Rosetta
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#include <LigandConformer.hh>
Public Member Functions | |
LigandConformer () | |
~LigandConformer () override | |
LigandConformer (core::pose::PoseCOP pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > movingscs, bool freeze_ligand_backbone=false, bool freeze_ligand=false) | |
void | init_params () |
void | initialize (core::pose::PoseCOP pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > movingscs, bool freeze_ligand_backbone, bool freeze_ligand) |
bool | defined () const |
void | update_conf (core::pose::PoseCOP pose) |
void | update_ligand_conf (core::pose::PoseCOP pose) |
void | to_pose (core::pose::PoseOP pose) const |
void | to_minipose (core::pose::PoseOP pose, LigandConformer &minilig) const |
create a reduced pose representation (to be used in minimization) More... | |
void | update_conf_from_minipose (core::pose::PoseCOP pose) |
update internal information from the reduced pose representation More... | |
numeric::Quaternion< core::Real > const | quat () const |
numeric::xyzVector< core::Real > const | trans () const |
utility::vector1< core::Vector > const & | ligand_xyz () |
core::Real | ligand_rg () const |
core::conformation::Residue | ligand_residue (core::Size ires) const |
core::conformation::Residue | protein_residue (core::Size ires) const |
core::pose::PoseOP | receptor () const |
utility::vector1< core::Size > | ligand_ids () const |
utility::vector1< core::Real > const & | get_ligandchis () const |
core::Real | get_ligandchi (core::Size ichi) const |
void | set_ligandchi (core::Size ichi, core::Real value) |
core::Size | n_ligandchis () const |
utility::vector1< core::Size > const & | moving_scs () const |
void | set_moving_scs (utility::vector1< core::Size > setting) |
void | set_protein_restype (core::Size ires, core::chemical::ResidueTypeCOP restype) |
void | set_protein_chis (core::Size ires, utility::vector1< core::Real > const &newchis) |
void | set_sample_ring_conformers (bool setting) |
bool | sample_ring_conformers () const |
core::chemical::ResidueTypeCOP | get_protein_restype (core::Size ires) const |
utility::vector1< core::Real > | get_protein_chis (core::Size ires) const |
void | randomize (core::Real transmax) |
void | sample_conformation (core::Real transmax, TorsionSamplerCOP const &sampler) |
void | set_rotwidth (core::Real setting) |
void | set_transwidth (core::Real setting) |
void | set_chiwidth (core::Real setting) |
void | set_torsmutrate (core::Real setting) |
void | set_rtmutrate (core::Real setting) |
void | assign_ligand_trans (core::Vector transv) |
void | score (core::Real scorein) |
core::Real | score () const |
void | density_score (core::Real scorein) |
core::Real | density_score () const |
void | rms (core::Real rmsin) |
core::Real | rms () const |
void | dump_pose (std::string pdbname) const |
void | set_generation_tag (std::string tag) |
std::string | generation_tag () const |
std::string | to_string () const |
core::kinematics::FoldTree const & | get_reference_ft () const |
core::Size | get_jumpid () const |
bool | is_ligand_terminal () const |
std::string | ligand_typename () const |
std::string | ligand_typename (core::Size i) const |
void | set_negTds (core::Real inval) |
core::Real | neg_Tds () const |
core::pose::PoseCOP | get_ref_pose () const |
void | update_ligchi_types (core::conformation::Residue const &ligres) |
TorsionType const & | get_ligchi_type (core::Size ndx) const |
utility::vector1< TorsionType > const & | get_ligchi_types () const |
void | superimpose_to_ref_pose (utility::vector1< core::id::AtomID > const &ids) |
void | set_has_density_map (bool setting) |
bool | has_density_map () const |
bool | is_ligand_frozen () const |
bool | is_ligand_bb_frozen () const |
Friends | |
LigandConformer | mutate (LigandConformer const &l) |
LigandConformer | crossover (LigandConformer const &l1, LigandConformer const &l2) |
core::Real | distance_fast (LigandConformer &gene1, LigandConformer &gene2) |
core::Real | distance_slow (LigandConformer &gene1, LigandConformer &gene2) |
std::pair< core::Real, core::Real > | distance_internal (LigandConformer const &gene1, LigandConformer const &gene2) |
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, |
utility::vector1< core::Size > const & | ligids, | ||
utility::vector1< core::Size > | movingscs, | ||
bool | freeze_ligand_backbone = false , |
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bool | freeze_ligand = false |
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References init_params(), and initialize().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::assign_ligand_trans | ( | core::Vector | transv | ) |
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References rb_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().
