The standard decorator for manipulating molecular structures. More...

#include <IMP/atom/Hierarchy.h>

Inheritance diagram for IMP::atom::Hierarchy:

Detailed Description

The standard decorator for manipulating molecular structures.

IMP represents molecular structures using the Hierarchy decorator. Molecules and collections of molecules each are stored as a hierarchy (or tree) where the resolution of the representation increases as you move further from the root. That is, if a parent has some particular property (eg, marks out a volume by having a x,y,z coordinates and a radius), then the children should have a higher resolution form of that information (eg, mark out a more detailed excluded volume by defining a set of balls which having approximately the same total volume).

Tree Basics

In a tree you have a set of nodes, represented by Hierarchy particles. Each node can have a node can have at most one parent. The node with no parent is known as the root of the tree.

Here is a simple example with a protein with three residues. Two of the residues have atoms, where as the third is coarse grained.

The nodes in the hierarchy can correspond to arbitrary bits of a molecule and do not need to have any biological significance. For example we could introduce a fragment containing residues 0 and 1:

A hierarchy can have any tree structure as long as:

the type of the parent makes sense for the child: eg a Residue cannot be the parent of a Chain.
the leaves always have coordinates, radius and mass
all particles in the hierarchy are from the same model
all Atoms have a Residue as the parent
any Atom with a non-heterogen atom type is part of a protein, DNA or RNA molecule.
all Residue children of a particle appear in order based on their index
all Atom children of a particle appear in order of their AtomType
if a node has residue indexes, all its descendants down to the residue level also do.

The get_is_valid() method checks some of these properties. Any method taking a hierarchy as an argument should do

IMP_USAGE_CHECK(h.get_is_valid(), "Invalid hierarchy as input");

to make sure the hierarchy makes sense.

A number of decorator types are associated with the Hierarchy to store the information associated with that node in the hierarchy. Examples include Residue, Atom, XYZ, Chain, XYZR, Mass, Domain, Molecule etc. We provide a get_as_x() function for each such decorator which returns either X() (a null type) if the node is not a particle of type x, or an X decorator wrapping the current particle if it is.

See Also: Atom; Residue; Chain; Molecule; Domain; Fragment; Mass; State

Definition at line 203 of file atom/Hierarchy.h.

Public Member Functions
	Hierarchy (kernel::Model *m, kernel::ParticleIndex pi)

	Hierarchy (kernel::ParticleAdaptor pi)

	Hierarchy ()
	null constructor More...

	Hierarchy (IMP::core::Hierarchy h)
	The traits must match. More...

void	add_child (Hierarchy o)
	Add a child and check that the types are appropriate. More...

Hierarchy	get_child (unsigned int i) const

Hierarchies	get_children () const
	Return the children in the order they were added. More...

template<class C >
C	get_children () const
	Get the children in a container of your choosing, eg kernel::ParticlesTemp. More...

bool	get_is_valid (bool print_info) const
	Return true if the hierarchy is valid. More...

Hierarchy	get_parent () const

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::core::Hierarchy
	Hierarchy (const IMP::kernel::ParticleAdaptor &d, const HierarchyTraits &tr=get_default_traits())

	Hierarchy (::IMP::kernel::Model *m,::IMP::kernel::ParticleIndex id, const HierarchyTraits &tr=get_default_traits())

void	add_child (Hierarchy h) const

void	add_child_at (Hierarchy h, unsigned int pos)

void	clear_children ()

Hierarchy	get_child (unsigned int i) const

kernel::ParticleIndex	get_child_index (unsigned int i) const

int	get_child_index () const
	Return i such that `get_parent().get_child(i) == this` More...

GenericHierarchies	get_children () const

kernel::ParticleIndexes	get_children_indexes () const

const DecoratorTraits &	get_decorator_traits () const

unsigned int	get_number_of_children () const

Hierarchy	get_parent () const

HierarchyTraits	get_traits ()

void	remove_child (unsigned int i)

void	remove_child (Hierarchy h)

void	show (std::ostream &out=std::cout) const

Public Member Functions inherited from IMP::kernel::Decorator
bool	get_is_valid () const

Model *	get_model () const
	Returns the Model containing the particle. More...

Particle *	get_particle () const
	Returns the particle decorated by this decorator. More...

