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Hierarchy.h File Reference

Decorator for helping deal with a hierarchy of molecules. More...

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Data Structures

class  IMP::atom::Hierarchies
class  IMP::atom::HierarchiesTemp
class  IMP::atom::Hierarchy
 The standard decorator for manipulating molecular structures. More...

Namespaces

namespace  IMP
 The IMP kernel provides base classes and key shared functionality.
namespace  IMP::atom
 This module contains functionality for dealing with atoms and proteins.

Defines

#define IMP_CAPS_NAME(UCName, lcname, CAPSNAME)   CAPSNAME,
#define IMP_FOREACH_HIERARCHY_TYPE(macro)
 Do an operation for each of the hierarchy types.
#define IMP_GET_AS_DECL(UCName, lcname, CAPSNAME)   UCName get_as_##lcname() const;
#define IMP_GET_AS_DEF(UCName, lcname, CAPSNAME)

Enumerations

enum  GetByType {
  ATOM_TYPE, RESIDUE_TYPE, CHAIN_TYPE, DOMAIN_TYPE,
  FRAGMENT_TYPE, XYZ_TYPE, XYZR_TYPE, MASS_TYPE
}

Functions

Hierarchy IMP::atom::create_clone (Hierarchy d)
 Clone the Hierarchy.
Hierarchy IMP::atom::create_clone_one (Hierarchy d)
 Clone the node in the Hierarchy.
Hierarchy IMP::atom::create_fragment (const HierarchiesTemp &ps)
 Create a fragment containing the specified nodes.
void IMP::atom::destroy (Hierarchy d)
 Delete the Hierarchy.
algebra::BoundingBoxD< 3 > IMP::atom::get_bounding_box (const Hierarchy &h)
 Get a bounding box for the Hierarchy.
algebra::SphereD< 3 > IMP::atom::get_bounding_sphere (const Hierarchy &h)
HierarchiesTemp IMP::atom::get_by_type (Hierarchy mhd, GetByType t)
Bonds IMP::atom::get_internal_bonds (Hierarchy mhd)
 Get the bonds internal to this tree.
bool IMP::atom::get_is_heterogen (Hierarchy h)
 Return true if the piece of hierarchy should be classified as a heterogen.
HierarchiesTemp IMP::atom::get_leaves (Hierarchy h)
Hierarchy IMP::atom::get_residue (Hierarchy mhd, unsigned int index)
 Get the residue with the specified index.
Hierarchy IMP::atom::get_root (Hierarchy h)
 Return the root of the hierarchy.
IMP::core::RigidBody IMP::atom::setup_as_rigid_body (Hierarchy h)
 Rigidify a molecule or collection of molecules.
void IMP::atom::show (Hierarchy h, std::ostream &out=std::cout)
 Print out a molecular hierarchy.

Detailed Description

Decorator for helping deal with a hierarchy of molecules.

Copyright 2007-2010 IMP Inventors. All rights reserved.


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