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Rosetta
2016.11
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Namespaces | |
membrane | |
orbitals | |
parametric | |
residue_datacache | |
RotamerSetCacheableDataType | |
signals | |
symmetry | |
Classes | |
class | AbstractRotamerTrie |
struct | AddEdgeVisitor |
class | Atom |
class | AtomGraphEdgeData |
class | AtomGraphVertexData |
class | Conformation |
A container of Residues and the kinematics to manage them. More... | |
class | ConformationKinWriter |
struct | DefaultCubeHash |
uses default boost::hash combine to hash Cubes More... | |
class | ExactResidueMatcher |
class | PointGraphEdgeData |
class | PointGraphVertexData |
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 | ResidueMatcher |
class | RotamerSetBase |
class | UltraLightResidue |
class | WatsonCrickResidueMatcher |
Typedefs | |
typedef utility::pointer::shared_ptr < AbstractRotamerTrie > | AbstractRotamerTrieOP |
typedef utility::pointer::shared_ptr < AbstractRotamerTrie const > | AbstractRotamerTrieCOP |
typedef utility::vector1< Atom > | Atoms |
typedef graph::UpperEdgeGraph < AtomGraphVertexData, AtomGraphEdgeData > | AtomGraph |
typedef utility::pointer::shared_ptr < AtomGraph > | AtomGraphOP |
typedef utility::pointer::shared_ptr < Conformation > | ConformationOP |
typedef utility::pointer::shared_ptr < Conformation const > | ConformationCOP |
typedef utility::pointer::weak_ptr < Conformation > | ConformationAP |
typedef utility::pointer::weak_ptr < Conformation const > | ConformationCAP |
typedef numeric::xyzTriple < core::Size > | CubeKey |
typedef numeric::xyzVector < core::Real > | PointPosition |
typedef graph::UpperEdgeGraph < PointGraphVertexData, PointGraphEdgeData > | PointGraph |
typedef utility::pointer::shared_ptr < PointGraph > | PointGraphOP |
typedef utility::vector0 < ppo_torsion_bin > | torsion_bin_string |
typedef utility::pointer::shared_ptr < PseudoBondCollection > | PseudoBondCollectionOP |
typedef utility::pointer::shared_ptr < PseudoBondCollection const > | PseudoBondCollectionCOP |
typedef utility::pointer::weak_ptr < Residue > | ResidueAP |
typedef utility::pointer::weak_ptr < Residue const > | ResidueCAP |
typedef utility::pointer::shared_ptr < Residue > | ResidueOP |
typedef utility::pointer::shared_ptr < Residue const > | ResidueCOP |
typedef utility::vector1 < ResidueOP > | ResidueOPs |
typedef utility::vector1 < ResidueCOP > | ResidueCOPs |
typedef utility::vector1 < ResidueCAP > | ResidueCAPs |
typedef utility::pointer::shared_ptr < ResidueKinWriter > | ResidueKinWriterOP |
typedef utility::pointer::shared_ptr < ResidueKinWriter const > | ResidueKinWriterCOP |
typedef utility::pointer::shared_ptr < ConformationKinWriter > | ConformationKinWriterOP |
typedef utility::pointer::shared_ptr < ConformationKinWriter const > | ConformationKinWriterCOP |
typedef utility::pointer::shared_ptr < ResidueMatcher > | ResidueMatcherOP |
typedef utility::pointer::shared_ptr < ResidueMatcher const > | ResidueMatcherCOP |
typedef utility::pointer::shared_ptr < RotamerSetBase > | RotamerSetBaseOP |
typedef utility::pointer::shared_ptr < RotamerSetBase const > | RotamerSetBaseCOP |
typedef utility::pointer::shared_ptr < UltraLightResidue > | UltraLightResidueOP |
Enumerations | |
enum | Strategy { NAIVE, AUTOMATIC, OCTREE, THREEDGRID, STRIPEHASH } |
enum | ppo_torsion_bin { ppo_torbin_A = 1, ppo_torbin_B, ppo_torbin_E, ppo_torbin_G, ppo_torbin_a, ppo_torbin_b, ppo_torbin_e, ppo_torbin_g, ppo_torbin_X, ppo_torbin_U, n_ppo_torsion_bins = ppo_torbin_U } |
Enumeration representing the different phi/psi/omega torsion bins. More... | |
Functions | |
std::ostream & | operator<< (std::ostream &out, 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::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff) |
template<class Vertex , class Edge > | |
void | find_neighbors_octree (utility::pointer::shared_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::shared_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::shared_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::shared_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::shared_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::shared_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::shared_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::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > point_graph, core::Real neighbor_cutoff) |
template<class Vertex , class Edge > | |
void | find_neighbors_restricted (utility::pointer::shared_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::shared_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) |
