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Namespaces | Functions
util.hh File Reference
#include <core/conformation/Conformation.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/types.hh>
#include <core/chemical/ResidueConnection.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/rings/AxEqDesignation.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/NamedStubID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/kinematics/tree/Atom.fwd.hh>
#include <core/kinematics/AtomTree.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/AtomPointer.fwd.hh>
#include <core/kinematics/Edge.fwd.hh>
#include <core/kinematics/Stub.fwd.hh>
#include <core/kinematics/RT.fwd.hh>
#include <iosfwd>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::conformation
 

Functions

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)
 
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) More...
 
void core::conformation::insert_ideal_mainchain_bonds (Size const seqpos, Conformation &conformation)
 
void core::conformation::idealize_position (Size const seqpos, Conformation &conformation)
 Idealize backbone and sidechain at seqpos. More...
 
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. More...
 
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. More...
 
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. More...
 
void core::conformation::check_good_cutpoint_neighbour (core::conformation::Residue const &thisres, core::conformation::Residue const &other_res)
 Given two residues, check that they are compatible types to be connected via a cutpoint. More...
 
void core::conformation::update_cutpoint_virtual_atoms_if_connected (core::conformation::Conformation &conf, core::Size const cutpoint_res, bool recurse)
 Given a conformation and a position that may or may not be CUTPOINT_UPPER or CUTPOINT_LOWER, determine whether this position has either of these variant types, and if it does, determine whether it's connected to anything. If it is, update the C-OVL1-OVL2 bond lengths and bond angle (for CUTPOINT_LOWER) or OVU1-N bond length (for CUTPOINT_UPPER) to match any potentially non-ideal geometry in the residue to which it's bonded. More...
 
void core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms (Residue const &source_rsd, Residue &target_rsd, utility::vector1< core::Size > const &mapping, Conformation const &conformation)
 Fills coords of target_rsd with coords from source_rsd using the provided mapping, rebuilds others The mapping is indexed by target_rsd atom index, giving source_rsd index or zero for not present. More...
 
void core::conformation::show_atom_tree (kinematics::tree::Atom const &atom, Conformation const &conf, std::ostream &os)
 
void core::conformation::replace_conformation_residue_copying_existing_coordinates (conformation::Conformation &conformation, Size const seqpos, chemical::ResidueType const &new_rsd_type)
 
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. More...
 
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. More...
 
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::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::build_tree (kinematics::FoldTree const &fold_tree, conformation::ResidueCOPs const &residues, kinematics::AtomPointer2D &atom_pointer)
 
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 More...
 
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 More...
 
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 More...
 
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. More...
 
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 More...
 
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. More...
 
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. More...
 
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" More...
 
Size core::conformation::get_root_residue_root_atomno (conformation::Residue const &rsd, kinematics::FoldTree const &fold_tree)
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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)
 
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 More...
 
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). More...
 
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. More...
 
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. More...
 
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. More...
 
void core::conformation::break_disulfide (core::conformation::Conformation &conformation, core::Size const res1, core::Size const res2)
 Breaks a disulfide bond. More...
 
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. More...
 
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. More...
 
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. More...
 
id::NamedAtomID core::conformation::atom_id_to_named_atom_id (id::AtomID const &atom_id, conformation::Residue const &rsd)
 
id::AtomID core::conformation::named_atom_id_to_atom_id (id::NamedAtomID const &named_atom_id, conformation::Residue const &rsd)
 
id::NamedStubID core::conformation::stub_id_to_named_stub_id (id::StubID const &stub_id, conformation::Residue const &rsd)
 
core::id::TorsionID core::conformation::find_bond_torsion_with_nearest_orientation (core::conformation::Conformation const &conf, utility::vector1< core::id::TorsionID > const &torsions, core::id::TorsionID const &query_torsion)
 Return a nearby TorsionID with approximately the same 3D orientation, selected from the give TorsionIDs. More...
 
core::uint core::conformation::position_of_atom_on_ring (Residue const &residue, core::uint query_atom, utility::vector1< core::uint > const &ring_atoms)
 What is the attachment position of the query atom on the given ring? More...
 
chemical::rings::AxEqDesignation core::conformation::is_atom_axial_or_equatorial_to_ring (Residue const &residue, core::uint query_atom, utility::vector1< core::uint > const &ring_atoms)
 Is the query atom in this residue axial or equatorial to the given ring or neither? More...
 
chemical::rings::AxEqDesignation core::conformation::is_atom_axial_or_equatorial (Residue const &residue, core::uint query_atom)
 Is the query atom in this residue axial or equatorial or neither? More...
 
chemical::ResidueTypeCOP core::conformation::virtual_type_for_conf (core::conformation::Conformation const &conformation)
 Return the appropritate ResidueType for the virtual residue for the "mode" (fullatom, centroid ...) the conformation is in. More...
 
chemical::ResidueTypeCOP core::conformation::inv_virtual_type_for_conf (core::conformation::Conformation const &conformation)
 Return the appropritate ResidueType for the inverse virtual residue for the "mode" (fullatom, centroid ...) the conformation is in. More...
 
core::Vector core::conformation::all_atom_center (core::conformation::Residue const &residue)
 Get the center of the Residue. More...
 
conformation::ResidueOP core::conformation::get_residue_from_name (std::string const &name, std::string const &residue_type_set="fa_standard")
 Returns a new residue based on a name. More...
 
conformation::ResidueOP core::conformation::get_residue_from_name1 (char name1, bool is_lower_terminus=false, bool is_upper_terminus=false, bool d_aa=false, std::string const &residue_type_set="fa_standard")
 Returns a new residue based on a name1. More...
 
bool core::conformation::get_second_atom_from_connection (core::Size &resno, core::Size &atomno, Residue const &rsd, Conformation const &conformation, core::Size const &conn_id)
 Given a residue and a connection id, get the heavyatom adjacent to the atom that makes that connection. More...
 
core::kinematics::Stub core::conformation::get_stub_from_residue (core::conformation::Residue const &res)
 Get stub from orient_atoms. More...
 
core::kinematics::RT core::conformation::get_rt_from_residue_pair (core::conformation::Residue const &res1, core::conformation::Residue const &res2)
 Get stub mapping that maps residue 1 to residue 2. More...
 

Detailed Description

Author
Phil Bradley