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Rosetta
2020.50
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Gene representation of ligand & flexible sidechains in receptor. More...
#include <LigandConformer.hh>
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core::pose::PoseCOP | ref_pose_ |
core::Size | ligid_ |
utility::vector1< core::Size > | movingscs_ |
utility::vector1 < core::chemical::ResidueTypeCOP > | proteinrestypes_ |
utility::vector1 < utility::vector1< core::Real > > | proteinchis_ |
bool | sample_ring_conformers_ |
core::Real | score_ |
core::Real | rms_ |
utility::vector1< core::Real > | rb_ |
utility::vector1< core::Real > | ligandchis_ |
utility::vector1< core::Real > | ligandnus_ |
utility::vector1< core::Real > | ligandtaus_ |
utility::vector1 < utility::vector1< core::Size > > | ligandchi_downstream_ |
core::Real | rg_ |
bool | ligandxyz_synced_ |
utility::vector1< core::Vector > | ligandxyz_ |
core::Real | torsmutationRate_ |
core::Real | rtmutationRate_ |
core::Real | transmutWidth_ |
core::Real | rotmutWidth_ |
core::Real | ligchimutWidth_ |
core::Real | protchimutWidth_ |
std::string | generation_tag_ |
std::string | ligand_typename_ |
core::Real | negTdS_ |
Friends | |
LigandConformer | mutate (LigandConformer const &l) |
LigandConformer | crossover (LigandConformer const &l1, LigandConformer const &l2) |
LigandConformer | crossover_ft (LigandConformer const &l1, LigandConformer const &l2) |
core::Real | distance_fast (LigandConformer &gene1, LigandConformer &gene2) |
std::pair< core::Real, core::Real > | distance_internal (LigandConformer const &gene1, LigandConformer const &gene2) |
core::Real | distance_slow (LigandConformer const &gene1, LigandConformer const &gene2) |
Gene representation of ligand & flexible sidechains in receptor.
Gene is preresented by rigid body (rb_), ligandchis, and receptorchis Also has functions to tranform back and forth to pose object Uses friend functions to perform mutation / crossovers with others within gene representation
protocols::ligand_docking::ga_ligand_dock::LigandConformer::LigandConformer | ( | ) |
References init_params().
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protocols::ligand_docking::ga_ligand_dock::LigandConformer::LigandConformer | ( | core::pose::PoseCOP | pose, |
core::Size | ligid, | ||
utility::vector1< core::Size > | movingscs | ||
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References init_params(), and initialize().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::assign_ligand_trans | ( | core::Vector | transv | ) |
References rb_.
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References rb_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::dump_pose | ( | std::string | pdbname | ) | const |
References to_pose().
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References generation_tag_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().
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References ligandchis_.
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().
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References ligandchis_.
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().
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References ref_pose_.
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::init_params | ( | ) |
References generation_tag_, ligand_typename_, ligchimutWidth_, negTdS_, protchimutWidth_, rg_, rotmutWidth_, rtmutationRate_, sample_ring_conformers_, torsmutationRate_, and transmutWidth_.
Referenced by LigandConformer().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::initialize | ( | core::pose::PoseCOP | pose, |
core::Size | ligid, | ||
utility::vector1< core::Size > | movingscs | ||
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References protocols::sewing::data_storage::ligand, ligand_typename_, ligandchi_downstream_, ligid_, movingscs_, ref_pose_, and update_conf().
Referenced by LigandConformer().
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References ligid_, and ref_pose_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer().
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References ligid_.
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().
core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue | ( | ) | const |
References ligid_, ref_pose_, and to_pose().
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_slow().
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References rg_.
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().
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References ligand_typename_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().
utility::vector1< core::Vector > const & protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz | ( | ) |
References protocols::membrane::com(), ligandxyz_, ligandxyz_synced_, ligid_, ref_pose_, rg_, to_pose(), and protocols::ligand_docking::ga_ligand_dock::TR().
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_fast(), and randomize().
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References movingscs_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::distance_internal(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_optimizer(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().
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References negTdS_.
core::conformation::Residue protocols::ligand_docking::ga_ligand_dock::LigandConformer::protein_residue | ( | core::Size | ires | ) | const |
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References rb_.
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize | ( | core::Real | transmax | ) |
References ligand_xyz(), ligandchis_, ligandnus_, ligandtaus_, ligandxyz_synced_, ligid_, core::chemical::ResidueType::n_rings(), protocols::simple_filters::R2quat(), core::scoring::motif::random_rotation(), rb_, ref_pose_, core::scoring::rg, core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_conformer_set(), sample_ring_conformers_, and protocols::ligand_docking::ga_ligand_dock::TR().
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().
core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::receptor | ( | ) | const |
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References rms_.
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References rms_.
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References sample_ring_conformers_.
Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), and protocols::ligand_docking::ga_ligand_dock::mutate().
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References score_.
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status(), and protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_pool().
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References score_.
