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 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 have approximately the same total volume).

Tree Basics

In a tree you have a set of nodes, represented by Hierarchy particles. Each 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.

Note: Deleting a Hierarchy, like deleting any decorator, will not delete the underlying Particle or remove any children. To do that, call destroy().

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

Definition at line 192 of file atom/Hierarchy.h.

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

	Hierarchy (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
	Get the ith child based on the order they were added. More...

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 ParticlesTemp. More...

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

Hierarchy	get_parent () const
	Get the parent particle. More...

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

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

	Hierarchy (::IMP::Model *m,::IMP::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

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

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::Decorator
bool	get_is_valid () const
	Returns true if constructed with a non-default constructor. More...

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 (Model *m, ParticleIndex p)
	Check if the particle has the needed attributes for a cast to succeed. More...

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

static Hierarchy	setup_particle (Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
	Create a Hierarchy of level t by adding the needed attributes. More...

Static Public Member Functions inherited from IMP::core::Hierarchy
static TriggerKey	get_changed_key ()
	The key used to signal to the Model that the Hierarchy has changed. More...

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::ParticleAdaptor &p, const HierarchyTraits &tr=get_default_traits())

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

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

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

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

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

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

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

Related Functions
(Note that these are not member functions.)
Hierarchy	create_clone (Hierarchy d)
	Clone the Hierarchy. More...

Hierarchy	create_clone_one (Hierarchy d)
	Clone the node in the Hierarchy. More...

Hierarchy	create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes. More...

void	destroy (Hierarchy d)
	Delete the Hierarchy. More...

algebra::BoundingBoxD< 3 >	get_bounding_box (const Hierarchy &h)
	Get a bounding box for the Hierarchy. More...

algebra::Sphere3D	get_bounding_sphere (const Hierarchy &h)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)
	Gather all the molecular particles of a certain level in the hierarchy. More...

Bonds	get_internal_bonds (Hierarchy mhd)
	Get the bonds internal to this tree. More...

bool	get_is_heterogen (Hierarchy h)
	Return true if the piece of hierarchy should be classified as a heterogen. More...

Hierarchies	get_leaves (Hierarchy h)

Hierarchies	get_leaves (const Hierarchies &h)

Hierarchy	get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index. More...

Hierarchy	get_root (Hierarchy h)
	Return the root of the hierarchy. More...

void	show (Hierarchy h, std::ostream &out=std::cout)
	Print out a molecular hierarchy. More...

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

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

	Decorator (ParticleAdaptor p)

Constructor & Destructor Documentation

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

Null constructor.

Definition at line 229 of file atom/Hierarchy.h.

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

explicit

The traits must match.

Definition at line 232 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 270 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 280 of file atom/Hierarchy.h.

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

Return the children in the order they were added.

Definition at line 285 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 ParticlesTemp.

Definition at line 295 of file atom/Hierarchy.h.

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

static

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

Definition at line 255 of file atom/Hierarchy.h.

bool IMP::atom::Hierarchy::get_is_valid ( bool print_info = false ) 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 304 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	(	Model *	m,
		ParticleIndex	pi,
		ParticleIndexesAdaptor	children = `ParticleIndexesAdaptor()`
	)

static

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

Definition at line 240 of file atom/Hierarchy.h.

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Friends And Related Function Documentation

Hierarchy create_clone ( Hierarchy d )

This method copies the Bond, Bonded, Atom, Residue, Domain, Mass, and provenance data and the particle name to the new copies in addition to the Hierarchy relationships.

Hierarchy create_clone_one ( Hierarchy d )

This method copies the Atom, Residue, Chain, Domain, Mass, and provenance data and the particle name.

Hierarchy create_fragment ( const Hierarchies & ps )

A particle representing the fragment is created and initialized.

The Fragment is inserted as a child of the parent (and the particles are removed). The particles become children of the fragment.

Exceptions

ValueException If all the particles do not have the same parent.

void destroy ( Hierarchy d )

All bonds connecting to these atoms are destroyed as are hierarchy links in the Hierarchy and the particles are removed from the Model. If this particle has a parent, it is removed from the parent. Any provenance information for this Hierarchy is also removed.

If any particle in the Hierarchy is a rigid body member, it is removed from the rigid body. (This is currently slow; if possible, destroy the rigid bodies first.)

algebra::BoundingBoxD< 3 > get_bounding_box ( const Hierarchy & h )

This bounding box is that of the highest (in the CS sense of a tree growing down from the root) cut through the tree where each node in the cut has x,y,z, and r. That is, if the root has x,y,z,r then it is the bounding box of that sphere. If only the leaves have radii, it is the bounding box of the leaves. If no such cut exists, the behavior is undefined.

See Also: IMP::algebra::BoundingBoxD

algebra::Sphere3D get_bounding_sphere ( const Hierarchy & h )

Hierarchies get_by_type	(	Hierarchy	mhd,
		GetByType	t
	)

Bonds get_internal_bonds ( Hierarchy mhd )

See Also: Bond

bool get_is_heterogen ( Hierarchy h )

For the purposes of classification, a heterogen is anything that

is a heterogen atom (one whose name starts with HET:)
is or is part of a Residue that is not a normal protein, rna or dna residue
or is not part of a Chain

For the moment, this can only be called on residues or atoms.

Hierarchies get_leaves ( Hierarchy h )

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Hierarchies get_leaves ( const Hierarchies & h )

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Hierarchy get_residue	(	Hierarchy	mhd,
		unsigned int	index
	)

Find the leaf containing the residue with the appropriate index. This is the PDB index, not the offset in the chain (if they are different).

The function returns a Hierarchy, rather than a Residue since the residue may not be explicitly represented and may just be part of some fragment.

Exceptions

ValueException if mhd's type is not one of CHAIN, PROTEIN, NUCLEOTIDE

Returns: Hierarchy() if that residue is not found.

Hierarchy get_root ( Hierarchy h )

Definition at line 380 of file atom/Hierarchy.h.

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void show	(	Hierarchy	h,
		std::ostream &	out = `std::cout`
	)

Definition at line 405 of file atom/Hierarchy.h.

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

Related Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation