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Rosetta
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Functions | |
| static basic::Tracer | TR ("protocols.toolbox.pose_manipulation") |
| static basic::Tracer | TR_DI ("protocols.toolbox.pose_manipulation.insert_pose_into_pose") |
| void | construct_poly_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys) |
| puts in ala residues at the positions specified in the 'positions' input array More... | |
| void | construct_poly_d_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys) |
| puts in D-ala residues at the positions specified in the 'positions' input array More... | |
| void | construct_poly_beta_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys) |
| puts in beta-3-ala residues at the positions specified in the 'positions' input array. More... | |
| void | construct_poly_d_beta_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys) |
| puts in D-beta-3-ala residues at the positions specified in the 'positions' input array More... | |
| void | construct_poly_uniq_restype_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, core::chemical::ResidueType const &restype, bool const keep_pro, bool const keep_gly, bool const keep_disulfide_cys) |
| allows construction of a polymer of any residue type More... | |
| void | construct_poly_XXX_pose (std::string const &aa, core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool keep_pro, bool keep_gly, bool keep_disulfide_cys) |
| puts in XXX residues at the positions specified in the 'positions' input array More... | |
| void | construct_poly_XXX_pose (std::string const &aa, core::pose::Pose &pose, utility::vector1< core::Size > const &positions, core::chemical::ResidueTypeSetCOP restype_set, bool keep_pro, bool keep_gly, bool keep_disulfide_cys) |
| puts in XXX residues at the positions from the given residue typeset specified in the 'positions' input array More... | |
| void | remove_non_protein_residues (core::pose::Pose &pose) |
| deletes all nonprotein residues from a pose More... | |
| void | add_chainbreaks_according_to_jumps (core::pose::Pose &pose) |
| adds chainbreak residue types depending on fold tree jumps More... | |
| void | add_chainbreaks_according_to_jumps (core::pose::Pose &pose, utility::vector1< core::Size > const &no_cutpoint_residues) |
| void | remove_chainbreaks_according_to_jumps (core::pose::Pose &pose) |
| removes chainbreak residue types depending on fold tree jumps More... | |
| core::Real | superimpose_pose_on_subset_CA (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< core::Size > const &positions, int const offset=0) |
| superimposes one pose onto the other at the positions specified and More... | |
| void | repack_this_residue (core::Size seq_pos, core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, bool include_current=true, std::string name1s_if_design="") |
| Repack a single residue @detail Repacks a single residue using the command-line flags A list of amino acid name1s may be provided if one wishes to design. Leaving this "" or default implies no design. More... | |
| void | repack_these_residues (core::select::residue_selector::ResidueSubset const &subset, core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, bool include_current=true, std::string name1s_if_design="") |
| Repack a subset of residues @detail Repacks a multiple residues using the command-line flags A list of amino acid name1s may be provided if one wishes to design. Leaving this "" or default implies no design. More... | |
| void | rigid_body_move (numeric::xyzVector< core::Real > const &rotation_unit_vector, core::Real angle_deg, numeric::xyzVector< core::Real > const &translation_vector, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0)) |
| Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More... | |
| void | rigid_body_move (numeric::xyzVector< core::Real > const &rotation_unit_vector, core::Real angle_deg, numeric::xyzVector< core::Real > const &translation_vector, core::Real translation_scalar, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0)) |
| Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More... | |
| void | rigid_body_move (numeric::xyzMatrix< core::Real > rotation, numeric::xyzVector< core::Real > const &translation_vector, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0)) |
| Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More... | |
| void | rigid_body_move (numeric::xyzMatrix< core::Real > rotation, numeric::xyzVector< core::Real > const &translation_vector, core::Real translation_scalar, core::pose::Pose &pose, core::select::residue_selector::ResidueSubset const &subset, numeric::xyzVector< core::Real > center_of_rotation=numeric::xyzVector< core::Real >(std::numeric_limits< core::Real >::quiet_NaN(), 0, 0)) |
| Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation. More... | |
| void protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps | ( | core::pose::Pose & | pose | ) |
adds chainbreak residue types depending on fold tree jumps
References core::pose::add_variant_type_to_pose_residue(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::residue_type(), and core::chemical::UPPER_TERMINUS_VARIANT.
Referenced by protocols::simple_filters::TruncatedScoreEvaluator::apply(), and protocols::simple_filters::ScoreEvaluator::apply().
| void protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps | ( | core::pose::Pose & | pose, |
| utility::vector1< core::Size > const & | no_cutpoint_residues | ||
| ) |
References core::pose::add_variant_type_to_pose_residue(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::residue_type(), and core::chemical::UPPER_TERMINUS_VARIANT.
| void protocols::toolbox::pose_manipulation::construct_poly_ala_pose | ( | core::pose::Pose & | pose, |
| utility::vector1< core::Size > const & | positions, | ||
| bool const | keep_pro, | ||
| bool const | keep_gly, | ||
| bool const | keep_disulfide_cys | ||
| ) |
puts in ala residues at the positions specified in the 'positions' input array
References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.
Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::forge::components::BDR::centroid_build(), protocols::denovo_design::construct_poly_ala_pose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around(), protocols::enzdes::PredesignPerturbMover::set_docking_pose(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().
| void protocols::toolbox::pose_manipulation::construct_poly_beta_ala_pose | ( | core::pose::Pose & | pose, |
| utility::vector1< core::Size > const & | positions, | ||
| bool const | keep_pro, | ||
| bool const | keep_gly, | ||
| bool const | keep_disulfide_cys | ||
| ) |
puts in beta-3-ala residues at the positions specified in the 'positions' input array.
References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.
Referenced by protocols::denovo_design::construct_poly_ala_pose().
| void protocols::toolbox::pose_manipulation::construct_poly_d_ala_pose | ( | core::pose::Pose & | pose, |
| utility::vector1< core::Size > const & | positions, | ||
| bool const | keep_pro, | ||
| bool const | keep_gly, | ||
| bool const | keep_disulfide_cys | ||
| ) |
puts in D-ala residues at the positions specified in the 'positions' input array
References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.
Referenced by protocols::denovo_design::construct_poly_ala_pose().
| void protocols::toolbox::pose_manipulation::construct_poly_d_beta_ala_pose | ( | core::pose::Pose & | pose, |
| utility::vector1< core::Size > const & | positions, | ||
| bool const | keep_pro, | ||
| bool const | keep_gly, | ||
| bool const | keep_disulfide_cys | ||
| ) |
puts in D-beta-3-ala residues at the positions specified in the 'positions' input array
References construct_poly_uniq_restype_pose(), and core::chemical::FA_STANDARD.
Referenced by protocols::denovo_design::construct_poly_ala_pose().
| void protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose | ( | core::pose::Pose & | pose, |
| utility::vector1< core::Size > const & | positions, | ||
| core::chemical::ResidueType const & | restype, | ||
| bool const | keep_pro, | ||
| bool const | keep_gly, | ||
| bool const | keep_disulfide_cys | ||
| ) |
allows construction of a polymer of any residue type
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_b3g, core::chemical::aa_b3p, core::chemical::aa_dpr, core::chemical::aa_gly, core::chemical::aa_pro, core::chemical::DISULFIDE, core::chemical::FA_STANDARD, core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::properties(), core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), TR(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::chemical::variants_match_with_exceptions().
Referenced by construct_poly_ala_pose(), construct_poly_beta_ala_pose(), construct_poly_d_ala_pose(), construct_poly_d_beta_ala_pose(), and protocols::motif_grafting::movers::MotifGraftMover::get_mono_aa_pose_copy().
| void protocols::toolbox::pose_manipulation::construct_poly_XXX_pose | ( | std::string const & | aa, |
| core::pose::Pose & | pose, | ||
| utility::vector1< core::Size > const & | positions, | ||
| bool | keep_pro, | ||
| bool | keep_gly, | ||
| bool | keep_disulfide_cys | ||
| ) |
puts in XXX residues at the positions specified in the 'positions' input array
References protocols::cluster::calibur::aa, and core::chemical::FA_STANDARD.
Referenced by protocols::denovo_design::components::SheetDB::add_sheets_from_pose(), protocols::pose_creation::MakePolyXMover::apply(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::hbnet::HBNet::get_native_networks(), and protocols::hbnet::HBNet::setup().
| void protocols::toolbox::pose_manipulation::construct_poly_XXX_pose | ( | std::string const & | aa, |
| core::pose::Pose & | pose, | ||
| utility::vector1< core::Size > const & | positions, | ||
| core::chemical::ResidueTypeSetCOP | restype_set, | ||
| bool | keep_pro, | ||
| bool | keep_gly, | ||
| bool | keep_disulfide_cys | ||
| ) |
puts in XXX residues at the positions from the given residue typeset specified in the 'positions' input array
References core::chemical::ResidueTypeBase::aa(), protocols::cluster::calibur::aa, core::chemical::aa_cys, core::chemical::aa_gly, core::chemical::aa_pro, core::chemical::DISULFIDE, core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::properties(), core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::chemical::variants_match().
| void protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps | ( | core::pose::Pose & | pose | ) |
removes chainbreak residue types depending on fold tree jumps
References core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::residue_type().