ppo_torsion_bin | get_torsion_bin (core::Real phi, core::Real psi, core::Real omega=180) |
determine the torsion bin for a given phi/psi/omega combination, assuming that omega is 180 if not specified More... | |
ppo_torsion_bin | remap_cis_omega_torsion_bins_to_trans (ppo_torsion_bin torbin) |
bool | cis_omega_torsion_bin (ppo_torsion_bin torbin) |
torsion_bin_string | map_string_to_torsion_bin_string (std::string const &torstring) |
convert a string of characters into a vector of the internally recognized ppo_torsion_bin enumeration More... | |
bool | char_valid_as_torsion_bin (char torbin) |
returns true if the input character represents a valid torsion bin More... | |
ppo_torsion_bin | map_char_to_torsion_bin (char torbin) |
returns the torsion bin that the input character represents More... | |
char | map_torsion_bin_to_char (ppo_torsion_bin torbin) |
convert a torsion bin to a character s.t. that character can be converted back to a torsion bin More... | |
static THREAD_LOCAL basic::Tracer | TR ("core.conformation.Residue") |
chemical::ResidueType const & | reference_from_restype_ptr (chemical::ResidueTypeCOP rsd_type) |
This function enforces the fact that ResidueTypes must be constructed with non-null-pointer ResidueTypeCOPs. More... | |
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 &conformation, bool const preserve_only_sidechain_dihedrals) |
Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others. More... | |
void | 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. 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 conformation 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 conformation 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::ResidueCOPs const &residues, kinematics::AtomPointer2D &atom_pointer) |
void | build_jump_edge (kinematics::Edge const &edge, conformation::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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::ResidueCOPs 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 const &cys_type_name3, Conformation &conf) |
Switch the disulfide state of a disulfide-forming residue (e.g. CYS->CYD or CYD->CYS or DCYD->DCYS or DCYS->DCYD or whatnot). 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) |
core::Size | get_disulf_partner (core::conformation::Conformation const &conformation, core::Size const res_index) |
Gets a disulfide-forming residue's partner in the disulfide bond. More... | |
void | break_disulfide (core::conformation::Conformation &conformation, core::Size const res1, core::Size const res2) |
Breaks a disulfide bond. More... | |
void | form_disulfide (Conformation &conformation, Size lower_res, Size upper_res, bool const preserve_d_residues, bool const force_d_residues) |
Introduce cysteines at the specified location and define a disulfide bond between them. More... | |
void | form_disulfide_helper (core::conformation::Conformation &conformation, core::Size const res_index, core::chemical::ResidueTypeSetCOP restype_set, bool const preserve_d_residues, bool const force_d_residues) |
Helper function for the form_disulfide function. More... | |
bool | upper_is_symm_equivalent_of_lower (core::conformation::Conformation const &conformation, core::Size const lower_res, core::Size const upper_res) |
Another helper function for the form_disulfide function. 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... | |
chemical::rings::AxEqDesignation | is_atom_axial_or_equatorial_to_ring (Residue const &residue, uint query_atom, utility::vector1< uint > const &ring_atoms) |
Is the query atom in this residue axial or equatorial to the given ring or neither? More... | |
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 utility::pointer::shared_ptr< AbstractRotamerTrie const > core::conformation::AbstractRotamerTrieCOP |
typedef utility::pointer::shared_ptr< AbstractRotamerTrie > core::conformation::AbstractRotamerTrieOP |
typedef utility::pointer::shared_ptr<AtomGraph > core::conformation::AtomGraphOP |
typedef utility::vector1< Atom > core::conformation::Atoms |
typedef utility::pointer::weak_ptr< Conformation > core::conformation::ConformationAP |
typedef utility::pointer::weak_ptr< Conformation const > core::conformation::ConformationCAP |
typedef utility::pointer::shared_ptr< Conformation const > core::conformation::ConformationCOP |
typedef utility::pointer::shared_ptr< ConformationKinWriter const > core::conformation::ConformationKinWriterCOP |
typedef utility::pointer::shared_ptr< ConformationKinWriter > core::conformation::ConformationKinWriterOP |
typedef utility::pointer::shared_ptr< Conformation > core::conformation::ConformationOP |
typedef numeric::xyzTriple< core::Size > core::conformation::CubeKey |
typedef graph::UpperEdgeGraph< PointGraphVertexData, PointGraphEdgeData > core::conformation::PointGraph |
typedef utility::pointer::shared_ptr< PointGraph > core::conformation::PointGraphOP |
typedef numeric::xyzVector< core::Real > core::conformation::PointPosition |
typedef utility::pointer::shared_ptr< PseudoBondCollection const > core::conformation::PseudoBondCollectionCOP |
typedef utility::pointer::shared_ptr< PseudoBondCollection > core::conformation::PseudoBondCollectionOP |
typedef utility::pointer::weak_ptr< Residue > core::conformation::ResidueAP |
typedef utility::pointer::weak_ptr< Residue const > core::conformation::ResidueCAP |
typedef utility::vector1< ResidueCAP > core::conformation::ResidueCAPs |
typedef utility::pointer::shared_ptr< Residue const > core::conformation::ResidueCOP |
typedef utility::vector1< ResidueCOP > core::conformation::ResidueCOPs |
typedef utility::pointer::shared_ptr< ResidueKinWriter const > core::conformation::ResidueKinWriterCOP |
typedef utility::pointer::shared_ptr< ResidueKinWriter > core::conformation::ResidueKinWriterOP |
typedef utility::pointer::shared_ptr< ResidueMatcher const > core::conformation::ResidueMatcherCOP |
typedef utility::pointer::shared_ptr< ResidueMatcher > core::conformation::ResidueMatcherOP |
typedef utility::pointer::shared_ptr< Residue > core::conformation::ResidueOP |
typedef utility::vector1< ResidueOP > core::conformation::ResidueOPs |
typedef utility::pointer::shared_ptr< RotamerSetBase const > core::conformation::RotamerSetBaseCOP |
typedef utility::pointer::shared_ptr< RotamerSetBase > core::conformation::RotamerSetBaseOP |
typedef utility::vector0< ppo_torsion_bin > core::conformation::torsion_bin_string |
typedef utility::pointer::shared_ptr< UltraLightResidue > core::conformation::UltraLightResidueOP |
void core::conformation::add_lower_terminus_type_to_conformation_residue | ( | conformation::Conformation & | conformation, |
Size const | seqpos | ||
) |
void core::conformation::add_upper_terminus_type_to_conformation_residue | ( | conformation::Conformation & | conformation, |
Size const | seqpos | ||
) |
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 conformation residue.
E.g., make a terminus variant, and replace the original in pose.
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
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 | ||
) |
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 | ||
) |
References core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::conformation::Residue::atoms(), core::id::AtomID::rsd(), and TR().
Referenced by core::conformation::Conformation::append_residue_by_bond(), protocols::farna::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::remapped_clone(), protocols::constraints_additional::COMCoordinateConstraint::remapped_clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::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::break_disulfide | ( | core::conformation::Conformation & | conformation, |
core::Size const | res1, | ||
core::Size const | res2 | ||
) |
Breaks a disulfide bond.
References change_cys_state(), get_disulf_partner(), core::chemical::ResidueType::is_disulfide_bonded(), core::conformation::Residue::name3(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), and core::conformation::Residue::type().
Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::break_disulfides().
void core::conformation::build_chemical_edge | ( | kinematics::Edge const & | edge, |
conformation::ResidueCOPs 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.
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::ResidueCOPs 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.
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::ResidueCOPs 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.
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::ResidueCOPs 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
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
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::ResidueCOPs 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
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(), core::kinematics::FoldTree::root(), and TR().
Referenced by core::conformation::Conformation::setup_atom_tree().
bool core::conformation::change_cys_state | ( | Size const | index, |
std::string const & | cys_type_name3, | ||
Conformation & | conf | ||
) |
Switch the disulfide state of a disulfide-forming residue (e.g. CYS->CYD or CYD->CYS or DCYD->DCYS or DCYS->DCYD or whatnot).
[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. DEPRECATED and kept only for backward-compatibility. |
[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.
[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. DEPRECATED and kept only for backward-compatibility. |
[in,out] | conf | The conformation to modify |
References copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::chemical::DISULFIDE, core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), core::chemical::ResidueType::residue_type_set(), TR(), and core::conformation::Residue::type().
Referenced by protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::CartesianSampler::apply_frame(), break_disulfide(), protocols::analysis::PeptideDeriverFilter::build_receptor_peptide_pose(), protocols::features::ProteinResidueConformationFeatures::check_num_requested_atoms(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::conformation::Conformation::fix_disulfides(), and form_disulfide().
bool core::conformation::char_valid_as_torsion_bin | ( | char | torbin | ) |
returns true if the input character represents a valid torsion bin
Referenced by map_string_to_torsion_bin_string().
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).
Referenced by setup_links_simple().
|
inline |
is atom2 the last atom of our chi angle ?
Referenced by setup_atom_links().
|
inline |
would we be breaking into a chi angle by adding atom2 to the tree now?
Referenced by setup_atom_links().
bool core::conformation::cis_omega_torsion_bin | ( | ppo_torsion_bin | torbin | ) |
References ppo_torbin_a, ppo_torbin_b, ppo_torbin_e, and ppo_torbin_g.
void core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms | ( | Residue const & | source_rsd, |
Residue & | target_rsd, | ||
Conformation const & | conformation, | ||
bool const | preserve_only_sidechain_dihedrals | ||
) |
Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.
If preserve_only_sidechain_dihedrals is true, then this function only copies mainchain coordinates, and rebuilds all sidechain coordinates from scratch, setting side-chain dihedrals based on the source residue. Otherwise, if false, it copies all the atoms that it can from the source residue, then rebuilds the rest.
References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::conformation::Residue::chain(), core::conformation::Residue::chi(), core::conformation::Residue::fill_missing_atoms(), core::conformation::Residue::has(), core::conformation::Residue::n_mainchain_atoms(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), core::conformation::Residue::seqpos(), core::conformation::Residue::set_chi(), TR(), and core::conformation::Atom::xyz().
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::pose::add_variant_type_to_residue(), protocols::simple_moves::MutateResidue::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), change_cys_state(), protocols::simple_filters::SidechainRmsdFilter::compute(), form_disulfide_helper(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::environment::Environment::remove_chainbreak_variants(), core::pose::remove_variant_type_from_residue(), replace_conformation_residue_copying_existing_coordinates(), core::pose::replace_pose_residue_copying_existing_coordinates(), and core::util::switch_to_residue_type_set().
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
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().
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.
References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, core::chemical::ResidueType::n_possible_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::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(), protocols::grafting::insert_pose_into_pose(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::store_disulfides(), and core::util::switch_to_residue_type_set().
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.
References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, core::chemical::ResidueType::n_possible_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::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(), protocols::grafting::insert_pose_into_pose(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::store_disulfides(), and core::util::switch_to_residue_type_set().
void core::conformation::find_neighbors | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Real | neighbor_cutoff, | ||
Strategy | strategy = AUTOMATIC |
||
) |
References AUTOMATIC, find_neighbors_3dgrid(), find_neighbors_naive(), find_neighbors_octree(), find_neighbors_stripe(), NAIVE, STRIPEHASH, and THREEDGRID.
Referenced by core::select::residue_selector::NumNeighborsSelector::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), and core::conformation::Conformation::detect_disulfides().
void core::conformation::find_neighbors_3dgrid | ( | utility::pointer::shared_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.
References core::sequence::end, and core::scoring::electron_density::square().
Referenced by find_neighbors(), and find_neighbors_restricted().
void core::conformation::find_neighbors_3dgrid_restricted | ( | utility::pointer::shared_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.
