Namespaces
	orbitals

	RotamerSetCacheableDataType

	signals

	symmetry

Classes
class	AbstractRotamerTrie

class	Atom
	A simple object with atom's position and its chemical type. More...

class	AtomGraphVertexData

class	AtomGraphEdgeData

class	Conformation
	A container of Residues and the kinematics to manage them. More...

struct	DefaultCubeHash
	uses default boost::hash combine to hash Cubes More...

struct	AddEdgeVisitor

class	PointGraphVertexData

class	PointGraphEdgeData

class	PseudoBond

class	PseudoBondCollection

class	Residue
	Instance Residue class, used for placed residues and rotamers. More...

class	ResidueFactory
	a collection of functions making a single residue More...

class	ResidueKinWriter

class	ConformationKinWriter

class	ResidueMatcher

class	WatsonCrickResidueMatcher

class	ExactResidueMatcher

class	RotamerSetBase

Typedefs
typedef utility::pointer::owning_ptr < AbstractRotamerTrie >	AbstractRotamerTrieOP

typedef utility::pointer::owning_ptr < AbstractRotamerTrie const >	AbstractRotamerTrieCOP

typedef utility::vector1< Atom >	Atoms

typedef graph::UpperEdgeGraph < AtomGraphVertexData, AtomGraphEdgeData >	AtomGraph

typedef utility::pointer::owning_ptr < AtomGraph >	AtomGraphOP

typedef utility::pointer::owning_ptr < Conformation >	ConformationOP

typedef utility::pointer::owning_ptr < Conformation const >	ConformationCOP

typedef numeric::xyzTriple < core::Size >	CubeKey

typedef numeric::xyzVector < core::Real >	PointPosition

typedef graph::UpperEdgeGraph < PointGraphVertexData, PointGraphEdgeData >	PointGraph

typedef utility::pointer::owning_ptr < PointGraph >	PointGraphOP

typedef utility::pointer::owning_ptr < PseudoBondCollection >	PseudoBondCollectionOP

typedef utility::pointer::owning_ptr < PseudoBondCollection const >	PseudoBondCollectionCOP

typedef utility::pointer::access_ptr < Residue >	ResidueAP

typedef utility::pointer::access_ptr < Residue const >	ResidueCAP

typedef utility::pointer::owning_ptr < Residue >	ResidueOP

typedef utility::pointer::owning_ptr < Residue const >	ResidueCOP

typedef utility::vector1 < ResidueOP >	ResidueOPs

typedef utility::vector1 < ResidueCOP >	ResidueCOPs

typedef utility::vector1 < ResidueCAP >	ResidueCAPs

typedef utility::pointer::owning_ptr < ResidueKinWriter >	ResidueKinWriterOP

typedef utility::pointer::owning_ptr < ResidueKinWriter const >	ResidueKinWriterCOP

typedef utility::pointer::owning_ptr < ConformationKinWriter >	ConformationKinWriterOP

typedef utility::pointer::owning_ptr < ConformationKinWriter const >	ConformationKinWriterCOP

typedef utility::pointer::owning_ptr < ResidueMatcher >	ResidueMatcherOP

typedef utility::pointer::owning_ptr < ResidueMatcher const >	ResidueMatcherCOP

typedef utility::pointer::owning_ptr < RotamerSetBase >	RotamerSetBaseOP

typedef utility::pointer::owning_ptr < RotamerSetBase const >	RotamerSetBaseCOP

Enumerations
enum	Strategy { NAIVE, AUTOMATIC, OCTREE, THREEDGRID, STRIPEHASH }

Functions
std::ostream &	operator<< (std::ostream &os, Atom const &atom)

void	atom_graph_from_conformation (Conformation const &conformation, AtomGraphOP atom_graph)

platform::Size	annotated_atom_graph_from_conformation (Conformation const &conformation, AtomGraphOP pg, PointPosition const &additional_point)
	create a pointgraph which consists of 1 node for every atom, plus 1 additional node which will be added as the last node. The index of the additional node is returned More...

std::ostream &	operator<< (std::ostream &os, Conformation const &conf)

template<class Vertex , class Edge >
void	find_neighbors_naive (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff)

template<class Vertex , class Edge >
void	find_neighbors_octree (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, Strategy strategy)
	Finds the residue neighbors efficiently using an octree-like spatial sort. More...

template<class Vertex , class Edge >
void	find_neighbors_3dgrid (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff)
	Create a 3D grid of points. O(N^3). For "spherical" conformations, Theta(N). Speeds neighbor detection in abinitio by a factor of 2. Definition: Spherical = span of x,y and z all O(N**1/3). Note circularity. Adendum: if the 3D grid used a list of point indices instead of a vector, then this would be Theta(N) for spherical conformations; however, with a vector, this is O(NlgN). With the additional assumption that each cube contains O(1) points, then this implementation is O(N). Such an assumption is unneccessary in the list implementation. More...

template<class Vertex , class Edge >
void	find_neighbors_naive_restricted (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, utility::vector1< bool > const &residue_selection)

template<class Vertex , class Edge >
void	find_neighbors_octree_restricted (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, utility::vector1< bool > const &residue_selection, Strategy strategy)
	Finds the residue neighbors efficiently using an octree-like spatial sort. More...

template<class Vertex , class Edge >
void	find_neighbors_3dgrid_restricted (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, utility::vector1< bool > const &residue_selection)
	Create a 3D grid of points. O(N^3). For "spherical" conformations, Theta(N). Speeds neighbor detection in abinitio by a factor of 2. Definition: Spherical = span of x,y and z all O(N**1/3). Note circularity. Adendum: if the 3D grid used a list of point indices instead of a vector, then this would be Theta(N) for spherical conformations; however, with a vector, this is O(NlgN). With the additional assumption that each cube contains O(1) points, then this implementation is O(N). Such an assumption is unneccessary in the list implementation. More...

template<class Vertex , class Edge >
core::Size	get_nearest_neighbor (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Size node_id, core::Real neighbor_cutoff, Strategy strategy=AUTOMATIC)

template<class Vertex , class Edge >
void	find_neighbors (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, Strategy strategy=AUTOMATIC)

template<class Vertex , class Edge >
void	find_neighbors_stripe (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff)

template<class Vertex , class Edge >
void	find_neighbors_restricted (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, utility::vector1< bool > const &residue_selection, Strategy strategy=AUTOMATIC)

template<class Vertex , class Edge >
void	find_neighbors_naive_surface (utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff, utility::vector1< std::pair< Size, Size > > const &non_surface_ranges, utility::vector1< bool > const &is_surface)

void	residue_point_graph_from_conformation (Conformation const &conformation, PointGraph &pg)

static basic::Tracer	TR ("core.conformation.Residue")

std::ostream &	operator<< (std::ostream &os, Residue const &res)

void	idealize_hydrogens (Residue &res, Conformation const &conf)

void	set_chi_according_to_coordinates (conformation::Residue &rotamer)
	rotamer chi-update from coords useful for building rotamers from coordinates More...

void	write_kinemage_header (std::ostream &ostr, Size const kin_number, std::string const &title, Vector const &ctr)

void	print_node (std::ostream &out, int residue_num, int atom_num, core::Vector const &atom_xyz, core::chemical::ResidueType const &res, std::string extras="")
	TWO FUNCTIONS STOLEN FROM IAN: and slightly modified. More...