Referenced by protocols::constraints_additional::ConstraintEvaluator::prepare_pose().
| void protocols::toolbox::pose_manipulation::remove_non_protein_residues | ( | core::pose::Pose & | pose | ) |
deletes all nonprotein residues from a pose
References core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::energies(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::size().
Referenced by protocols::enzdes::DesignVsNativeComparison::compare_to_native(), protocols::pose_metric_calculators::HPatchCalculator::recompute(), protocols::pose_metric_calculators::PackstatCalculator::recompute(), protocols::pose_metric_calculators::SurfaceCalculator::recompute(), and protocols::enzdes::RemoveLigandFilter::report_sm().
| void protocols::toolbox::pose_manipulation::repack_these_residues | ( | core::select::residue_selector::ResidueSubset const & | subset, |
| core::pose::Pose & | pose, | ||
| core::scoring::ScoreFunctionOP | scorefxn, | ||
| bool | include_current = true, |
||
| std::string | name1s_if_design = "" |
||
| ) |
Repack a subset of residues @detail Repacks a multiple residues using the command-line flags A list of amino acid name1s may be provided if one wishes to design. Leaving this "" or default implies no design.
References core::select::get_residue_selector_from_subset(), and protocols::antibody::design::repack.
| void protocols::toolbox::pose_manipulation::repack_this_residue | ( | core::Size | seq_pos, |
| core::pose::Pose & | pose, | ||
| core::scoring::ScoreFunctionOP | scorefxn, | ||
| bool | include_current = true, |
||
| std::string | name1s_if_design = "" |
||
| ) |
Repack a single residue @detail Repacks a single residue using the command-line flags A list of amino acid name1s may be provided if one wishes to design. Leaving this "" or default implies no design.
References protocols::antibody::design::repack, and core::id::to_string().
| void protocols::toolbox::pose_manipulation::rigid_body_move | ( | numeric::xyzMatrix< core::Real > | rotation, |
| numeric::xyzVector< core::Real > const & | translation_vector, | ||
| core::pose::Pose & | pose, | ||
| core::select::residue_selector::ResidueSubset const & | subset, | ||
| numeric::xyzVector< core::Real > | center_of_rotation | ||
| ) |
Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.
References core::conformation::Residue::atom(), core::pose::center_of_mass(), core::select::get_residues_from_subset(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), and core::conformation::Atom::xyz().
| void protocols::toolbox::pose_manipulation::rigid_body_move | ( | numeric::xyzMatrix< core::Real > | rotation, |
| numeric::xyzVector< core::Real > const & | translation_vector, | ||
| core::Real | translation_scalar, | ||
| core::pose::Pose & | pose, | ||
| core::select::residue_selector::ResidueSubset const & | subset, | ||
| numeric::xyzVector< core::Real > | center_of_rotation | ||
| ) |
Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.
References rigid_body_move(), and protocols::toolbox::rigid_body::translate().
| void protocols::toolbox::pose_manipulation::rigid_body_move | ( | numeric::xyzVector< core::Real > const & | rotation_unit_vector, |
| core::Real | angle_deg, | ||
| numeric::xyzVector< core::Real > const & | translation_vector, | ||
| core::pose::Pose & | pose, | ||
| core::select::residue_selector::ResidueSubset const & | subset, | ||
| numeric::xyzVector< core::Real > | center_of_rotation | ||
| ) |
Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.
Referenced by protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), and rigid_body_move().
| void protocols::toolbox::pose_manipulation::rigid_body_move | ( | numeric::xyzVector< core::Real > const & | rotation_unit_vector, |
| core::Real | angle_deg, | ||
| numeric::xyzVector< core::Real > const & | translation_vector, | ||
| core::Real | translation_scalar, | ||
| core::pose::Pose & | pose, | ||
| core::select::residue_selector::ResidueSubset const & | subset, | ||
| numeric::xyzVector< core::Real > | center_of_rotation | ||
| ) |
Performs a rigid body rotation then translation of a section of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.
References rigid_body_move(), and protocols::toolbox::rigid_body::translate().
| core::Real protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA | ( | core::pose::Pose & | pose, |
| core::pose::Pose const & | ref_pose, | ||
| utility::vector1< core::Size > const & | positions, | ||
| int const | offset = 0 |
||
| ) |
superimposes one pose onto the other at the positions specified and
with the offset specified
References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), and core::scoring::superimpose_pose().
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Referenced by construct_poly_uniq_restype_pose().
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1.9.1