References core::sequence::end, and core::scoring::electron_density::square().
void core::conformation::find_neighbors_naive | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Real | neighbor_cutoff | ||
) |
Referenced by find_neighbors().
void core::conformation::find_neighbors_naive_restricted | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Real | neighbor_cutoff, | ||
utility::vector1< bool > const & | residue_selection | ||
) |
void core::conformation::find_neighbors_naive_surface | ( | utility::pointer::shared_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 core::conformation::find_neighbors_octree | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Real | neighbor_cutoff, | ||
Strategy | strategy | ||
) |
Finds the residue neighbors efficiently using an octree-like spatial sort.
References OCTREE, and core::scoring::electron_density::square().
Referenced by find_neighbors().
void core::conformation::find_neighbors_octree_restricted | ( | utility::pointer::shared_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.
References OCTREE, and core::scoring::electron_density::square().
void core::conformation::find_neighbors_restricted | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Real | neighbor_cutoff, | ||
utility::vector1< bool > const & | residue_selection, | ||
Strategy | strategy = AUTOMATIC |
||
) |
References AUTOMATIC, find_neighbors_3dgrid(), NAIVE, and THREEDGRID.
void core::conformation::find_neighbors_stripe | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Real | neighbor_cutoff | ||
) |
Referenced by find_neighbors().
void core::conformation::form_disulfide | ( | Conformation & | conformation, |
Size | lower_res, | ||
Size | upper_res, | ||
bool const | preserve_d_residues, | ||
bool const | force_d_residues | ||
) |
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.
References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), change_cys_state(), core::conformation::Residue::connect_map(), core::conformation::Conformation::declare_chemical_bond(), core::chemical::DISULFIDE, core::chemical::FA_STANDARD, form_disulfide_helper(), core::chemical::ResidueType::get_disulfide_atom_name(), core::conformation::Residue::has_variant_type(), core::conformation::Conformation::is_fullatom(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::name3(), core::chemical::ResConnID::resid(), core::conformation::Conformation::residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Conformation::residue_type(), TR(), core::conformation::Residue::type(), and upper_is_symm_equivalent_of_lower().
Referenced by protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::forge::remodel::build_and_score_disulfide(), protocols::cyclic_peptide::TryDisulfPermutations::generate_disulfides(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::denovo_design::DisulfidizeMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::rebuild_disulfides().
void core::conformation::form_disulfide_helper | ( | core::conformation::Conformation & | conformation, |
core::Size const | res_index, | ||
core::chemical::ResidueTypeSetCOP | restype_set, | ||
bool const | preserve_d_residues, | ||
bool const | force_d_residues | ||
) |
Helper function for the form_disulfide function.
This function ensures that as a residue is mutated to a disulfide-bonding residue type, all other variant types are preserved; it is used to avoid code duplication.
References core::chemical::aa_cys, core::chemical::aa_dcs, copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_d_aa(), core::chemical::ResidueType::properties(), core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), and core::conformation::Residue::type().
Referenced by form_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.
References core::conformation::Residue::atom_index(), core::kinematics::dir_jump, core::kinematics::Edge::downstream_atom(), get_anchor_atomno(), get_chemical_root_and_anchor_atomnos(), get_root_atomno(), core::kinematics::Edge::has_atom_info(), core::kinematics::Edge::is_chemical_bond(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::is_polymer(), core::kinematics::Edge::polymer_direction(), core::conformation::Residue::seqpos(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and core::kinematics::Edge::upstream_atom().
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.
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.
References protocols::loops::loop_closure::ccd::backward, core::kinematics::dir_jump, protocols::loops::loop_closure::ccd::forward, 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 | ||
) |
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().
core::Size core::conformation::get_disulf_partner | ( | core::conformation::Conformation const & | conformation, |
core::Size const | res_index | ||
) |
Gets a disulfide-forming residue's partner in the disulfide bond.
References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::ResidueType::get_disulfide_atom_name(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueType::n_possible_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 break_disulfide().
core::Size core::conformation::get_nearest_neighbor | ( | utility::pointer::shared_ptr< graph::UpperEdgeGraph< Vertex, Edge > > | point_graph, |
core::Size | node_id, | ||
core::Real | neighbor_cutoff, | ||
Strategy | strategy = AUTOMATIC |
||
) |
void core::conformation::get_residue_connections | ( | conformation::Residue const & | new_rsd, |
kinematics::FoldTree const & | fold_tree, | ||
conformation::ResidueCOPs 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
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"
References core::chemical::ResidueType::atom_index(), protocols::loops::loop_closure::ccd::backward, core::kinematics::dir_jump, protocols::loops::loop_closure::ccd::forward, core::chemical::ResidueType::has_variant_type(), 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::chemical::N_ACETYLATION, core::conformation::Residue::n_mainchain_atoms(), core::chemical::ResidueType::root_atom(), core::conformation::Residue::type(), 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)
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(), and core::conformation::Residue::seqpos().
