Functions
void	construct_poly_ala_pose (core::pose::Pose &pose, utility::vector1< core::Size > const &positions, bool keep_pro, bool keep_gly, bool keep_disulfide_cys)
	puts in 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 keep_pro, bool keep_gly, bool 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	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...

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

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

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::ResidueType::has_variant_type(), core::chemical::ResidueType::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::ResidueType::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	keep_pro,
		bool	keep_gly,
		bool	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(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), and residue_type_set.

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::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_uniq_restype_pose	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	positions,
		core::chemical::ResidueType const &	restype,
		bool	keep_pro,
		bool	keep_gly,
		bool	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::FA_STANDARD, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::type().

Referenced by construct_poly_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, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), and runtime_assert.

Referenced by protocols::simple_moves::MakePolyXMover::apply(), and protocols::fldsgn::BluePrintBDR::centroid_build().

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::ResidueType::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::ResidueType::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::enzdes::DesignVsNativeComparison::compare_to_native(), protocols::toolbox::pose_metric_calculators::HPatchCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SurfaceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::PackstatCalculator::recompute(), and protocols::enzdes::RemoveLigandFilter::report_sm().

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(), BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), core::pose::Pose::residue(), and core::scoring::superimpose_pose().

Variable Documentation

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

static

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

static

Functions

Variables

Function Documentation

Variable Documentation