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/Particle.h>
#include <IMP/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
	Base functionality and abstract base classes for representation, scoring and sampling.

	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::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 }
	The different types which can be passed to get_by_type() More...

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)
	Gather all the molecular particles of a certain level in the hierarchy. More...

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.

Definition in file atom/Hierarchy.h.

Classes

Namespaces

Macros

Typedefs

Enumerations

Functions

Detailed Description