Referenced by build_residue_tree(), get_residue_connections(), and protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map().
ppo_torsion_bin core::conformation::get_torsion_bin | ( | core::Real | phi, |
core::Real | psi, | ||
core::Real | omega | ||
) |
determine the torsion bin for a given phi/psi/omega combination, assuming that omega is 180 if not specified
placed here to make it accessible to a wide range of applications, but it's quite possible that placing this code elsewhere would be better bin boundaries are currently hard-coded – ideally in the future these can be read from external files, and thus adapted if desired
References ppo_torbin_A, ppo_torbin_a, ppo_torbin_B, ppo_torbin_b, ppo_torbin_E, ppo_torbin_e, ppo_torbin_G, ppo_torbin_g, and ppo_torbin_X.
Referenced by core::scoring::Ramachandran::init_rama_sampling_table(), core::scoring::Ramachandran2B::init_rama_sampling_table(), 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 | ||
) |
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(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::sewing::Assembly::to_multichain_pose(), and protocols::sewing::Assembly::to_pose().
void core::conformation::idealize_position | ( | Size const | seqpos, |
Conformation & | conformation | ||
) |
Idealize backbone and sidechain at seqpos.
References core::id::BB, core::chemical::rna::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::oop::OopPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::hybridization::MRMover::apply(), protocols::antibody::ModelCDRH3::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::relax::RangeRelaxMover::idealize_pose(), 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::forge::build::SegmentInsert::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
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 | ||
) |
void core::conformation::insert_residue_into_atom_tree | ( | conformation::Residue const & | new_rsd, |
kinematics::FoldTree const & | fold_tree, | ||
conformation::ResidueCOPs const & | residues, | ||
kinematics::AtomTree & | atom_tree | ||
) |
Inserts/ appends new residue subtree into an existing atomtree.
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(), core::conformation::Conformation::insert_residue_by_bond(), and core::conformation::Conformation::insert_residue_by_jump().
chemical::rings::AxEqDesignation core::conformation::is_atom_axial_or_equatorial_to_ring | ( | Residue const & | residue, |
uint | query_atom, | ||
utility::vector1< uint > const & | ring_atoms | ||
) |
Is the query atom in this residue axial or equatorial to the given ring or neither?
This function calculates an average plane and determines whether the coordinates of a given atom are axial or equatorial to it (or neither). The attachment atom is auto-detected.
<residue> | The Residue containing the atoms in question. |
<query_atom> | The index of the atom in question. |
<ring_atoms> | A list of indices for the atoms of a monocyclic ring system in sequence. |
References core::conformation::Residue::get_adjacent_heavy_atoms(), core::chemical::rings::is_atom_axial_or_equatorial_to_ring(), core::chemical::rings::NEITHER, TR(), and core::conformation::Residue::xyz().
Referenced by core::pose::is_atom_axial_or_equatorial_to_ring(), and core::conformation::Residue::show().
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
References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::chemical::element::B, core::conformation::Residue::connect_map(), core::chemical::ResidueType::get_disulfide_atom_name(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_disulfide_bonded(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::is_sidechain_thiol(), core::chemical::ResidueType::n_possible_residue_connections(), 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
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(), protocols::features::ProteinResidueConformationFeatures::report_features(), and protocols::features::PoseConformationFeatures::report_features_implementation().
ppo_torsion_bin core::conformation::map_char_to_torsion_bin | ( | char | torbin | ) |
returns the torsion bin that the input character represents
References ppo_torbin_A, ppo_torbin_a, ppo_torbin_B, ppo_torbin_b, ppo_torbin_E, ppo_torbin_e, ppo_torbin_G, ppo_torbin_g, ppo_torbin_U, and ppo_torbin_X.