void	print_node (std::ostream &out, int residue_num, int atom_num, core::conformation::Residue const &res, std::string extras="")

void	print_node (std::ostream &out, int residue_num, std::string atom_name, core::conformation::Residue const &res, std::string extras="")

void	orient_residue_for_ideal_bond (Residue &moving_rsd, chemical::ResidueConnection const &moving_connection, Residue const &fixed_rsd, chemical::ResidueConnection const &fixed_connection, Conformation const &conformation, bool lookup_bond_length)

void	insert_ideal_mainchain_bonds (Size const seqpos, Conformation &conformation)

void	insert_ideal_bonds_at_polymer_junction (Size const seqpos, Conformation &conformation)
	Sets the two bond angles and the bond length across the junction, rebuilds dependent atoms (eg O,H) More...

void	idealize_position (Size const seqpos, Conformation &conformation)
	Idealize backbone and sidechain at seqpos. More...

bool	is_ideal_position (Size const seqpos, Conformation const &conformation, Real theta_epsilon=0.005,Real D_epsilon=0.02)
	Return true if position contains an ideal geometry up to some epsilon. More...

void	copy_residue_coordinates_and_rebuild_missing_atoms (Residue const &source_rsd, Residue &target_rsd, Conformation const &conf)
	Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others. More...

std::ostream &	print_atom (id::AtomID const &id, Conformation const &conf, std::ostream &os)

void	show_atom_tree (kinematics::tree::Atom const &atom, Conformation const &conf, std::ostream &os)

void	replace_conformation_residue_copying_existing_coordinates (conformation::Conformation &conformation, Size const seqpos, chemical::ResidueType const &new_rsd_type)

void	add_variant_type_to_conformation_residue (conformation::Conformation &conformation, chemical::VariantType const &variant_type, Size const seqpos)
	construct a variant of an existing pose residue More...

void	remove_variant_type_from_conformation_residue (conformation::Conformation &conformation, chemical::VariantType const &variant_type, Size const seqpos)
	construct a non-variant of an existing pose residue More...

void	add_lower_terminus_type_to_conformation_residue (conformation::Conformation &conformation, Size const seqpos)

void	remove_lower_terminus_type_from_conformation_residue (conformation::Conformation &conformation, Size const seqpos)

void	add_upper_terminus_type_to_conformation_residue (conformation::Conformation &conformation, Size const seqpos)

void	remove_upper_terminus_type_from_conformation_residue (conformation::Conformation &conformation, Size const seqpos)

void	build_tree (kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)

void	build_jump_edge (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
	build a sub atom-tree for a jump edge and attach it to main atom-tree More...

void	build_polymer_edge (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
	build a sub atom-tree for a polymer edge and attach it to main atom-tree More...

void	build_chemical_edge (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
	build a sub atom-tree for a chemical edge and attach it to main atom-tree More...

int	get_root_atomno (conformation::Residue const &rsd, int const dir)
	get the root atom for building residue atom-tree given the folding direction "dir" More...

Size	get_root_residue_root_atomno (conformation::Residue const &rsd, kinematics::FoldTree const &fold_tree)

void	build_residue_tree (conformation::ResidueCAPs const &residues, conformation::Residue const &rsd, kinematics::FoldTree const &fold_tree, kinematics::AtomPointer1D &atom_ptr)
	build_residue_tree function that uses the foldtree info More...

bool	check_good_neighbor (Size const &atom_index, utility::vector1< Size > const &cut_nbrs)
	Check if this atom neighbor has been black-listed ("CUT_BOND" in params file). More...

bool	chi_continuation (Size const atom1, Size const atom2, utility::vector1< utility::vector1< Size > > const &chi_atoms)
	is atom2 the last atom of our chi angle ? More...

bool	chi_interruption (Size const atom1, Size const atom2, utility::vector1< utility::vector1< Size > > const &chi_atoms, utility::vector1< bool > const &is_done)
	would we be breaking into a chi angle by adding atom2 to the tree now? More...

void	setup_links_simple (conformation::Residue const &rsd, kinematics::Links &links)
	simply fill the "links" by adding, for each atom, its bonded neighbors More...

void	setup_atom_links (int const atom1, kinematics::Links const &full_links, utility::vector1< bool > &is_done, utility::vector1< bool > const &is_mainchain, utility::vector1< bool > const &is_chi, utility::vector1< bool > const &is_hydrogen, utility::vector1< utility::vector1< Size > > const &chi_atoms, kinematics::Links &new_links)
	set correct order for how atoms are linked to each other. More...

void	setup_links (conformation::Residue const &rsd, int const root_atomno, kinematics::Links &links)
	given the root_atomno, set up rules for how other atoms are linked for this residue a wrapper function calling setup_atom_links recursively . More...

void	build_residue_tree (int const root_atomno, conformation::Residue const &rsd, kinematics::AtomPointer1D &atom_ptr, bool const root_is_jump_atom)
	set up a local atom-tree for a residue from the defined root atom. More...

void	get_residue_connections (conformation::Residue const &new_rsd, kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, id::BondID &new_rsd_in, utility::vector1< id::BondID > &new_rsd_out)

void	replace_residue_in_atom_tree (conformation::Residue const &new_rsd, kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, kinematics::AtomTree &atom_tree)
	Helper function for conformation routines. More...

void	insert_residue_into_atom_tree (conformation::Residue const &new_rsd, kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, kinematics::AtomTree &atom_tree)
	Inserts/ appends new residue subtree into an existing atomtree. More...

int	get_anchor_atomno (conformation::Residue const &anchor_rsd, Size const seqpos, kinematics::FoldTree const &fold_tree)
	Get the atom-index of the atom to which the residue at position seqpos should be anchored. More...

int	get_anchor_atomno (conformation::Residue const &rsd, int const dir)
	get anchor atom to which the atom-tree of next residue in the edge is attached. More...

void	get_anchor_and_root_atoms (conformation::Residue const &anchor_rsd, conformation::Residue const &root_rsd, kinematics::Edge const &edge, Size &anchor_atomno, Size &root_atomno)
	Use this routine to deduce atom indices of connect atoms in the tree. More...

void	promote_sameresidue_child_of_jump_atom (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomTree &atom_tree)
	Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list. More...

void	promote_sameresidue_child_of_jump_atom (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D const &atom_pointer)
	Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list. More...

void	get_chemical_root_and_anchor_atomnos (conformation::Residue const &rsd_anchor, conformation::Residue const &rsd_root, Size &anchor_atom_no, Size &root_atom_no)

void	setup_corresponding_atoms (id::AtomID_Map< id::AtomID > &atom_map, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
	set up a map to match mainchain atoms from residue1 to residue2 More...

bool	change_cys_state (Size const index, std::string cys_type_name3, Conformation &conf)
	Replace a CYS with a CYD or vice-versa for changing disulfide bonds. More...

id::NamedAtomID	atom_id_to_named_atom_id (id::AtomID const &atom_id, conformation::Residue const &rsd)

id::AtomID	named_atom_id_to_atom_id (id::NamedAtomID const &named_atom_id, conformation::Residue const &rsd)

id::NamedStubID	stub_id_to_named_stub_id (id::StubID const &stub_id, conformation::Residue const &rsd)

id::StubID	named_stub_id_to_stub_id (id::NamedStubID const &named_stub_id, conformation::Residue const &rsd)

void	form_disulfide (Conformation &conformation, Size lower_res, Size upper_res)
	Introduce cysteines at the specified location and define a disulfide bond between them. More...

bool	is_disulfide_bond (conformation::Conformation const &conformation, Size residueA_pos, Size residueB_pos)
	Find whether there is a disulfide defined between two residues. More...

void	disulfide_bonds (conformation::Conformation const &conformation, utility::vector1< std::pair< Size, Size > > &disulfides)
	Generate a list of all disulfide bonds in the conformation. More...

char	get_torsion_bin (core::Real phi, core::Real psi, core::Real omega)

void	disulfide_bonds (core::conformation::Conformation const &conformation, utility::vector1< std::pair< core::Size, core::Size > > &disulfides)
	Generate a list of all disulfide bonds in the conformation. More...

Typedef Documentation

typedef utility::pointer::owning_ptr< AbstractRotamerTrie const > core::conformation::AbstractRotamerTrieCOP

Definition at line 27 of file AbstractRotamerTrie.fwd.hh.

typedef utility::pointer::owning_ptr< AbstractRotamerTrie > core::conformation::AbstractRotamerTrieOP

Definition at line 24 of file AbstractRotamerTrie.fwd.hh.

typedef graph::UpperEdgeGraph<AtomGraphVertexData, AtomGraphEdgeData> core::conformation::AtomGraph

Definition at line 23 of file AtomGraph.fwd.hh.

typedef utility::pointer::owning_ptr<AtomGraph > core::conformation::AtomGraphOP

Definition at line 24 of file AtomGraph.fwd.hh.

typedef utility::vector1< Atom > core::conformation::Atoms

Definition at line 22 of file Atom.fwd.hh.

typedef utility::pointer::owning_ptr< Conformation const > core::conformation::ConformationCOP

Definition at line 33 of file Conformation.fwd.hh.

typedef utility::pointer::owning_ptr< ConformationKinWriter const > core::conformation::ConformationKinWriterCOP

Definition at line 31 of file ResidueKinWriter.fwd.hh.

typedef utility::pointer::owning_ptr< ConformationKinWriter > core::conformation::ConformationKinWriterOP

Definition at line 30 of file ResidueKinWriter.fwd.hh.

typedef utility::pointer::owning_ptr< Conformation > core::conformation::ConformationOP

Definition at line 31 of file Conformation.fwd.hh.

typedef numeric::xyzTriple< core::Size > core::conformation::CubeKey

Definition at line 70 of file find_neighbors.fwd.hh.

typedef graph::UpperEdgeGraph< PointGraphVertexData, PointGraphEdgeData > core::conformation::PointGraph

Definition at line 30 of file PointGraph.fwd.hh.

typedef utility::pointer::owning_ptr< PointGraph > core::conformation::PointGraphOP

Definition at line 32 of file PointGraph.fwd.hh.

typedef numeric::xyzVector< core::Real > core::conformation::PointPosition

Definition at line 71 of file find_neighbors.fwd.hh.

typedef utility::pointer::owning_ptr< PseudoBondCollection const > core::conformation::PseudoBondCollectionCOP

Definition at line 29 of file PseudoBond.fwd.hh.

typedef utility::pointer::owning_ptr< PseudoBondCollection > core::conformation::PseudoBondCollectionOP

Definition at line 26 of file PseudoBond.fwd.hh.

typedef utility::pointer::access_ptr< Residue > core::conformation::ResidueAP

Definition at line 27 of file Residue.fwd.hh.

typedef utility::pointer::access_ptr< Residue const > core::conformation::ResidueCAP

Definition at line 30 of file Residue.fwd.hh.

typedef utility::vector1< ResidueCAP > core::conformation::ResidueCAPs

Definition at line 36 of file Residue.fwd.hh.

typedef utility::pointer::owning_ptr< Residue const > core::conformation::ResidueCOP

Definition at line 32 of file Residue.fwd.hh.

typedef utility::vector1< ResidueCOP > core::conformation::ResidueCOPs

Definition at line 35 of file Residue.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueKinWriter const > core::conformation::ResidueKinWriterCOP

Definition at line 28 of file ResidueKinWriter.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueKinWriter > core::conformation::ResidueKinWriterOP

Definition at line 25 of file ResidueKinWriter.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueMatcher const > core::conformation::ResidueMatcherCOP

Definition at line 34 of file ResidueMatcher.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueMatcher > core::conformation::ResidueMatcherOP

Definition at line 31 of file ResidueMatcher.fwd.hh.

typedef utility::pointer::owning_ptr< Residue > core::conformation::ResidueOP

Definition at line 31 of file Residue.fwd.hh.

typedef utility::vector1< ResidueOP > core::conformation::ResidueOPs

Definition at line 34 of file Residue.fwd.hh.

typedef utility::pointer::owning_ptr< RotamerSetBase const > core::conformation::RotamerSetBaseCOP

Definition at line 29 of file RotamerSetBase.fwd.hh.

typedef utility::pointer::owning_ptr< RotamerSetBase > core::conformation::RotamerSetBaseOP

Definition at line 26 of file RotamerSetBase.fwd.hh.

Enumeration Type Documentation

enum core::conformation::Strategy

Enumerator
NAIVE
AUTOMATIC
OCTREE
THREEDGRID
STRIPEHASH

Definition at line 60 of file find_neighbors.fwd.hh.

Function Documentation

void core::conformation::add_lower_terminus_type_to_conformation_residue	(	conformation::Conformation &	conformation,
		Size const	seqpos
	)

Definition at line 649 of file util.cc.

References add_variant_type_to_conformation_residue(), and core::chemical::LOWER_TERMINUS.

void core::conformation::add_upper_terminus_type_to_conformation_residue	(	conformation::Conformation &	conformation,
		Size const	seqpos
	)

Definition at line 669 of file util.cc.

References add_variant_type_to_conformation_residue(), and core::chemical::UPPER_TERMINUS.

void core::conformation::add_variant_type_to_conformation_residue	(	conformation::Conformation &	conformation,
		chemical::VariantType const &	variant_type,
		Size const	seqpos
	)

construct a variant of an existing pose residue

eg make a terminus variant, and replace the orignal in pose.

Note: this copies any atoms in common between old and new residues, rebuild the others

Definition at line 609 of file util.cc.

References replace_conformation_residue_copying_existing_coordinates(), and core::conformation::Conformation::residue().

Referenced by add_lower_terminus_type_to_conformation_residue(), and add_upper_terminus_type_to_conformation_residue().

platform::Size core::conformation::annotated_atom_graph_from_conformation	(	Conformation const &	conformation,
		AtomGraphOP	atom_graph,
		PointPosition const &	additional_point
	)

create a pointgraph which consists of 1 node for every atom, plus 1 additional node which will be added as the last node. The index of the additional node is returned

Definition at line 65 of file AtomGraph.cc.

References core::conformation::AtomGraphVertexData::atom_name(), core::chemical::ResidueType::natoms(), core::pose::num_atoms(), core::conformation::Conformation::residue(), core::conformation::AtomGraphVertexData::residue_id(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::size(), and core::conformation::PointGraphVertexData::xyz().

void core::conformation::atom_graph_from_conformation	(	Conformation const &	conformation,
		AtomGraphOP	atom_graph
	)

Definition at line 31 of file AtomGraph.cc.

