protocols::metal_interface::MatchGrafter Class Reference

#include <MatchGrafter.hh>

Inheritance diagram for protocols::metal_interface::MatchGrafter:

Public Types
typedef core::pose::Pose	Pose

Public Member Functions
	MatchGrafter ()
	~MatchGrafter () override
virtual Pose	graft (Pose &match, Pose &partner_ungrafted)
	Takes match pose (2 residues + zinc) and partner pose, grafts match onto partner, returns grafted partner. More...
virtual Pose	build_combined_pose_with_zinc_overlay (Pose &partner1, Pose &partner2)
	Takes two matches (for residue number info) and two grafted poses, overlays the zinc atoms, and uses a partner2 fold tree to combine the two poses. More...
virtual void	ensure_proper_his_tautomers (Pose &combined, utility::vector1< core::Size > metalsite_seqpos)

Member Typedef Documentation

Pose

typedef core::pose::Pose protocols::metal_interface::MatchGrafter::Pose

Constructor & Destructor Documentation

MatchGrafter()

protocols::metal_interface::MatchGrafter::MatchGrafter ( )

default

~MatchGrafter()

protocols::metal_interface::MatchGrafter::~MatchGrafter ( )

overridedefault

Member Function Documentation

build_combined_pose_with_zinc_overlay()

Pose protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay ( Pose &  partner1, Pose &  partner2  )

virtual

Takes two matches (for residue number info) and two grafted poses, overlays the zinc atoms, and uses a partner2 fold tree to combine the two poses.

References core::kinematics::FoldTree::add_edge(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_chain_ending(), core::pose::Pose::jump(), core::chemical::LOWER_TERMINUS_VARIANT, core::kinematics::Edge::PEPTIDE, core::pose::remove_variant_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_jump(), core::pose::Pose::size(), protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

ensure_proper_his_tautomers()

void protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers ( Pose &  combined, utility::vector1< core::Size >  metalsite_seqpos  )

virtual

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_his, core::conformation::Residue::atom(), core::conformation::Residue::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::kinematics::distance(), core::pose::get_restype_for_pose(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

graft()

Pose protocols::metal_interface::MatchGrafter::graft ( Pose &  match, Pose &  partner_ungrafted  )

virtual

Takes match pose (2 residues + zinc) and partner pose, grafts match onto partner, returns grafted partner.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::pose::Pose::append_residue_by_jump(), core::pose::Pose::conformation(), core::chemical::FA_STANDARD, core::chemical::LOWER_TERMINUS_VARIANT, core::pose::remove_variant_type_from_pose_residue(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::TR(), core::conformation::Conformation::update_polymeric_connection(), and core::chemical::UPPER_TERMINUS_VARIANT.

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The documentation for this class was generated from the following files:

• src/protocols/metal_interface/MatchGrafter.hh
• src/protocols/metal_interface/MatchGrafter.cc