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References density_score_.
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References density_score_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::dump_pose | ( | std::string | pdbname | ) | const |
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References generation_tag_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().
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References jumpid_.
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), 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_ligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().
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References ligandchis_.
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References ligandchis_.
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References ligandchi_types_.
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References ligandchi_types_.
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References ref_pose_.
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void protocols::ligand_docking::ga_ligand_dock::LigandConformer::init_params | ( | ) |
References freeze_ligand_, freeze_ligand_backbone_, generation_tag_, jumpid_, ligchimutWidth_, negTdS_, 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, |
utility::vector1< core::Size > const & | ligids, | ||
utility::vector1< core::Size > | movingscs, | ||
bool | freeze_ligand_backbone, | ||
bool | freeze_ligand | ||
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References core::pose::addVirtualResAsRoot(), freeze_ligand_, freeze_ligand_backbone_, jumpid_, ligand_typenames_, ligids_, movingscs_, ref_pose_, ref_pose_ligand_, and update_conf().
Referenced by LigandConformer().
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References freeze_ligand_, and freeze_ligand_backbone_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().
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References freeze_ligand_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop().
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References ligids_.
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(), 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_ligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin_helper(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_optH(), 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::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), 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 | ( | core::Size | ires | ) | const |
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References rg_.
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References ligand_typenames_.
utility::vector1< core::Vector > const& protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz | ( | ) |
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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::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin(), 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(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().
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References ligandchis_.
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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_.
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize | ( | core::Real | transmax | ) |
core::pose::PoseOP protocols::ligand_docking::ga_ligand_dock::LigandConformer::receptor | ( | ) | const |
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References rms_.
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References rms_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_conformation | ( | core::Real | transmax, |
TorsionSamplerCOP const & | sampler | ||
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References sample_ring_conformers_.
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References score_.
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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::GALigandDock::load_template_pool(), and protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().
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References ligchimutWidth_.
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References generation_tag_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation().
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References has_density_map_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply().
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References ligandchis_.
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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 torsmutationRate_.
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References transmutWidth_.
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_ref_pose | ( | utility::vector1< core::id::AtomID > const & | ids | ) |
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose | ( | core::pose::PoseOP | pose, |
LigandConformer & | minilig | ||
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create a reduced pose representation (to be used in minimization)
References core::pose::addVirtualResAsRoot(), jumpid_, ligids_, 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 jumpid_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligids_, 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::MCSAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score_init(), 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_.
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf | ( | core::pose::PoseCOP | pose | ) |
References protocols::ligand_docking::ga_ligand_dock::TorsionType::at1, protocols::ligand_docking::ga_ligand_dock::TorsionType::at2, protocols::ligand_docking::ga_ligand_dock::TorsionType::at3, protocols::ligand_docking::ga_ligand_dock::TorsionType::at4, core::conformation::Residue::atom_type_index(), core::id::AtomID::atomno(), core::id::BB, protocols::ligand_docking::ga_ligand_dock::TorsionType::bn, core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), protocols::ligand_docking::ga_ligand_dock::TorsionType::br, core::conformation::Residue::chi(), core::id::CHI, protocols::membrane::com(), freeze_ligand_, freeze_ligand_backbone_, core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), jumpid_, ligandchi_types_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligandxyz_, ligandxyz_synced_, ligid_restype_map_, ligids_, core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), movingscs_, core::chemical::ResidueType::n_rings(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::id::NU, core::chemical::ResidueType::nu_atoms(), proteinchis_, proteinrestypes_, protocols::simple_filters::R2quat(), rb_, rg_, core::chemical::ResidueType::ring_atoms(), sample_ring_conformers_, protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::conformation::Residue::xyz().