Referenced by map_string_to_torsion_bin_string().
torsion_bin_string core::conformation::map_string_to_torsion_bin_string | ( | std::string const & | torstring | ) |
convert a string of characters into a vector of the internally recognized ppo_torsion_bin enumeration
utility::excn::EXCN_MsgException | if any of the input characters in this string are invalid |
References char_valid_as_torsion_bin(), map_char_to_torsion_bin(), and core::id::to_string().
Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().
char core::conformation::map_torsion_bin_to_char | ( | ppo_torsion_bin | torbin | ) |
convert a torsion bin to a character s.t. that character can be converted back to a torsion bin
References ppo_torbin_A, ppo_torbin_a, ppo_torbin_B, ppo_torbin_b, ppo_torbin_E, ppo_torbin_e, ppo_torbin_G, ppo_torbin_g, and ppo_torbin_X.
id::AtomID core::conformation::named_atom_id_to_atom_id | ( | id::NamedAtomID const & | named_atom_id, |
conformation::Residue const & | rsd | ||
) |
References core::id::NamedAtomID::atom(), core::conformation::Residue::atom_index(), and core::id::NamedAtomID::rsd().
Referenced by protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_forward_backward_res_by_backtracking(), protocols::toolbox::AtomLevelDomainMap::get_domain(), protocols::farna::fragments::FullAtomRNA_Fragments::insert_fragment(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN(), named_stub_id_to_stub_id(), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::remapped_clone(), protocols::constraints_additional::COMCoordinateConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), protocols::toolbox::AtomLevelDomainMap::set(), protocols::toolbox::AtomLevelDomainMap::set_domain(), protocols::toolbox::AtomLevelDomainMap::set_phosphate_domain(), protocols::toolbox::AtomLevelDomainMap::set_sugar_domain(), protocols::farna::setup::RNA_DeNovoPoseSetup::setup_jumps(), protocols::farna::movers::RNA_Minimizer::setup_movemap(), and protocols::farna::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res().
id::StubID core::conformation::named_stub_id_to_stub_id | ( | id::NamedStubID const & | named_stub_id, |
conformation::Residue const & | rsd | ||
) |
std::ostream & core::conformation::operator<< | ( | std::ostream & | out, |
Atom const & | atom | ||
) |
References core::conformation::Atom::show().
std::ostream & core::conformation::operator<< | ( | std::ostream & | os, |
Residue const & | res | ||
) |
References core::conformation::Residue::show().
std::ostream & core::conformation::operator<< | ( | std::ostream & | os, |
Conformation const & | conf | ||
) |
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 | ||
) |
References protocols::comparative_modeling::features::A, core::conformation::Residue::actcoord(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueConnection::atomno(), core::chemical::element::B, core::chemical::AtomICoor::build(), core::chemical::FA_STANDARD, 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(), TR(), 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(), core::conformation::Conformation::insert_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
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.
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 = "" |
||
) |
void core::conformation::print_node | ( | std::ostream & | out, |
int | residue_num, | ||
std::string | atom_name, | ||
core::conformation::Residue const & | res, | ||
std::string | extras = "" |
||
) |
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::ResidueCOPs 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 ); debug_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 ) { debug_assert( new_rsd_out[i].atom2 == old_rsd_out[i].atom2 ); } }
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::ResidueCOPs 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.
References get_anchor_and_root_atoms(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and TR().
chemical::ResidueType const& core::conformation::reference_from_restype_ptr | ( | chemical::ResidueTypeCOP | rsd_type | ) |
This function enforces the fact that ResidueTypes must be constructed with non-null-pointer ResidueTypeCOPs.
This must be a function as the initialization of the Residue's rsd_type_ reference must occur in the constructor.
ppo_torsion_bin core::conformation::remap_cis_omega_torsion_bins_to_trans | ( | ppo_torsion_bin | torbin | ) |
References ppo_torbin_A, ppo_torbin_a, ppo_torbin_B, ppo_torbin_b, ppo_torbin_E, ppo_torbin_e, ppo_torbin_G, ppo_torbin_g, and ppo_torbin_X.
Referenced by protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), and protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain().
void core::conformation::remove_lower_terminus_type_from_conformation_residue | ( | conformation::Conformation & | conformation, |
Size const | seqpos | ||
) |
void core::conformation::remove_upper_terminus_type_from_conformation_residue | ( | conformation::Conformation & | conformation, |
Size const | 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 conformation residue.