References core::conformation::AtomGraphVertexData::atom_name(), core::conformation::AtomGraphVertexData::atom_radius_squared(), core::chemical::ResidueType::natoms(), core::pose::num_atoms(), core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::size(), and core::conformation::PointGraphVertexData::xyz().

id::NamedAtomID core::conformation::atom_id_to_named_atom_id	(	id::AtomID const &	atom_id,
		conformation::Residue const &	rsd
	)

Definition at line 1829 of file util.cc.

References core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::conformation::Residue::atoms(), core::id::AtomID::rsd(), and TR().

Referenced by protocols::toolbox::AllowInsert::append_residue(), core::conformation::Conformation::append_residue_by_bond(), core::scoring::constraints::AngleConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::show_def(), core::scoring::constraints::AngleConstraint::show_def(), core::scoring::constraints::AtomPairConstraint::show_def(), and stub_id_to_named_stub_id().

void core::conformation::build_chemical_edge	(	kinematics::Edge const &	edge,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomPointer2D &	atom_pointer
	)

build a sub atom-tree for a chemical edge and attach it to main atom-tree

assumes that the start residue of edge has already been built. Traverse the chemical edge residue by residue and after building sub atom-tree for this residue, attaches the edge's subtree to the anchor_atom in the previous residue.

Definition at line 837 of file util.cc.

References build_residue_tree(), get_anchor_and_root_atoms(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

Referenced by build_tree().

void core::conformation::build_jump_edge	(	kinematics::Edge const &	edge,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomPointer2D &	atom_pointer
	)

build a sub atom-tree for a jump edge and attach it to main atom-tree

root_atomno is the root for the sub atom-tree of this edge. anchor_atomno is the entry point of this sub atom-tree into the main atom-tree.

Definition at line 751 of file util.cc.

References build_residue_tree(), get_anchor_and_root_atoms(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

Referenced by build_tree().

void core::conformation::build_polymer_edge	(	kinematics::Edge const &	edge,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomPointer2D &	atom_pointer
	)

build a sub atom-tree for a polymer edge and attach it to main atom-tree

assumes that the start residue of edge has already been built. Traverse the polymer edge residue by residue and after building sub atom-tree for this residue, attaches the edge's subtree to the anchor_atom in the previous residue.

Definition at line 794 of file util.cc.

References build_residue_tree(), get_anchor_and_root_atoms(), core::kinematics::Edge::polymer_direction(), core::kinematics::Edge::start(), protocols::loops::start, core::kinematics::Edge::stop(), and protocols::loops::stop.

Referenced by build_tree().

void core::conformation::build_residue_tree	(	conformation::ResidueCAPs const &	residues,
		conformation::Residue const &	rsd,
		kinematics::FoldTree const &	fold_tree,
		kinematics::AtomPointer1D &	atom_ptr
	)

build_residue_tree function that uses the foldtree info

A wrapper function to build an atom-tree for a residue. Uses information from the foldtree to find the proper root atom if it is not defined, and determine the direction in which to build the residue. The goal of this function is to allow the Conformation to rebuild parts of the AtomTree in a way that is compatible with what would be built if we erased the entire atomtree and rebuilt it using the foldtree. Also used to build the atomtree for the root residue when we are building the atomtree from scratch.

also used in build_tree to build the residue tree for the root residue

Definition at line 960 of file util.cc.

References core::conformation::Residue::atom_index(), core::kinematics::dir_jump, get_anchor_and_root_atoms(), core::kinematics::FoldTree::get_residue_edge(), get_root_atomno(), get_root_residue_root_atomno(), core::kinematics::FoldTree::root(), and core::conformation::Residue::seqpos().

Referenced by build_chemical_edge(), build_jump_edge(), build_polymer_edge(), build_tree(), core::conformation::Conformation::fill_missing_atoms(), replace_residue_in_atom_tree(), and core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection().

void core::conformation::build_residue_tree	(	int const	root_atomno,
		conformation::Residue const &	rsd,
		kinematics::AtomPointer1D &	atom_ptr,
		bool const	root_is_jump_atom
	)

set up a local atom-tree for a residue from the defined root atom.

build the tree of atoms for this residue, anchored at root_atomno

Definition at line 1334 of file util.cc.

References core::kinematics::add_atom(), core::conformation::Residue::atom(), core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), setup_links(), and core::conformation::Atom::xyz().

void core::conformation::build_tree	(	kinematics::FoldTree const &	fold_tree,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomPointer2D &	atom_pointer
	)

Build an atom-tree from a fold-tree and a set of residues atoms in the tree are allocated with new (on the heap) and held in owning pointers in atom_pointer

Note: atom_pointer is cleared at the beginning and then filled with AtomOPs to all the atoms

Definition at line 695 of file util.cc.

References core::kinematics::FoldTree::begin(), build_chemical_edge(), build_jump_edge(), build_polymer_edge(), build_residue_tree(), core::kinematics::Edge::CHEMICAL, core::id::AtomID_Map< T >::clear(), core::kinematics::FoldTree::end(), core::kinematics::Edge::PEPTIDE, promote_sameresidue_child_of_jump_atom(), core::id::AtomID_Map< T >::resize(), and core::kinematics::FoldTree::root().

Referenced by core::conformation::Conformation::setup_atom_tree().

bool core::conformation::change_cys_state	(	Size const	index,
		std::string	cys_type_name3,
		Conformation &	conf
	)

Replace a CYS with a CYD or vice-versa for changing disulfide bonds.

Parameters

[in]	index	Position of the residue to replace.
[in]	cys_type_name3	The 3-letter name of the cys type to use: e.g. CYS or CYD.
[in,out]	conf	The conformation to modify

Substitutes a residue with the given cys type, keeping as many of the existing atom positions as possible. If the original residue has a disulfide variant it will be removed, otherwise a disulfide variant will be added. Should work with any ResidueTypeSet that has the proper disulfide variants. If the replacement fails for any reason a warning will be printed.

Returns: true if the replacement was successful, false otherwise.

Parameters

[in]	index	Position of the residue to replace.
[in]	cys_type_name3	The 3-letter name of the cys type to use: either CYS or CYD.
[in,out]	conf	The conformation to modify

Returns: true if the replacement was successful, false otherwise.

Definition at line 1770 of file util.cc.

References core::chemical::aa_cys, copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::chemical::DISULFIDE, core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), and TR().

Referenced by core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::conformation::Conformation::fix_disulfides(), and form_disulfide().

bool core::conformation::check_good_neighbor	(	Size const &	atom_index,
		utility::vector1< Size > const &	cut_nbrs
	)

Check if this atom neighbor has been black-listed ("CUT_BOND" in params file).

Definition at line 1015 of file util.cc.

Referenced by setup_links_simple().

bool core::conformation::chi_continuation	(	Size const	atom1,
		Size const	atom2,
		utility::vector1< utility::vector1< Size > > const &	chi_atoms
	)

inline

is atom2 the last atom of our chi angle ?

Definition at line 1026 of file util.cc.

Referenced by setup_atom_links().

bool core::conformation::chi_interruption	(	Size const	atom1,
		Size const	atom2,
		utility::vector1< utility::vector1< Size > > const &	chi_atoms,
		utility::vector1< bool > const &	is_done
	)

inline

would we be breaking into a chi angle by adding atom2 to the tree now?

Definition at line 1050 of file util.cc.

Referenced by setup_atom_links().

void core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms	(	Residue const &	source_rsd,
		Residue &	target_rsd,
		Conformation const &	conformation
	)

Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.