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References ligchimutWidth_.
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References movingscs_.
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References negTdS_.
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References ligandxyz_synced_, and proteinchis_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop().
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References ligandxyz_synced_, proteinchis_, and proteinrestypes_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop().
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References rotmutWidth_.
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References rtmutationRate_.
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References sample_ring_conformers_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply().
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References torsmutationRate_.
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References transmutWidth_.
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References ligand_typename_.
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame | ( | LigandConformer const & | refconf | ) |
References core::pose::addVirtualResAsRoot(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::id::AtomID::BOGUS_ATOM_ID(), core::conformation::Residue::chi_atoms(), core::pose::initialize_atomid_map(), protocols::sewing::data_storage::ligand, ligandchis_, ligid_, core::conformation::Residue::nbr_atom(), core::conformation::Residue::nheavyatoms(), core::scoring::rg, core::scoring::superimpose_pose(), to_pose(), protocols::ligand_docking::ga_ligand_dock::TR(), update_conf(), and core::conformation::Residue::xyz().
Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose | ( | core::pose::PoseOP | pose, |
LigandConformer & | minilig | ||
) | const |
create a reduced pose representation (to be used in minimization)
References core::pose::addVirtualResAsRoot(), ligid_, movingscs_, and to_pose().
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose | ( | core::pose::PoseOP | pose | ) | const |
References ligandchis_, ligandnus_, ligandtaus_, ligid_, movingscs_, core::chemical::ResidueType::n_rings(), core::id::NU, core::chemical::ResidueType::nu_atoms(), proteinchis_, proteinrestypes_, protocols::simple_filters::quat2R(), rb_, ref_pose_, core::chemical::ResidueType::ring_atoms(), sample_ring_conformers_, core::kinematics::Jump::set_rotation(), and core::kinematics::Jump::set_translation().
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), dump_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), ligand_residue(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protein_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), superimpose_to_alternative_frame(), to_minipose(), and update_conf_from_minipose().
std::string protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_string | ( | ) | const |
References core::chemical::element::F, ligandchis_, and rb_.
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References rb_.
Referenced by protocols::ligand_docking::ga_ligand_dock::distance_internal().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf | ( | core::pose::PoseCOP | pose | ) |
References protocols::membrane::com(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), ligandchis_, ligandnus_, ligandtaus_, ligandxyz_, ligandxyz_synced_, ligid_, movingscs_, core::chemical::ResidueType::n_rings(), core::id::NU, core::chemical::ResidueType::nu_atoms(), proteinchis_, proteinrestypes_, protocols::simple_filters::R2quat(), rb_, rg_, core::chemical::ResidueType::ring_atoms(), and sample_ring_conformers_.
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), initialize(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), superimpose_to_alternative_frame(), and update_conf_from_minipose().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf_from_minipose | ( | core::pose::PoseCOP | pose | ) |
update internal information from the reduced pose representation
References ligid_, movingscs_, to_pose(), and update_conf().
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().
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Referenced by generation_tag(), init_params(), and set_generation_tag().
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Referenced by init_params(), initialize(), ligand_typename(), and set_typename().
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Referenced by protocols::ligand_docking::ga_ligand_dock::crossover_ft(), and initialize().
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Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), protocols::ligand_docking::ga_ligand_dock::crossover_ft(), get_ligandchi(), get_ligandchis(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), superimpose_to_alternative_frame(), to_pose(), to_string(), and update_conf().
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Referenced by ligand_xyz(), and update_conf().
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Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_chiwidth().
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Referenced by protocols::ligand_docking::ga_ligand_dock::crossover(), initialize(), is_ligand_terminal(), ligand_id(), ligand_residue(), ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::mutate(), randomize(), receptor(), superimpose_to_alternative_frame(), to_minipose(), to_pose(), update_conf(), and update_conf_from_minipose().
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Referenced by initialize(), moving_scs(), set_moving_scs(), to_minipose(), to_pose(), update_conf(), and update_conf_from_minipose().
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Referenced by init_params(), neg_Tds(), and set_negTds().
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Referenced by init_params().
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Referenced by get_protein_chis(), set_protein_chis(), set_protein_restype(), to_pose(), and update_conf().
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Referenced by get_protein_restype(), set_protein_restype(), to_pose(), and update_conf().
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Referenced by assign_ligand_trans(), defined(), protocols::ligand_docking::ga_ligand_dock::mutate(), quat(), randomize(), to_pose(), to_string(), trans(), and update_conf().
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Referenced by init_params(), ligand_rg(), ligand_xyz(), and update_conf().
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Referenced by rms().
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Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_rotwidth().
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Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_rtmutrate().
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Referenced by init_params(), randomize(), sample_ring_conformers(), set_sample_ring_conformers(), to_pose(), and update_conf().
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Referenced by score().
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Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_torsmutrate().
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Referenced by init_params(), protocols::ligand_docking::ga_ligand_dock::mutate(), and set_transwidth().