chi_bins_, n_chi_products_, n_possible_rots_, n_rotameric_bins_for_aa(), n_rotameric_chi_, read_options(), rotno_2_packed_rotno_, and rotwell_exists_.
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Definition at line 124 of file SingleResidueDunbrackLibrary.cc.
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inline |
The amino acid this library is representing.
Definition at line 286 of file SingleResidueDunbrackLibrary.hh.
References aa_.
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inline |
This is not the right place for this code, but the numeric interpolation library uselessly indexes by 0 and the basic functions aren't inlined...
Definition at line 260 of file SingleResidueDunbrackLibrary.hh.
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inline |
, Turns out, when non-rotameric chi are taken out of the picture, all remaining chi are binned the same way, except proline. Valid only for Dun10 libraries.
Definition at line 236 of file SingleResidueDunbrackLibrary.hh.
References aa_, core::chemical::aa_pro, and dun02_.
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After the derived class has marked all the rotwells that do exist, the base class will create the rotwell to packerot conversion data.
Definition at line 294 of file SingleResidueDunbrackLibrary.cc.
References n_packed_rots_, n_possible_rots_, packed_rotno_2_rotno_, packed_rotno_2_rotwell_, packed_rotno_conversion_data_current_, rotno_2_packed_rotno_, rotno_2_rotwell(), and rotwell_exists_.
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Read access for the derived class.
Definition at line 140 of file SingleResidueDunbrackLibrary.hh.
References dun02_.
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pure virtual |
Return all of the rotamer sample data given a particular phi/psi. For N-terminus residues, hand in the phi value SingleResidueDunbrackLibrary::PHI_NEUTRAL and for C-terminus residues, hand in the psi value SingleResidueDunbrackLibrary::PSI_NEUTRAL. The returned samples should be in semi-decrasing order by probability; semi, because the rotamers are constructed in sorted order by their probability in the lower phi-psi bin that the input phi/psi perscribes.
Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
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pure virtual |
Implemented in core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
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pure virtual |
Return the probability for a particular rotamer where rotamers are indexed in order of decreasing probability (or something very close to decreasing probability).
Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
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Implemented in core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
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pure virtual |
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pure virtual |
Convert a vector of chi angles (degrees) into a integer vector of rotamer wells. Derived class should be consistent, but may be arbitrary in how wells divide angle space.
Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
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private |
This function forces the instantiation of virtual templated methods in the derived classes. Functions like this one are necessary when combining polymorphism and templates. Though these functions must be compiled, they need never be called. Do not call this function.
forces instantiation of virtual functions for templated derived classes... part of the uglyness of mixing templates and polymorphism. Never invoke this function.
Definition at line 580 of file SingleResidueDunbrackLibrary.cc.
References core::chemical::aa_ala, core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::find_another_representative_for_unlikely_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_probability_for_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::memory_usage_dynamic(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::memory_usage_dynamic(), memory_usage_in_bytes(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::memory_usage_static(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::memory_usage_static(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::n_rotamer_bins(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::n_rotamer_bins(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::nchi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::nchi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_binary(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_from_binary(), core::pack::RG(), rot(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::write_to_binary(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::write_to_binary(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::write_to_file(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::write_to_file().
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The base class needs to be informed about which rotamer wells exist in order to create the rotwell to packed rot conversion data. set_chi_nbins must be called first.
Definition at line 282 of file SingleResidueDunbrackLibrary.cc.
References packed_rotno_conversion_data_current_, rotwell_2_rotno(), and rotwell_exists_.
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Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
Definition at line 560 of file SingleResidueDunbrackLibrary.cc.
References n_chi_bins_, n_chi_products_, packed_rotno_2_rotno_, packed_rotno_2_rotwell_, rotno_2_packed_rotno_, and rotwell_exists_.
Referenced by memory_usage_in_bytes().
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Virtual functions the derived classes must implement.
Derived classes should invoke base class function as well.
Definition at line 555 of file SingleResidueDunbrackLibrary.cc.
References memory_usage_dynamic(), and memory_usage_static().
Referenced by hokey_template_workaround().
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protectedpure virtual |
Worker functions available to the derived classes.
Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
Referenced by memory_usage_in_bytes().
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Read access to the n_chi_bins_ vector.
Definition at line 149 of file SingleResidueDunbrackLibrary.hh.
References n_chi_bins_.
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The number of existing rotamers.
Definition at line 166 of file SingleResidueDunbrackLibrary.hh.
References n_packed_rots_.
Referenced by read_from_binary(), and write_to_binary().
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The number of possible rotamers – product of the chi_nbins_ array.
Definition at line 172 of file SingleResidueDunbrackLibrary.hh.
References n_possible_rots_.
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Hard coded specifics about the amino acids.
the number of wells defined for the 08 library; includes the number of wells for the semi-rotameric chi (arbitrarily chosen).
