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IMP Reference Guide  2.5.0
The Integrative Modeling Platform
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/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.

Copyright 2007-2015 IMP Inventors. All rights reserved.

Definition in file atom/Hierarchy.h.