E.g., remove a terminus variant, and replace the original in pose.
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
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::ResidueCOPs 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
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 | ||
) |
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::select::residue_selector::NumNeighborsSelector::apply(), core::select::util::calc_interacting_vector(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), protocols::toolbox::CalcInterNeighborGroup::compute(), 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::select::util::find_jump_partners_within_CB_cutoff(), core::select::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(), 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.
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::rotamers::SingleLigandRotamerLibrary::build_base_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), 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.
References chi_continuation(), chi_interruption(), and protocols::sic_dock::scores::nbr.
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.
References core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::atoms(), core::conformation::Residue::chi_atoms(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_RNA(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name1(), core::chemical::ResidueType::name3(), core::conformation::Residue::natoms(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::seqpos(), core::id::AtomID_Map< T >::set(), and core::conformation::Residue::type().
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 .
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(), core::conformation::Residue::has_variant_type(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::natoms(), setup_atom_links(), setup_links_simple(), and TR().
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
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 | ||
) |
id::NamedStubID core::conformation::stub_id_to_named_stub_id | ( | id::StubID const & | stub_id, |
conformation::Residue const & | rsd | ||
) |
|
static |
Referenced by protocols::simple_moves::hbs::add_hbs_constraint(), core::conformation::Conformation::append_residue(), protocols::simple_moves::a3b_hbs::A3BHbsMover::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsRandomSmallMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), core::conformation::Residue::apply_transform_downstream(), atom_id_to_named_atom_id(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), build_tree(), change_cys_state(), core::conformation::Residue::copy_residue_connections(), copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::membrane::SpanningTopology::create_from_spanfile(), core::conformation::membrane::SpanningTopology::create_from_structure(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::Conformation::detect_pseudobonds(), disulfide_bonds(), core::conformation::membrane::SpanningTopology::fill_from_spanfile(), core::conformation::membrane::SpanningTopology::fill_from_structure(), core::conformation::Conformation::fill_missing_atoms(), core::conformation::Residue::fill_missing_atoms(), core::conformation::Residue::first_adjacent_heavy_atom(), core::conformation::Conformation::fix_disulfides(), core::conformation::Conformation::fold_tree(), form_disulfide(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::residue_optimization::MetapatchEnumeration::generate_metapatched_variants(), protocols::simple_moves::chiral::get_chiral_residue_type(), get_disulf_partner(), core::conformation::Conformation::get_torsion_angle_atom_ids(), insert_ideal_bonds_at_polymer_junction(), is_atom_axial_or_equatorial_to_ring(), is_ideal_position(), core::conformation::Conformation::is_residue_typeset(), core::conformation::membrane::Span::is_valid(), core::conformation::membrane::SpanningTopology::is_valid(), core::conformation::membrane::LipidAccInfo::LipidAccInfo(), protocols::ncbb::ncbb_design_main_loop(), orient_residue_for_ideal_bond(), promote_sameresidue_child_of_jump_atom(), core::conformation::Residue::Residue(), core::conformation::Conformation::residues_append(), core::conformation::membrane::MembraneInfo::set_membrane_jump(), core::conformation::Conformation::set_torsion(), core::conformation::Conformation::set_torsion_angle(), setup_links(), core::conformation::membrane::Span::show(), core::conformation::membrane::SpanningTopology::show(), core::conformation::Conformation::show_residue_connections(), protocols::residue_optimization::MetapatchEnumeration::tabooed(), core::conformation::Residue::update_connections_to_other_residue(), and core::conformation::membrane::SpanningTopology::write_spanfile().
bool core::conformation::upper_is_symm_equivalent_of_lower | ( | core::conformation::Conformation const & | conformation, |
core::Size const | lower_res, | ||
core::Size const | upper_res | ||
) |
Another helper function for the form_disulfide function.
Returns true if and only if the conformation is symmetric and upper_res is a symmetric copy of lower_res.
References core::conformation::Conformation::get_self_ptr().
Referenced by form_disulfide().
void core::conformation::write_kinemage_header | ( | std::ostream & | ostr, |
Size const | kin_number, | ||
std::string const & | title, | ||
Vector const & | ctr | ||
) |
Referenced by core::conformation::ResidueKinWriter::write_kin_header().