atom/Hierarchy.h File Reference

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

#include <IMP/atom/atom_config.h>
#include <IMP/core/utility.h>
#include <IMP/core/Hierarchy.h>
#include "bond_decorators.h"
#include "atom_macros.h"
#include <IMP/core/XYZR.h>
#include <IMP/core/rigid_bodies.h>
#include <IMP/kernel/Particle.h>
#include <IMP/kernel/Model.h>
#include <vector>
#include <deque>

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

Namespaces
	IMP
	Synonym for IMP::kernel.
	IMP::atom
	Functionality for loading, creating, manipulating and scoring atomic structures.

Macros
#define	IMP_ATOM_CAPS_NAME(UCName, lcname, CAPSNAME)   CAPSNAME
#define	IMP_ATOM_FOREACH_HIERARCHY_TYPE_FUNCTIONS(macro)
#define	IMP_ATOM_FOREACH_HIERARCHY_TYPE_LIST(macro)
#define	IMP_ATOM_FOREACH_HIERARCHY_TYPE_STATEMENTS(macro)
#define	IMP_ATOM_GET_AS_DECL(UCName, lcname, CAPSNAME)   UCName get_as_##lcname() const;
#define	IMP_ATOM_GET_AS_DEF(UCName, lcname, CAPSNAME)

Typedefs
typedef IMP::base::Vector < Hierarchy >	IMP::atom::Hierarchies

Enumerations
enum	IMP::atom::GetByType {   ATOM_TYPE, RESIDUE_TYPE, CHAIN_TYPE, MOLECULE_TYPE,   DOMAIN_TYPE, FRAGMENT_TYPE, XYZ_TYPE, XYZR_TYPE,   MASS_TYPE, STATE_TYPE }

Functions
Hierarchy	IMP::atom::create_clone (Hierarchy d)
	Clone the Hierarchy. More...
Hierarchy	IMP::atom::create_clone_one (Hierarchy d)
	Clone the node in the Hierarchy. More...
IMP::core::RigidBody	IMP::atom::create_compatible_rigid_body (Hierarchy h, Hierarchy reference)
	Rigidify a molecule or collection of molecules. More...
Hierarchy	IMP::atom::create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes. More...
IMP::core::RigidBody	IMP::atom::create_rigid_body (const Hierarchies &h, std::string name=std::string("created rigid body"))
	Rigidify a molecule or collection of molecules. More...
IMP::core::RigidBody	IMP::atom::create_rigid_body (Hierarchy h)
void	IMP::atom::destroy (Hierarchy d)
	Delete the Hierarchy. More...
algebra::BoundingBoxD< 3 >	IMP::atom::get_bounding_box (const Hierarchy &h)
	Get a bounding box for the Hierarchy. More...
algebra::Sphere3D	IMP::atom::get_bounding_sphere (const Hierarchy &h)
Hierarchies	IMP::atom::get_by_type (Hierarchy mhd, GetByType t)
Bonds	IMP::atom::get_internal_bonds (Hierarchy mhd)
	Get the bonds internal to this tree. More...
bool	IMP::atom::get_is_heterogen (Hierarchy h)
	Return true if the piece of hierarchy should be classified as a heterogen. More...
Hierarchies	IMP::atom::get_leaves (Hierarchy h)
Hierarchies	IMP::atom::get_leaves (const Hierarchies &h)
Hierarchy	IMP::atom::get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index. More...
Hierarchy	IMP::atom::get_root (Hierarchy h)
	Return the root of the hierarchy. More...
void	IMP::atom::show (Hierarchy h, std::ostream &out=std::cout)
	Print out a molecular hierarchy. More...

Detailed Description

Decorator for helping deal with a hierarchy of molecules.

Copyright 2007-2014 IMP Inventors. All rights reserved.

Definition in file atom/Hierarchy.h.