Referenced by protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), initialize(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), 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 ligids_, 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().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf | ( | core::pose::PoseCOP | pose | ) |
References protocols::ligand_docking::ga_ligand_dock::TorsionType::at1, protocols::ligand_docking::ga_ligand_dock::TorsionType::at2, protocols::ligand_docking::ga_ligand_dock::TorsionType::at3, protocols::ligand_docking::ga_ligand_dock::TorsionType::at4, core::conformation::Residue::atom_type_index(), core::id::AtomID::atomno(), core::id::BB, protocols::ligand_docking::ga_ligand_dock::TorsionType::bn, core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), protocols::ligand_docking::ga_ligand_dock::TorsionType::br, core::conformation::Residue::chi(), core::id::CHI, protocols::membrane::com(), freeze_ligand_, freeze_ligand_backbone_, ligandchi_types_, ligandchis_, ligandnus_, ligandtaus_, ligandtorsionids_, ligandxyz_, ligandxyz_synced_, ligid_restype_map_, ligids_, core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), core::chemical::ResidueType::n_rings(), core::conformation::Residue::nchi(), core::conformation::Residue::nheavyatoms(), core::id::NU, core::chemical::ResidueType::nu_atoms(), rg_, core::chemical::ResidueType::ring_atoms(), sample_ring_conformers_, protocols::ligand_docking::ga_ligand_dock::TR(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::conformation::Residue::xyz().
Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool().
void protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types | ( | core::conformation::Residue const & | ligres | ) |
References protocols::ligand_docking::ga_ligand_dock::TorsionType::at1, protocols::ligand_docking::ga_ligand_dock::TorsionType::at2, protocols::ligand_docking::ga_ligand_dock::TorsionType::at3, protocols::ligand_docking::ga_ligand_dock::TorsionType::at4, core::conformation::Residue::atom_type_index(), protocols::ligand_docking::ga_ligand_dock::TorsionType::bn, core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), protocols::ligand_docking::ga_ligand_dock::TorsionType::br, core::conformation::Residue::chi_atoms(), ligandchi_types_, core::conformation::Residue::nchi(), and core::conformation::Residue::type().
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Referenced by density_score().
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Referenced by init_params(), initialize(), is_ligand_bb_frozen(), is_ligand_frozen(), update_conf(), and update_ligand_conf().
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Referenced by init_params(), initialize(), is_ligand_bb_frozen(), update_conf(), and update_ligand_conf().
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Referenced by generation_tag(), init_params(), and set_generation_tag().
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Referenced by has_density_map(), and set_has_density_map().
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Referenced by get_jumpid(), init_params(), initialize(), to_minipose(), to_pose(), and update_conf().
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Referenced by initialize(), and ligand_typename().
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Referenced by get_ligchi_type(), get_ligchi_types(), update_conf(), update_ligand_conf(), and update_ligchi_types().
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Referenced by get_ligandchi(), get_ligandchis(), n_ligandchis(), set_ligandchi(), to_pose(), to_string(), update_conf(), and update_ligand_conf().
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Referenced by to_pose(), update_conf(), and update_ligand_conf().
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Referenced by to_pose(), update_conf(), and update_ligand_conf().
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Referenced by to_pose(), update_conf(), and update_ligand_conf().
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Referenced by update_conf(), and update_ligand_conf().
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Referenced by set_protein_chis(), set_protein_restype(), update_conf(), and update_ligand_conf().
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Referenced by init_params(), and set_chiwidth().
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Referenced by update_conf(), and update_ligand_conf().
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Referenced by initialize(), is_ligand_terminal(), ligand_ids(), to_minipose(), to_pose(), update_conf(), update_conf_from_minipose(), and update_ligand_conf().
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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 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 defined(), quat(), to_pose(), to_string(), trans(), and update_conf().
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Referenced by get_ref_pose(), get_reference_ft(), initialize(), is_ligand_terminal(), and to_pose().
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Referenced by initialize().
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Referenced by init_params(), ligand_rg(), update_conf(), and update_ligand_conf().
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Referenced by rms().
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Referenced by init_params(), and set_rotwidth().
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Referenced by init_params(), and set_rtmutrate().
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Referenced by init_params(), sample_ring_conformers(), set_sample_ring_conformers(), to_pose(), update_conf(), and update_ligand_conf().
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Referenced by score().
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Referenced by init_params(), and set_torsmutrate().
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Referenced by init_params(), and set_transwidth().