Definition at line 139 of file SingleResidueDunbrackLibrary.cc.
References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, 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, and core::chemical::aa_val.
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Hard coded rotamer well info for the 2002 library.
To continue supporting the 2002 Dunbrack library, we need to preserve the rotamer well definitions that it made.
Definition at line 216 of file SingleResidueDunbrackLibrary.cc.
References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, 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, and core::chemical::aa_val.
Referenced by n_rotameric_bins_for_aa().
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Reports information about the rotameric chi only; no details about the non rotameric chi.
For the rotameric chi – not all chi are rotameric
Definition at line 174 of file SingleResidueDunbrackLibrary.cc.
References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, 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_val, and n_rotamer_bins_for_aa_02().
Referenced by SingleResidueDunbrackLibrary().
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The number of chi represented by the library.
Implemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell | ( | Size const | packed_rotno, |
| utility::vector1< Size > & | rotwell | ||
| ) | const |
Convert from the packed rotamer number to the rotamer well.
Definition at line 388 of file SingleResidueDunbrackLibrary.cc.
References packed_rotno_2_rotwell_.
Referenced by protocols::features::RotamerInitializer< T >::initialize_rotamer(), read_from_binary(), and write_to_binary().
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell | ( | Size const | packed_rotno, |
| Size4 & | rotwell | ||
| ) | const |
Definition at line 397 of file SingleResidueDunbrackLibrary.cc.
References core::sequence::end, packed_rotno_2_rotwell_, and core::io::serialization::size().
| utility::vector1< Size > const & core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell | ( | Size const | packed_rotno) | const |
Definition at line 407 of file SingleResidueDunbrackLibrary.cc.
References packed_rotno_2_rotwell_.
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate | ( | Real | buried, |
| Real | nonburied | ||
| ) |
setters for accumulation probability cutoff (to support externally-controlled option dependence)
Definition at line 537 of file SingleResidueDunbrackLibrary.cc.
References prob_to_accumulate_buried(), and prob_to_accumulate_nonburied().
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_buried | ( | Real | buried) |
Definition at line 543 of file SingleResidueDunbrackLibrary.cc.
References prob_to_accumulate_buried_.
Referenced by prob_to_accumulate(), and read_options().
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::prob_to_accumulate_nonburied | ( | Real | nonburied) |
Definition at line 549 of file SingleResidueDunbrackLibrary.cc.
References prob_to_accumulate_nonburied_.
Referenced by prob_to_accumulate(), and read_options().
| Real core::pack::dunbrack::SingleResidueDunbrackLibrary::probability_to_accumulate_while_building_rotamers | ( | bool | buried) | const |
When creating rotamer, what position in the CDF should one build until? Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.
Definition at line 528 of file SingleResidueDunbrackLibrary.cc.
References prob_to_accumulate_buried_, and prob_to_accumulate_nonburied_.
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virtual |
Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
Definition at line 457 of file SingleResidueDunbrackLibrary.cc.
References n_packed_rots(), n_packed_rots_, n_possible_rots_, n_rotameric_chi_, packed_rotno_2_rotno_, packed_rotno_2_rotwell(), packed_rotno_2_rotwell_, packed_rotno_conversion_data_current_, rotno_2_packed_rotno(), and rotno_2_packed_rotno_.
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::read_options | ( | ) |
Definition at line 127 of file SingleResidueDunbrackLibrary.cc.
References prob_to_accumulate_buried(), and prob_to_accumulate_nonburied().
Referenced by SingleResidueDunbrackLibrary().
| Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_packed_rotno | ( | Size const | rotno) | const |
Convert from the rotamer number to the compacted "packed rotamer number". Returns 0 if rotno has no corresponding packed rotno.
Definition at line 360 of file SingleResidueDunbrackLibrary.cc.
References packed_rotno_conversion_data_current_, and rotno_2_packed_rotno_.
Referenced by read_from_binary(), rotwell_2_packed_rotno(), and write_to_binary().
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::rotno_2_rotwell | ( | Size const | rotno, |
| utility::vector1< Size > & | rotwell | ||
| ) | const |
Convert from the rotamer number to the rotamer well.
not as fast as going through the packed_rotno_2_rotwell_ lookup table, but does the modulo converstion from a 1-based index to a lexicographical index ordering.
if there are 3 chi, and 3 rotamer bins per chi, then 21 would represent (3-1) * 3**2 + (1-1) * 3**1 + (3-1) * 3**0 + 1 = [ 3, 1, 3 ];
Definition at line 509 of file SingleResidueDunbrackLibrary.cc.
References n_chi_products_, and n_rotameric_chi_.
Referenced by declare_all_existing_rotwells_encountered().
| Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno | ( | utility::vector1< Size > const & | rotwell) | const |
Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno.
Definition at line 369 of file SingleResidueDunbrackLibrary.cc.
