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Rosetta Protocols
2014.35
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#include <PcsEnergy.hh>
Public Types | |
typedef core::scoring::methods::WholeStructureEnergy | parent |
typedef core::scoring::methods::WholeStructureEnergy protocols::scoring::methods::pcs2::PcsEnergy::parent |
protocols::scoring::methods::pcs2::PcsEnergy::PcsEnergy | ( | ) |
c-tor
Referenced by clone().
protocols::scoring::methods::pcs2::PcsEnergy::~PcsEnergy | ( | ) |
protocols::scoring::methods::pcs2::PcsEnergy::PcsEnergy | ( | PcsEnergy const & | other | ) |
core::Real protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors | ( | utility::vector1< core::Real > & | vec_best_score, |
utility::vector1< PcsTensor > & | vec_best_tensor, | ||
numeric::xyzVector< core::Real > & | best_coo, | ||
core::pose::Pose const & | pdb, | ||
PcsDataCenter & | pcs_d, | ||
core::Size | i_multi_data, | ||
GridSearchIteratorCA & | grid_it | ||
) | const |
Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number, return the vec of best score, vec of best tensor, and the vec of best x-y-z coordinate.
References numeric::xyzVector< class >::assign(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_only_with_svd(), epsilon, protocols::scoring::methods::pcs2::PcsTensor::get_chi_xx(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_xy(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_xz(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_yy(), protocols::scoring::methods::pcs2::PcsTensor::get_chi_yz(), protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all(), minimize_tensors_from_PCS_data(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::next_center(), options, protocols::scoring::methods::pcs2::GridSearchIteratorCA::reset(), score, protocols::scoring::methods::pcs2::TR_PcsEnergy, protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_svd(), utility_exit_with_message, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().
Referenced by calculate_pcs_score_on_PCS_data_center_CA().
core::Real protocols::scoring::methods::pcs2::PcsEnergy::CA_search_scores_and_tensors_with_svd | ( | utility::vector1< core::Real > & | vec_best_score, |
utility::vector1< PcsTensor > & | vec_best_tensor, | ||
numeric::xyzVector< core::Real > & | best_coo, | ||
core::pose::Pose const & | , | ||
PcsDataCenter & | pcs_d_c, | ||
core::Size | , | ||
GridSearchIteratorCA & | grid_it | ||
) | const |
References numeric::xyzVector< class >::assign(), epsilon, protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all(), minimize_tensors_from_PCS_data_with_svd(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::next_center(), options, protocols::scoring::methods::pcs2::GridSearchIteratorCA::reset(), score, protocols::scoring::methods::pcs2::TR_PcsEnergy, utility_exit_with_message, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().
core::Real protocols::scoring::methods::pcs2::PcsEnergy::calculate_pcs_score_on_PCS_data_center_CA | ( | core::pose::Pose & | pose, |
bool | print_to_tracer, | ||
PcsDataCenter & | pcs_d, | ||
core::Size | i_multi_data, | ||
GridSearchIteratorCA & | grid_it | ||
) | const |
Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number.
References CA_search_scores_and_tensors(), dump_PCS_info(), protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_instance(), protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), and protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all().
Referenced by finalize_total_energy().
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virtual |
clone
References PcsEnergy().
void protocols::scoring::methods::pcs2::PcsEnergy::dump_PCS_info | ( | utility::vector1< PcsTensor > const & | vec_tensor, |
numeric::xyzVector< core::Real > const & | best_coo, | ||
PcsDataCenter const & | pcs_d | ||
) | const |
References FACT_USI_PRECALC_FOR_A_3, protocols::scoring::methods::pcs2::fill_A_line_fast(), protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides(), protocols::scoring::methods::pcs2::PcsDataCenter::get_PCS_data_line_all_spin(), protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all(), protocols::scoring::methods::pcs2::PcsDataCenter::get_X_all(), protocols::scoring::methods::pcs2::PcsDataCenter::get_Y_all(), protocols::scoring::methods::pcs2::PcsDataCenter::get_Z_all(), option, user, utility_exit, basic::options::OptionKeys::PCS::write_extra, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().
Referenced by calculate_pcs_score_on_PCS_data_center_CA().
void protocols::scoring::methods::pcs2::PcsEnergy::finalize_total_energy | ( | core::pose::Pose & | pose, |
core::scoring::ScoreFunction const & | , | ||
core::scoring::EnergyMap & | totals | ||
) | const |
This is called to start the PCS machinerie and get the score (set in totals)
References calculate_pcs_score_on_PCS_data_center_CA(), protocols::scoring::methods::pcs2::PcsDataCenterManager::get_n_multi_data(), protocols::scoring::methods::pcs2::PcsDataCenterManager::get_PCS_data_all(), core::scoring::pcs2, PCS_multi_data_from_pose(), protocols::scoring::methods::pcs2::TR_PcsEnergy, and protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all().
void protocols::scoring::methods::pcs2::PcsEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | ) | const |
core::Real protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_fix_from_PCS_data | ( | utility::vector1< PcsTensor > & | vec_best_tensor, |
PcsDataCenter const & | pcs_d | ||
) | const |
core::Real protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_from_PCS_data | ( | utility::vector1< PcsTensor > & | vec_best_tensor, |
numeric::xyzVector< core::Real > & | best_coo, | ||
PcsDataCenter const & | pcs_d, | ||
core::optimization::Minimizer & | minimizer, | ||
utility::vector1< core::Real > & | vect_to_opti | ||
) | const |
References numeric::xyzVector< class >::assign(), and core::optimization::Minimizer::run().
Referenced by CA_search_scores_and_tensors().
core::Real protocols::scoring::methods::pcs2::PcsEnergy::minimize_tensors_from_PCS_data_with_svd | ( | utility::vector1< PcsTensor > & | vec_best_tensor, |
numeric::xyzVector< core::Real > & | best_coo, | ||
PcsDataCenter const & | , | ||
core::optimization::Minimizer & | minimizer, | ||
utility::vector1< core::Real > & | vect_to_opti | ||
) | const |
References numeric::xyzVector< class >::assign(), and core::optimization::Minimizer::run().
Referenced by CA_search_scores_and_tensors_with_svd().
References utility_exit_with_message.
PcsDataCenterManagerSingleton & protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_noone | ( | ) | const |
PcsDataCenterManager & protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_pose | ( | core::pose::Pose & | pose | ) | const |
References core::pose::Pose::data(), end, protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_instance(), protocols::scoring::methods::pcs2::PcsInputCenterManager::get_instance(), protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_n_multi_data(), protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_PcsEnergyParameter_for(), protocols::scoring::methods::pcs2::PcsInputCenterManager::get_PcsInputCenter_for(), basic::datacache::BasicDataCache::get_ptr(), protocols::scoring::methods::pcs2::PcsEnergyParameter::get_vector_filename(), protocols::scoring::methods::pcs2::PcsEnergyParameter::get_vector_weight(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::PSEUDOCONTACT_SHIFT_MULTI_DATA, basic::datacache::BasicDataCache::set(), protocols::loops::start, and utility_exit_with_message.
Referenced by finalize_total_energy().
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