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util.cc File Reference
#include <core/conformation/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/Stub.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/IdealBondLengthSet.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/NamedStubID.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/constants.hh>
#include <core/kinematics/util.hh>
#include <numeric/util.hh>
#include <numeric/xyz.functions.hh>
#include <utility/assert.hh>
#include <utility/exit.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/pointer/access_ptr.hh>
#include <utility/io/izstream.hh>
#include <cassert>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <utility/vector1.hh>

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::conformation
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::conformation
 

Functions

static basic::Tracer TR ("core.conformation.util")
 
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_mainchain_bonds (Size const seqpos, Conformation &conformation)
 
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::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 &conf)
 Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others. More...
 
std::ostream & core::conformation::print_atom (id::AtomID const &id, Conformation const &conf, std::ostream &os)
 
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 pose 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 pose residue More...
 
void core::conformation::add_lower_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::add_upper_terminus_type_to_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::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
 
void core::conformation::build_jump_edge (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
 build a sub atom-tree for a jump edge and attach it to main atom-tree More...
 
void core::conformation::build_polymer_edge (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
 build a sub atom-tree for a polymer edge and attach it to main atom-tree More...
 
void core::conformation::build_chemical_edge (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D &atom_pointer)
 build a sub atom-tree for a chemical edge and attach it to main atom-tree 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)
 
void core::conformation::build_residue_tree (conformation::ResidueCAPs const &residues, conformation::Residue const &rsd, kinematics::FoldTree const &fold_tree, kinematics::AtomPointer1D &atom_ptr)
 build_residue_tree function that uses the foldtree info More...
 
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). More...
 
bool core::conformation::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 core::conformation::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 core::conformation::setup_links_simple (conformation::Residue const &rsd, kinematics::Links &links)
 simply fill the "links" by adding, for each atom, its bonded neighbors More...
 
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. More...
 
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 . 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::get_residue_connections (conformation::Residue const &new_rsd, kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, id::BondID &new_rsd_in, utility::vector1< id::BondID > &new_rsd_out)
 
void core::conformation::replace_residue_in_atom_tree (conformation::Residue const &new_rsd, kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, kinematics::AtomTree &atom_tree)
 Helper function for conformation routines. More...
 
void core::conformation::insert_residue_into_atom_tree (conformation::Residue const &new_rsd, kinematics::FoldTree const &fold_tree, conformation::ResidueCAPs const &residues, kinematics::AtomTree &atom_tree)
 Inserts/ appends new residue subtree into an existing atomtree. More...
 
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::ResidueCAPs const &residues, kinematics::AtomTree &atom_tree)
 Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list. More...
 
void core::conformation::promote_sameresidue_child_of_jump_atom (kinematics::Edge const &edge, conformation::ResidueCAPs const &residues, kinematics::AtomPointer2D const &atom_pointer)
 Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list. 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 cys_type_name3, Conformation &conf)
 Replace a CYS with a CYD or vice-versa for changing disulfide bonds. 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)
 
id::StubID core::conformation::named_stub_id_to_stub_id (id::NamedStubID const &named_stub_id, conformation::Residue const &rsd)
 
void core::conformation::form_disulfide (Conformation &conformation, Size lower_res, Size upper_res)
 Introduce cysteines at the specified location and define a disulfide bond between them. 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 (conformation::Conformation const &conformation, utility::vector1< std::pair< Size, Size > > &disulfides)
 Generate a list of all disulfide bonds in the conformation. More...
 
char core::conformation::get_torsion_bin (core::Real phi, core::Real psi, core::Real omega)
 

Detailed Description

Author
Phil Bradley

Function Documentation

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