protocols::toolbox::pose_manipulation Namespace Reference

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 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 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...

Function Documentation

void protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps

(

core::pose::Pose &

pose

)

adds chainbreak residue types depending on fold tree jumps

Author

Florian Richter( flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), nov 11

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::kinematics::FoldTree::num_jump(), core::pose::Pose::residue_type(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by protocols::simple_filters::ScoreEvaluator::apply(), and protocols::simple_filters::TruncatedScoreEvaluator::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::kinematics::FoldTree::num_jump(), 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

Author

Florian Richter( flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu) , june 08

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.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

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

Author

Possu Huang ( possu.nosp@m.@uw..nosp@m.edu)

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(), 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

Author

Nobuyasu Koga ( nobuy.nosp@m.asu@.nosp@m.uw.ed.nosp@m.u ), Oct 09

References 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

Author

Nobuyasu Koga ( nobuy.nosp@m.asu@.nosp@m.uw.ed.nosp@m.u ), Oct 09; Tom Linsky (tlins.nosp@m.ky@u.nosp@m.w.edu), Nov 2014

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::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(), 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

Author

Florian Richter( flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), nov 11

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::kinematics::FoldTree::num_jump(), 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

Author

Florian Richter( flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu) , aug 08

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::SurfaceCalculator::recompute(), protocols::pose_metric_calculators::PackstatCalculator::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 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.

Author

Brian Coventry (bcov@.nosp@m.uw.e.nosp@m.du)

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 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.

Author

Brian Coventry (bcov@.nosp@m.uw.e.nosp@m.du)

References protocols::antibody::design::repack, and core::id::to_string().

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().

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::pose::center_of_mass(), core::select::get_residues_from_subset(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::set_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().

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

Author

Florian Richter( flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu) , sep 08 with the offset specified

References core::conformation::Residue::atom_index(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID::set(), and core::scoring::superimpose_pose().

static basic::Tracer protocols::toolbox::pose_manipulation::TR ( "protocols.toolbox.pose_manipulation"  )

static

static basic::Tracer protocols::toolbox::pose_manipulation::TR_DI ( "protocols.toolbox.pose_manipulation.insert_pose_into_pose"  )

static