For building variant residues, eg

Note: Need conformation for context in case we have to rebuild atoms, eg backbone H

Definition at line 526 of file util.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::conformation::Residue::chain(), core::conformation::Residue::fill_missing_atoms(), core::conformation::Residue::has(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), TR(), and core::conformation::Atom::xyz().

Referenced by core::pose::add_variant_type_to_residue(), protocols::simple_moves::O2M_MutateMover::apply(), protocols::simple_moves::MutateResidue::apply(), change_cys_state(), protocols::simple_filters::SidechainRmsdFilter::compute(), form_disulfide(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), core::pose::remove_variant_type_from_residue(), replace_conformation_residue_copying_existing_coordinates(), core::pose::replace_pose_residue_copying_existing_coordinates(), protocols::hybridization::FoldTreeHybridize::set_loops_to_virt_ala(), and core::util::switch_to_residue_type_set().

void core::conformation::disulfide_bonds	(	core::conformation::Conformation const &	conformation,
		utility::vector1< std::pair< core::Size, core::Size > > &	disulfides
	)

Generate a list of all disulfide bonds in the conformation.

void core::conformation::disulfide_bonds	(	conformation::Conformation const &	conformation,
		utility::vector1< std::pair< Size, Size > > &	disulfides
	)

Generate a list of all disulfide bonds in the conformation.

Definition at line 2030 of file util.cc.

References core::chemical::aa_cys, core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, core::chemical::ResidueType::n_residue_connections(), core::chemical::ResConnID::resid(), core::conformation::Conformation::residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Conformation::size(), TR(), and core::conformation::Residue::type().

Referenced by protocols::swa::protein::StepWiseProteinPoseMinimizer::apply(), core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(), and core::util::switch_to_residue_type_set().

template<class Vertex , class Edge >

void core::conformation::find_neighbors	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		Strategy	strategy = `AUTOMATIC`
	)

Definition at line 86 of file find_neighbors.hh.

References AUTOMATIC, find_neighbors_3dgrid(), find_neighbors_naive(), find_neighbors_octree(), find_neighbors_stripe(), NAIVE, STRIPEHASH, and THREEDGRID.

Referenced by protocols::forge::remodel::RemodelDesignMover::apply(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), and core::conformation::Conformation::detect_disulfides().

template<class Vertex , class Edge >

void core::conformation::find_neighbors_3dgrid	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff
	)

Create a 3D grid of points. O(N^3). For "spherical" conformations, Theta(N). Speeds neighbor detection in abinitio by a factor of 2. Definition: Spherical = span of x,y and z all O(N**1/3). Note circularity. Adendum: if the 3D grid used a list of point indices instead of a vector, then this would be Theta(N) for spherical conformations; however, with a vector, this is O(NlgN). With the additional assumption that each cube contains O(1) points, then this implementation is O(N). Such an assumption is unneccessary in the list implementation.

Shameless code duplication below based on Stuart's stl-map-based-neighbor-detection code. Note that the FArray3D is an index-from-1 data structure.

Definition at line 368 of file find_neighbors.hh.

References core::sequence::end, core::io::serialization::size(), and core::scoring::electron_density::square().

Referenced by find_neighbors(), and find_neighbors_restricted().

template<class Vertex , class Edge >

void core::conformation::find_neighbors_3dgrid_restricted	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		utility::vector1< bool > const &	residue_selection
	)

Create a 3D grid of points. O(N^3). For "spherical" conformations, Theta(N). Speeds neighbor detection in abinitio by a factor of 2. Definition: Spherical = span of x,y and z all O(N**1/3). Note circularity. Adendum: if the 3D grid used a list of point indices instead of a vector, then this would be Theta(N) for spherical conformations; however, with a vector, this is O(NlgN). With the additional assumption that each cube contains O(1) points, then this implementation is O(N). Such an assumption is unneccessary in the list implementation.

Definition at line 762 of file find_neighbors.hh.

References core::sequence::end, core::io::serialization::size(), and core::scoring::electron_density::square().

template<class Vertex , class Edge >

void core::conformation::find_neighbors_naive	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff
	)

Definition at line 113 of file find_neighbors.hh.

Referenced by find_neighbors().

template<class Vertex , class Edge >

void core::conformation::find_neighbors_naive_restricted	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		utility::vector1< bool > const &	residue_selection
	)

Definition at line 555 of file find_neighbors.hh.

template<class Vertex , class Edge >

void core::conformation::find_neighbors_naive_surface	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		utility::vector1< std::pair< Size, Size > > const &	non_surface_ranges,
		utility::vector1< bool > const &	is_surface
	)

Definition at line 952 of file find_neighbors.hh.

template<class Vertex , class Edge >

void core::conformation::find_neighbors_octree	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		Strategy	strategy
	)

Finds the residue neighbors efficiently using an octree-like spatial sort.

Remarks

The "octree" algorithm isn't a real octree since we don't want/need the tree structure: we are only interested in one distance cutoff criterion
The octree algorithm is O( R log R ) for R residues vs. O( R^2 ) for the naive algorithm
The octree algorithm seems to be faster for R >= 150 or so: this may come down as it gets refined
This is an initial implementation of a more scalable neighbor detection algorithm: it will be further tuned as more tests cases are run. This type of algorithm may be of greater benefit for atom neighbor detection because the numbers involved are greater and the neighbor regions encompass a smaller fraction of the other atoms in typical structures.
The spatial sorting is essentially an octree method but with the important distinction that is doesn't have full a full tree structure: That would change the log R search complexity to log C where C is the number of cubes in the whole bounding box, which could be as much O( R^3 ) ( O( log C ) == O( log R ) would still be true but the constant would be 3x worse). Instead we let the map build a tree of just the active cubes, keeping the depth minimal. If we needed to access the parent meta-cubes we would need the full octree, but we don't here.
The use of std::map to hold the octree should be compared against hash maps and other methods.

Definition at line 191 of file find_neighbors.hh.

References OCTREE, and core::scoring::electron_density::square().

Referenced by find_neighbors().

template<class Vertex , class Edge >

void core::conformation::find_neighbors_octree_restricted	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		utility::vector1< bool > const &	residue_selection,
		Strategy	strategy
	)

Finds the residue neighbors efficiently using an octree-like spatial sort.

Definition at line 587 of file find_neighbors.hh.

References OCTREE, and core::scoring::electron_density::square().

template<class Vertex , class Edge >

void core::conformation::find_neighbors_restricted	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff,
		utility::vector1< bool > const &	residue_selection,
		Strategy	strategy = `AUTOMATIC`
	)

Definition at line 530 of file find_neighbors.hh.

References AUTOMATIC, find_neighbors_3dgrid(), NAIVE, and THREEDGRID.

template<class Vertex , class Edge >

void core::conformation::find_neighbors_stripe	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Real	neighbor_cutoff
	)

Definition at line 155 of file find_neighbors.hh.

Referenced by find_neighbors().

void core::conformation::form_disulfide	(	Conformation &	conformation,
		Size	lower_res,
		Size	upper_res
	)

Introduce cysteines at the specified location and define a disulfide bond between them.

Does not do the repacking & minimization required to place the disulfide correctly.

Definition at line 1907 of file util.cc.

Referenced by protocols::forge::remodel::RemodelDesignMover::make_disulfide().

void core::conformation::get_anchor_and_root_atoms	(	conformation::Residue const &	anchor_rsd,
		conformation::Residue const &	root_rsd,
		kinematics::Edge const &	edge,
		Size &	anchor_atomno,
		Size &	root_atomno
	)

Use this routine to deduce atom indices of connect atoms in the tree.

