Rosetta Core  2014.35
Namespaces | Functions
util.hh File Reference
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/chemical/ResidueConnection.fwd.hh>
#include <core/chemical/VariantType.fwd.hh>
#include <core/chemical/ResidueType.fwd.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/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 <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 &conf)
 Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others. 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 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::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::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...
 
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::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...
 
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_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::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::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::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...
 
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...
 
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...
 
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)
 

Detailed Description

Author
Phil Bradley