References packed_rotno_conversion_data_current_, rotno_2_packed_rotno(), and rotwell_2_rotno().
Referenced by protocols::features::RotamerInitializer< T >::initialize_rotamer().
| Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_packed_rotno | ( | Size4 const & | rotwell) | const |
Convert from the rotamer bin indices for each chi to the compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno.
Definition at line 380 of file SingleResidueDunbrackLibrary.cc.
References packed_rotno_conversion_data_current_, rotno_2_packed_rotno(), and rotwell_2_rotno().
| Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno | ( | utility::vector1< Size > const & | rotwell) | const |
Conversion functions.
Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number"
Definition at line 330 of file SingleResidueDunbrackLibrary.cc.
References n_chi_products_.
Referenced by protocols::features::RotamerInitializer< T >::initialize_rotamer(), mark_rotwell_exists(), and rotwell_2_packed_rotno().
| Size core::pack::dunbrack::SingleResidueDunbrackLibrary::rotwell_2_rotno | ( | Size4 const & | rotwell) | const |
Convert from the rotamer bin indices for each chi to the (non-compact) "rotamer number".
Definition at line 345 of file SingleResidueDunbrackLibrary.cc.
References n_chi_products_.
| void core::pack::dunbrack::SingleResidueDunbrackLibrary::set_n_chi_bins | ( | utility::vector1< Size > const & | n_chi_bins) |
Tell the base class the number of chi bins for each rotameric chi dimension.
Sets the number of bins for a particular chi angle, used for the NCAAs, info for CAAs is hardcoded bellow
Definition at line 105 of file SingleResidueDunbrackLibrary.cc.
References n_chi_bins_, n_chi_products_, n_possible_rots_, n_rotameric_chi_, rotno_2_packed_rotno_, and rotwell_exists_.
Referenced by core::pack::dunbrack::RotamerLibrary::get_NCAARotamerLibrary().
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Reimplemented in core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >, and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >.
Definition at line 414 of file SingleResidueDunbrackLibrary.cc.
References n_packed_rots(), n_packed_rots_, n_possible_rots_, n_rotameric_chi_, packed_rotno_2_rotno_, packed_rotno_2_rotwell(), packed_rotno_2_rotwell_, rotno_2_packed_rotno(), and rotno_2_packed_rotno_.
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Definition at line 337 of file SingleResidueDunbrackLibrary.hh.
Referenced by aa(), bin_rotameric_chi(), and SingleResidueDunbrackLibrary().
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data
Definition at line 336 of file SingleResidueDunbrackLibrary.hh.
Referenced by bin_rotameric_chi(), and dun02().
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Definition at line 339 of file SingleResidueDunbrackLibrary.hh.
Referenced by memory_usage_dynamic(), n_chi_bins(), set_n_chi_bins(), and SingleResidueDunbrackLibrary().
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Definition at line 340 of file SingleResidueDunbrackLibrary.hh.
Referenced by memory_usage_dynamic(), rotno_2_rotwell(), rotwell_2_rotno(), set_n_chi_bins(), and SingleResidueDunbrackLibrary().
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Definition at line 342 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), n_packed_rots(), read_from_binary(), and write_to_binary().
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Definition at line 343 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), n_possible_rots(), read_from_binary(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().
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Definition at line 338 of file SingleResidueDunbrackLibrary.hh.
Referenced by read_from_binary(), rotno_2_rotwell(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().
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constants
A good "phi" value to use for N-term residues
Definition at line 53 of file SingleResidueDunbrackLibrary.hh.
Referenced by protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue().
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A good "psi" value to use for C-term residues.
Definition at line 56 of file SingleResidueDunbrackLibrary.hh.
Referenced by protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue().
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Definition at line 351 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), read_from_binary(), and write_to_binary().
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Definition at line 352 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), packed_rotno_2_rotwell(), read_from_binary(), and write_to_binary().
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Definition at line 348 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), mark_rotwell_exists(), read_from_binary(), rotno_2_packed_rotno(), and rotwell_2_packed_rotno().
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Definition at line 345 of file SingleResidueDunbrackLibrary.hh.
Referenced by prob_to_accumulate_buried(), and probability_to_accumulate_while_building_rotamers().
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Definition at line 345 of file SingleResidueDunbrackLibrary.hh.
Referenced by prob_to_accumulate_nonburied(), and probability_to_accumulate_while_building_rotamers().
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Definition at line 350 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), memory_usage_dynamic(), read_from_binary(), rotno_2_packed_rotno(), set_n_chi_bins(), SingleResidueDunbrackLibrary(), and write_to_binary().
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Definition at line 347 of file SingleResidueDunbrackLibrary.hh.
Referenced by declare_all_existing_rotwells_encountered(), mark_rotwell_exists(), memory_usage_dynamic(), set_n_chi_bins(), and SingleResidueDunbrackLibrary().
1.8.4