Determines the anchor and root atom indices based on residue types and the foldtree edge.

Definition at line 1561 of file util.cc.

Referenced by protocols::rigid::RotateJumpAxisMover::apply(), build_chemical_edge(), build_jump_edge(), build_polymer_edge(), build_residue_tree(), get_residue_connections(), and promote_sameresidue_child_of_jump_atom().

int core::conformation::get_anchor_atomno	(	conformation::Residue const &	anchor_rsd,
		Size const	seqpos,
		kinematics::FoldTree const &	fold_tree
	)

Get the atom-index of the atom to which the residue at position seqpos should be anchored.

Get the atom-index of the atom to which the residue at position seqpos should be anchored in constructing the atomtree.

Definition at line 1475 of file util.cc.

References core::conformation::Residue::atom_index(), core::kinematics::dir_jump, core::kinematics::FoldTree::get_residue_edge(), core::kinematics::FoldTree::root(), and core::conformation::Residue::seqpos().

Referenced by get_anchor_and_root_atoms(), get_anchor_atomno(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentRebuild::modify_impl(), and protocols::forge::build::SegmentInsert::modify_impl().

int core::conformation::get_anchor_atomno	(	conformation::Residue const &	rsd,
		int const	dir
	)

get anchor atom to which the atom-tree of next residue in the edge is attached.

Definition at line 1506 of file util.cc.

References core::kinematics::dir_jump, get_anchor_atomno(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), and core::conformation::Residue::upper_connect_atom().

void core::conformation::get_chemical_root_and_anchor_atomnos	(	conformation::Residue const &	rsd_anchor,
		conformation::Residue const &	rsd_root,
		Size &	anchor_atom_no,
		Size &	root_atom_no
	)

Definition at line 1661 of file util.cc.

References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::conformation::Residue::connections_to_residue(), core::chemical::ResConnID::connid(), core::conformation::Residue::is_bonded(), and core::conformation::Residue::residue_connection().

Referenced by get_anchor_and_root_atoms().

template<class Vertex , class Edge >

core::Size core::conformation::get_nearest_neighbor	(	utility::pointer::owning_ptr< graph::UpperEdgeGraph< Vertex, Edge > >	point_graph,
		core::Size	node_id,
		core::Real	neighbor_cutoff,
		Strategy	strategy = `AUTOMATIC`
	)

Definition at line 926 of file find_neighbors.hh.

References core::graph::UEVertex< V, E >::data(), core::graph::UEVertex< V, E >::upper_edge_list_begin(), and core::graph::UEVertex< V, E >::upper_edge_list_end().

void core::conformation::get_residue_connections	(	conformation::Residue const &	new_rsd,
		kinematics::FoldTree const &	fold_tree,
		conformation::ResidueCAPs const &	residues,
		id::BondID &	new_rsd_in,
		utility::vector1< id::BondID > &	new_rsd_out
	)

Get the incoming connection and all outgoing connections from a residue

Definition at line 1363 of file util.cc.

References core::id::BondID::atom1, core::id::BondID::atom2, core::id::BOGUS_ATOM_ID, get_anchor_and_root_atoms(), core::kinematics::FoldTree::get_outgoing_edges(), core::kinematics::FoldTree::get_residue_edge(), get_root_residue_root_atomno(), core::kinematics::FoldTree::is_root(), core::kinematics::Edge::polymer_direction(), and core::conformation::Residue::seqpos().

Referenced by replace_residue_in_atom_tree().

int core::conformation::get_root_atomno	(	conformation::Residue const &	rsd,
		int const	dir
	)

get the root atom for building residue atom-tree given the folding direction "dir"

Definition at line 864 of file util.cc.

References core::kinematics::dir_jump, core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), and core::conformation::Residue::upper_connect_atom().

Referenced by build_residue_tree(), get_anchor_and_root_atoms(), get_root_residue_root_atomno(), and core::conformation::Conformation::jump_atom_id().

Size core::conformation::get_root_residue_root_atomno	(	conformation::Residue const &	rsd,
		kinematics::FoldTree const &	fold_tree
	)

Determine which atom to use as the root of the root residue in the atomtree. It is sometimes useful to be able to control the atom chosen as the root of the atomtree, eg in graphics. The logic below uses atom_info stored in the foldtree for jump edges emanating from the root residue to override the default atom (if the root residue is a jump_point and said atom_info exists)

Definition at line 929 of file util.cc.

References core::conformation::Residue::atom_index(), core::kinematics::dir_jump, get_root_atomno(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::root(), core::conformation::Residue::seqpos(), and TR().

Referenced by build_residue_tree(), and get_residue_connections().

char core::conformation::get_torsion_bin	(	core::Real	phi,
		core::Real	psi,
		core::Real	omega
	)

Definition at line 2076 of file util.cc.

Referenced by core::scoring::Ramachandran::init_rama_sampling_table(), core::scoring::Ramachandran2B::init_rama_sampling_table_left(), core::scoring::Ramachandran2B::init_rama_sampling_table_right(), protocols::loops::loop_mover::LoopMover::torsion_features_string(), and protocols::loops::loop_closure::kinematic_closure::KinematicMover::torsion_features_string().

void core::conformation::idealize_hydrogens	(	Residue &	res,
		Conformation const &	conf
	)

Definition at line 35 of file Residue.functions.cc.

References core::conformation::Residue::atom_name(), core::chemical::ICoorAtomID::atomno(), core::chemical::AtomICoor::build(), core::conformation::Residue::icoor(), core::chemical::ICoorAtomID::is_internal(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::set_xyz(), and core::chemical::AtomICoor::stub_atom().

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), and core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers().

void core::conformation::idealize_position	(	Size const	seqpos,
		Conformation &	conformation
	)

Idealize backbone and sidechain at seqpos.

Definition at line 303 of file util.cc.

References core::id::BB, core::id::CHI, core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::size(), and core::conformation::Residue::type().

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::idealize::basic_idealize(), protocols::star::Extender::extend_unaligned(), protocols::loops::idealize_loop(), protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation(), core::fragment::make_pose_from_frags(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_cter_perturbation(), protocols::jumping::remove_cut(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), and protocols::loops::set_extended_torsions_and_idealize_loops().

void core::conformation::insert_ideal_bonds_at_polymer_junction	(	Size const	seqpos,
		Conformation &	conformation
	)

Sets the two bond angles and the bond length across the junction, rebuilds dependent atoms (eg O,H)

Just sets the two bond angles and the bond length between seqpos and seqpos+1

Definition at line 246 of file util.cc.

References core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::residue(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::size(), TR(), and core::conformation::Residue::type().

Referenced by protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop().

void core::conformation::insert_ideal_mainchain_bonds	(	Size const	seqpos,
		Conformation &	conformation
	)

Definition at line 163 of file util.cc.

References core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::residue(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::size(), and core::conformation::Residue::type().

void core::conformation::insert_residue_into_atom_tree	(	conformation::Residue const &	new_rsd,
		kinematics::FoldTree const &	fold_tree,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomTree &	atom_tree
	)

Inserts/ appends new residue subtree into an existing atomtree.

Note: The foldtree must already have been changed to reflect the new residue; The residues array should already have been inserted into; The sequence position of the new residue is deduced from new_rsd.seqpos(); This function handles renumbering of the atomtree if necessary; The foldtree must already have been changed to reflect the new residue; The sequence position of the new residue is deduced from new_rsd.seqpos(); This function handles renumbering of the atomtree if necessary

Definition at line 1441 of file util.cc.