ParticleIndex	get_particle_index () const
	Returns the particle index decorated by this decorator. More...

	operator Particle * () const

	operator ParticleIndex () const

Particle *	operator-> () const

Static Public Member Functions
static bool	get_is_setup (kernel::Model *m, kernel::ParticleIndex p)

static const IMP::core::HierarchyTraits &	get_traits ()
	Get the molecular hierarchy HierarchyTraits. More...

static Hierarchy	setup_particle (kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())

Static Public Member Functions inherited from IMP::core::Hierarchy
static const DecoratorTraits &	get_default_decorator_traits ()

static const HierarchyTraits &	get_default_traits ()
	Get the default hierarchy traits. More...

static bool	get_is_setup (const IMP::kernel::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits())

static bool	get_is_setup (kernel::Model *, kernel::ParticleIndex, HierarchyTraits=Hierarchy::get_default_traits())

static Hierarchy	setup_particle (IMP::kernel::ParticleAdaptor d, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (kernel::Model *m, ParticleIndex pi, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (IMP::kernel::ParticleAdaptor d, kernel::ParticleIndexes children, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (IMP::kernel::ParticleAdaptor d, kernel::ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())

static Hierarchy	setup_particle (kernel::Model *m, ParticleIndex pi, kernel::ParticlesTemp children, DecoratorTraits tr=get_default_decorator_traits())

Methods to get associated decorators
We provide a number of helper methods to get associated decorators for the current node in the hierarchy. As an example, if the particle decorated by this decorator is a Residue particle, then get_as_residue() returns Residue(get_particle()), if not it returns Residue().
Atom	get_as_atom () const

Residue	get_as_residue () const

Chain	get_as_chain () const

Molecule	get_as_molecule () const

Domain	get_as_domain () const

Fragment	get_as_fragment () const

core::XYZ	get_as_xyz () const

core::XYZR	get_as_xyzr () const

Mass	get_as_mass () const

State	get_as_state () const

Additional Inherited Members
Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits	DecoratorTraits

Protected Member Functions inherited from IMP::kernel::Decorator
	Decorator (Model *m, ParticleIndex pi)

	Decorator (ParticleAdaptor p)

Constructor & Destructor Documentation

IMP::atom::Hierarchy::Hierarchy ( )

null constructor

Definition at line 258 of file atom/Hierarchy.h.

IMP::atom::Hierarchy::Hierarchy ( IMP::core::Hierarchy h )

explicit

The traits must match.

Definition at line 261 of file atom/Hierarchy.h.

Member Function Documentation

void IMP::atom::Hierarchy::add_child ( Hierarchy o )

Add a child and check that the types are appropriate.

A child must have a type that is listed before the parent in the Type enum list.

Examples:: atom/dope_and_excluded_volume.cpp.

Definition at line 300 of file atom/Hierarchy.h.

Hierarchy IMP::atom::Hierarchy::get_child ( unsigned int i ) const

Get the ith child based on the order they were added.

Definition at line 310 of file atom/Hierarchy.h.

Hierarchies IMP::atom::Hierarchy::get_children ( ) const

Return the children in the order they were added.

Definition at line 315 of file atom/Hierarchy.h.

template<class C >

C IMP::atom::Hierarchy::get_children ( ) const

Get the children in a container of your choosing, eg kernel::ParticlesTemp.

Definition at line 325 of file atom/Hierarchy.h.

static bool IMP::atom::Hierarchy::get_is_setup	(	kernel::Model *	m,
		kernel::ParticleIndex	p
	)

static

Check if the particle has the needed attributes for a cast to succeed

Definition at line 286 of file atom/Hierarchy.h.

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bool IMP::atom::Hierarchy::get_is_valid ( bool print_info ) const

Return true if the hierarchy is valid.

Print information about the hierarchy if print_info is true and things are invalid.

Note: Returning true only means that no problems were found, it can't check everything.

Hierarchy IMP::atom::Hierarchy::get_parent ( ) const

Get the parent particle.

Definition at line 334 of file atom/Hierarchy.h.

static const IMP::core::HierarchyTraits& IMP::atom::Hierarchy::get_traits ( )

static

Get the molecular hierarchy HierarchyTraits.

static Hierarchy IMP::atom::Hierarchy::setup_particle	(	kernel::Model *	m,
		kernel::ParticleIndex	pi,
		kernel::ParticleIndexesAdaptor	children = `kernel::ParticleIndexesAdaptor()`
	)

static

Create a Hierarchy of level t by adding the needed attributes.

Definition at line 270 of file atom/Hierarchy.h.

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The documentation for this class was generated from the following file:

atom/Hierarchy.h

Detailed Description

Tree Basics

Public Member Functions

Static Public Member Functions

Methods to get associated decorators

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation