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external support for manipulating the ResidueType's icoor/ideal_xyz More...

#include <core/chemical/icoor_support.hh>
#include <core/chemical/MutableResidueType.hh>
#include <core/chemical/AtomICoor.fwd.hh>
#include <core/chemical/MutableICoorRecord.hh>
#include <core/chemical/MutableResidueConnection.hh>
#include <core/chemical/bond_support.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/tree/BondedAtom.hh>
#include <core/kinematics/tree/JumpAtom.hh>
#include <core/id/AtomID.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <numeric/xyz.functions.hh>
#include <utility/graph/DFS_sort.hh>
#include <set>
#include <queue>


class  core::chemical::RerootRestypeVisitor
class  core::chemical::RerootEdgeSorter
 Edge sorting: Return true if we should prefer edge1 over edge2. More...


 A class for reading in the atom type properties.


static basic::Tracer core::chemical::TR ("core.chemical.icoor_support")
VD core::chemical::walk_back_to_find_usable_base (core::chemical::MutableResidueType const &restype, VD start, utility::vector1< VD > const &exclusions)
 Walk up the icoor tree to find alternate reference atoms Utility function for clean_up_dangling_connect() – we only go up the tree to make sure we don't get cycles. Won't choose atoms in exclusions (or the start) More...
void core::chemical::clean_up_dangling_connect (core::chemical::MutableResidueType &restype, ICoordAtomIDType remove_type)
 Attempt to find new ICOOR definitions for entries in the ResidueType which rely on a now-deleted upper/lower connection (Connection type is specified by the passed type.) More...
void core::chemical::reroot_restype (core::chemical::MutableResidueType &restype, core::chemical::ResidueGraph const &graph, core::chemical::VD root)
 Reroot the Icoord records of a ResidueType on the given atom We need direct access to the ResidueGraph, so this function can only be called by ResidueType itself. More...
bool core::chemical::has_assigned_coords (std::string const &stub, std::set< VD > const &assigned, core::chemical::MutableResidueType const &restype)
 Utility function for fill_ideal_xyz_from_icoor() – does this ICoorAtomID have all the dependancies filled? More...
void core::chemical::fill_ideal_xyz_from_icoor (core::chemical::MutableResidueType &restype, core::chemical::ResidueGraph const &graph)

Detailed Description

external support for manipulating the ResidueType's icoor/ideal_xyz

Rocco Moretti (