References core::kinematics::FoldTree::nres(), replace_residue_in_atom_tree(), core::conformation::Residue::seqpos(), core::kinematics::AtomTree::size(), and core::kinematics::AtomTree::update_sequence_numbering().

Referenced by core::conformation::Conformation::append_residue(), core::conformation::Conformation::insert_polymer_residue(), and core::conformation::Conformation::insert_residue_by_jump().

bool core::conformation::is_disulfide_bond	(	conformation::Conformation const &	conformation,
		Size	residueA_pos,
		Size	residueB_pos
	)

Find whether there is a disulfide defined between two residues.

We define a disulfide to exist between a pair of residues iff

They are both cysteines
They are bonded by their sidechains

Definition at line 1997 of file util.cc.

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), protocols::comparative_modeling::features::B, core::conformation::Residue::connect_map(), core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueType::name1(), core::chemical::ResConnID::resid(), core::conformation::Conformation::residue(), core::chemical::ResidueType::residue_connection(), and core::conformation::Residue::type().

Referenced by core::util::rebuild_disulfide().

bool core::conformation::is_ideal_position	(	Size const	seqpos,
		Conformation const &	conformation,
		Real	theta_epsilon = `0.005`,
		Real	D_epsilon = `0.02`
	)

Return true if position contains an ideal geometry up to some epsilon.

seqpos - sequence position conformation - conformation object theta_epsilon - permitted deviation from ideal bond angles, in Radians D_epsilon - permitted deviation from ideal bond length

Remarks: conformation is needed for context of polymer nbrs

Definition at line 439 of file util.cc.

References core::conformation::Conformation::append_residue_by_bond(), core::conformation::ResidueFactory::create_residue(), core::id::D, core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), core::id::THETA, TR(), and core::conformation::Residue::type().

Referenced by core::pose::is_ideal_position(), protocols::features::ResidueConformationFeatures::report_features(), and protocols::features::ProteinResidueConformationFeatures::report_features().

id::AtomID core::conformation::named_atom_id_to_atom_id	(	id::NamedAtomID const &	named_atom_id,
		conformation::Residue const &	rsd
	)

Definition at line 1848 of file util.cc.

References core::id::NamedAtomID::atom(), core::conformation::Residue::atom_index(), and core::id::NamedAtomID::rsd().

id::StubID core::conformation::named_stub_id_to_stub_id	(	id::NamedStubID const &	named_stub_id,
		conformation::Residue const &	rsd
	)

Definition at line 1878 of file util.cc.

References core::id::NamedStubID::atom(), core::id::NamedStubID::center(), named_atom_id_to_atom_id(), and core::id::NamedAtomID::valid().

Referenced by protocols::topology_broker::CoordConstraintClaimer::generate_constraints().

std::ostream & core::conformation::operator<<	(	std::ostream &	os,
		Atom const &	atom
	)

Definition at line 1151 of file Residue.cc.

References core::conformation::Atom::type(), and core::conformation::Atom::xyz().

std::ostream & core::conformation::operator<<	(	std::ostream &	os,
		Residue const &	res
	)

Definition at line 1136 of file Residue.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), and core::conformation::Residue::seqpos().

std::ostream & core::conformation::operator<<	(	std::ostream &	os,
		Conformation const &	conf
	)

Definition at line 3479 of file Conformation.cc.

References core::conformation::Conformation::show_residue_connections().

void core::conformation::orient_residue_for_ideal_bond	(	Residue &	moving_rsd,
		chemical::ResidueConnection const &	moving_connection,
		Residue const &	fixed_rsd,
		chemical::ResidueConnection const &	fixed_connection,
		Conformation const &	conformation,
		bool	lookup_bond_length
	)

Definition at line 86 of file util.cc.

References protocols::comparative_modeling::features::A, core::conformation::Residue::actcoord(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueConnection::atomno(), protocols::comparative_modeling::features::B, core::chemical::AtomICoor::build(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::kinematics::Stub::global2local(), core::chemical::ResidueConnection::icoor(), core::chemical::ChemicalManager::ideal_bond_length_set(), core::chemical::AtomICoor::is_internal(), core::conformation::Residue::natoms(), core::conformation::Residue::set_xyz(), core::chemical::AtomICoor::stub_atom2(), core::chemical::ICoorAtomID::xyz(), and core::conformation::Residue::xyz().

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), and core::conformation::Conformation::prepend_polymer_residue_before_seqpos().

std::ostream& core::conformation::print_atom	(	id::AtomID const &	id,
		Conformation const &	conf,
		std::ostream &	os
	)

Helper function for below

Definition at line 560 of file util.cc.

References core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::conformation::Conformation::residue(), and core::conformation::Residue::seqpos().

Referenced by show_atom_tree().

void core::conformation::print_node	(	std::ostream &	out,
		int	residue_num,
		int	atom_num,
		core::Vector const &	atom_xyz,
		core::chemical::ResidueType const &	res,
		std::string	extras = `""`
	)

TWO FUNCTIONS STOLEN FROM IAN: and slightly modified.

Definition at line 47 of file ResidueKinWriter.cc.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), protocols::loops::extras, core::chemical::AtomType::name(), and core::chemical::ResidueType::name3().

Referenced by print_node(), core::conformation::ConformationKinWriter::write_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

void core::conformation::print_node	(	std::ostream &	out,
		int	residue_num,
		int	atom_num,
		core::conformation::Residue const &	res,
		std::string	extras = `""`
	)

Definition at line 70 of file ResidueKinWriter.cc.

References protocols::loops::extras, print_node(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

void core::conformation::print_node	(	std::ostream &	out,
		int	residue_num,
		std::string	atom_name,
		core::conformation::Residue const &	res,
		std::string	extras = `""`
	)

Definition at line 82 of file ResidueKinWriter.cc.

References core::conformation::Residue::atom_index(), protocols::loops::extras, and print_node().

void core::conformation::promote_sameresidue_child_of_jump_atom	(	kinematics::Edge const &	edge,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomTree &	atom_tree
	)

Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list.

if ( debug ) { BondID old_rsd_in; vector1< BondID > old_rsd_out; get_residue_connections( old_rsd, fold_tree, residues, old_rsd_in, old_rsd_out ); assert( new_rsd_in.atom1 == old_rsd_in.atom1 && new_rsd_out.size() == old_rsd_out.size() ); for ( Size i=1; i<= new_rsd_out.size(); ++i ) { assert( new_rsd_out[i].atom2 == old_rsd_out[i].atom2 ); } }

Definition at line 1618 of file util.cc.

References get_anchor_and_root_atoms(), core::kinematics::Edge::is_jump(), core::kinematics::AtomTree::promote_sameresidue_nonjump_child(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

Referenced by build_tree(), and replace_residue_in_atom_tree().

void core::conformation::promote_sameresidue_child_of_jump_atom	(	kinematics::Edge const &	edge,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomPointer2D const &	atom_pointer
	)

Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list.

Definition at line 1632 of file util.cc.

References get_anchor_and_root_atoms(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and TR().

void core::conformation::remove_lower_terminus_type_from_conformation_residue	(	conformation::Conformation &	conformation,
		Size const	seqpos
	)

Definition at line 659 of file util.cc.

References core::chemical::LOWER_TERMINUS, and remove_variant_type_from_conformation_residue().

Referenced by protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), and core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos().

void core::conformation::remove_upper_terminus_type_from_conformation_residue	(	conformation::Conformation &	conformation,
		Size const	seqpos
	)

Definition at line 679 of file util.cc.

References remove_variant_type_from_conformation_residue(), and core::chemical::UPPER_TERMINUS.

Referenced by protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), and core::conformation::Conformation::safely_append_polymer_residue_after_seqpos().

void core::conformation::remove_variant_type_from_conformation_residue	(	conformation::Conformation &	conformation,
		chemical::VariantType const &	variant_type,
		Size const	seqpos
	)

construct a non-variant of an existing pose residue

eg remove a terminus variant, and replace the orignal in pose.

Note: this copies any atoms in common between old and new residues, rebuild the others

Definition at line 630 of file util.cc.

References replace_conformation_residue_copying_existing_coordinates(), and core::conformation::Conformation::residue().

Referenced by remove_lower_terminus_type_from_conformation_residue(), and remove_upper_terminus_type_from_conformation_residue().

void core::conformation::replace_conformation_residue_copying_existing_coordinates	(	conformation::Conformation &	conformation,
		Size const	seqpos,
		chemical::ResidueType const &	new_rsd_type
	)

helper function for residue replacement/residuetype switching

Note: Will call new_rsd->fill_missing_atoms if the new residue has atoms that the old one doesn't

Definition at line 589 of file util.cc.

References copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::replace_residue(), and core::conformation::Conformation::residue().

Referenced by add_variant_type_to_conformation_residue(), and remove_variant_type_from_conformation_residue().

void core::conformation::replace_residue_in_atom_tree	(	conformation::Residue const &	new_rsd,
		kinematics::FoldTree const &	fold_tree,
		conformation::ResidueCAPs const &	residues,
		kinematics::AtomTree &	atom_tree
	)

Helper function for conformation routines.

Helper function for conformation routines. Uses fold_tree to deduce the incoming/outgoing connections for the new residue and the old residue We want it to be the case that the tree we get after this call is the same one that we would have gotten by calling build_tree

Definition at line 1406 of file util.cc.

References build_residue_tree(), get_residue_connections(), core::kinematics::FoldTree::get_residue_edge(), core::kinematics::Edge::is_jump(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::is_root(), core::kinematics::Edge::keep_stub_in_residue(), promote_sameresidue_child_of_jump_atom(), core::kinematics::AtomTree::replace_residue_subtree(), and core::conformation::Residue::seqpos().

Referenced by insert_residue_into_atom_tree(), and core::conformation::Conformation::replace_residue().

void core::conformation::residue_point_graph_from_conformation	(	Conformation const &	conformation,
		PointGraph &	pg
	)

Definition at line 34 of file PointGraph.cc.

References core::graph::UEVertex< V, E >::data(), core::graph::UpperEdgeGraph< V, E >::get_vertex(), core::conformation::Residue::nbr_atom(), core::conformation::Conformation::residue(), core::graph::UpperEdgeGraph< V, E >::set_num_vertices(), core::conformation::Conformation::size(), and core::conformation::Residue::xyz().

Referenced by protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), core::pack::task::operation::util::calc_interacting_vector(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pack::create_packer_graph(), protocols::toolbox::pose_metric_calculators::SequenceComparison::fill_num_neighbors(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), core::scoring::solid_surface::SurfaceEnergies::fill_point_graph(), core::scoring::Energies::fill_point_graph(), core::pack::task::operation::util::find_jump_partners_within_CB_cutoff(), core::pack::task::operation::util::find_neighbors_within_CB_cutoff(), core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::recompute(), core::scoring::NeighborList::setup(), and protocols::simple_moves::setup_dme_point_graph().

void core::conformation::set_chi_according_to_coordinates ( conformation::Residue & rotamer)

rotamer chi-update from coords useful for building rotamers from coordinates

hokey "update chi from coordinates" useful for when the coordinates are known for a rotamer (specifically, a residue living outside of a conformation object); after the coordinates are set, the chis have to be updated – that won't happen automatically.

Definition at line 95 of file Residue.functions.cc.

References core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::conformation::Residue::is_protein(), core::conformation::Residue::nchi(), and core::conformation::Residue::xyz().

Referenced by core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::dunbrack::SingleLigandRotamerLibrary::init_from_file(), and protocols::motifs::load_build_position_data().

void core::conformation::setup_atom_links	(	int const	atom1,
		kinematics::Links const &	full_links,
		utility::vector1< bool > &	is_done,
		utility::vector1< bool > const &	is_mainchain,
		utility::vector1< bool > const &	is_chi,
		utility::vector1< bool > const &	is_hydrogen,
		utility::vector1< utility::vector1< Size > > const &	chi_atoms,
		kinematics::Links &	new_links
	)

set correct order for how atoms are linked to each other.

this function is called recursively.

atom1 is the root of links at the current level.
full_links store information about UNORDERED bonded neighbors for each atom in this residue.
is_done indicates which atoms have already been linked.
is_mainchain, is_chi, is_hydrogen and chi atoms are self explanatory
new_links store information about ORDERED bonded neighbors (links) for each atom in this residue.

Definition at line 1137 of file util.cc.

References chi_continuation(), and chi_interruption().

Referenced by setup_links().

void core::conformation::setup_corresponding_atoms	(	id::AtomID_Map< id::AtomID > &	atom_map,
		conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

set up a map to match mainchain atoms from residue1 to residue2

only map by atom number, not by identity currently.

Definition at line 1695 of file util.cc.

void core::conformation::setup_links	(	conformation::Residue const &	rsd,
		int const	root_atomno,
		kinematics::Links &	links
	)

given the root_atomno, set up rules for how other atoms are linked for this residue a wrapper function calling setup_atom_links recursively .

Definition at line 1256 of file util.cc.

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::chi_atoms(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::natoms(), setup_atom_links(), and setup_links_simple().

Referenced by build_residue_tree().

void core::conformation::setup_links_simple	(	conformation::Residue const &	rsd,
		kinematics::Links &	links
	)

simply fill the "links" by adding, for each atom, its bonded neighbors

Definition at line 1094 of file util.cc.

References check_good_neighbor(), core::conformation::Residue::cut_bond_neighbor(), core::conformation::Residue::natoms(), and core::conformation::Residue::nbrs().

Referenced by setup_links().

void core::conformation::show_atom_tree	(	kinematics::tree::Atom const &	atom,
		Conformation const &	conf,
		std::ostream &	os
	)

Definition at line 569 of file util.cc.

References core::kinematics::tree::Atom::child(), core::kinematics::tree::Atom::id(), core::kinematics::tree::Atom::n_children(), and print_atom().

id::NamedStubID core::conformation::stub_id_to_named_stub_id	(	id::StubID const &	stub_id,
		conformation::Residue const &	rsd
	)

Definition at line 1856 of file util.cc.

References core::id::StubID::atom(), atom_id_to_named_atom_id(), core::id::StubID::center(), and core::id::AtomID::valid().

static basic::Tracer core::conformation::TR ( "core.conformation.Residue" )

static

void core::conformation::write_kinemage_header	(	std::ostream &	ostr,
		Size const	kin_number,
		std::string const &	title,
		Vector const &	ctr
	)

Definition at line 33 of file ResidueKinWriter.cc.

Referenced by core::conformation::ResidueKinWriter::write_kin_header().

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