IMP  2.0.1
The Integrative Modeling Platform
IMP::atom::Hierarchy Class Reference

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

#include <IMP/atom/Hierarchy.h>

+ Inheritance diagram for IMP::atom::Hierarchy:

Public Member Functions

 Hierarchy (Particle *p)
 
 Hierarchy (Model *m, ParticleIndex pi)
 
 Hierarchy ()
 null constructor
 
 Hierarchy (IMP::core::Hierarchy h)
 The traits must match.
 
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.
 
template<class C >
get_children () const
 Get the children in a container of your choosing, eg ParticlesTemp.
 
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 (Model *m, ParticleIndex id, const HierarchyTraits &tr)
 
 Hierarchy (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())
 
 Hierarchy (const HierarchyTraits &tr)
 
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
 
int get_child_index () const
 
GenericHierarchies get_children () const
 
const DecoratorTraitsget_decorator_traits () const
 
unsigned int get_number_of_children () const
 
Hierarchy get_parent () const
 
const HierarchyTraitsget_traits () const
 
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
ParticleIndex get_particle_index () const
 
Particleget_particle () const
 
Modelget_model () const
 Returns the Model containing the particle.
 
 Decorator (Particle *p)
 
 Decorator ()
 

Static Public Member Functions

static Hierarchy decorate_particle (Particle *p)
 cast a particle which has the needed attributes
 
static const
IMP::core::HierarchyTraits
get_traits ()
 Get the molecular hierarchy HierararchyTraits.
 
static bool particle_is_instance (Particle *p)
 
static bool particle_is_instance (Model *m, ParticleIndex p)
 
static Hierarchy setup_particle (Particle *p, const ParticlesTemp &children)
 
static Hierarchy setup_particle (Model *m, ParticleIndex pi, const ParticlesTemp &children=ParticlesTemp())
 
static Hierarchy setup_particle (Particle *p)
 
- Static Public Member Functions inherited from IMP::core::Hierarchy
static Hierarchy decorate_particle (::IMP::kernel::Particle *p, const HierarchyTraits &tr=get_default_traits())
 
static const DecoratorTraitsget_default_decorator_traits ()
 
static const HierarchyTraitsget_default_traits ()
 Get the default hierarchy traits.
 
static bool particle_is_instance (Particle *, HierarchyTraits=Hierarchy::get_default_traits())
 
static Hierarchy setup_particle (Particle *p, HierarchyTraits traits=Hierarchy::get_default_traits())
 Add the needed attributes to a particle.
 
static Hierarchy setup_particle (Particle *p, const Particles &children, HierarchyTraits traits=Hierarchy::get_default_traits())
 Add the needed attributes to a particle and add the particles as children. More...
 
- Static Public Member Functions inherited from IMP::kernel::Decorator
static bool particle_is_instance (Particle *p)
 Return true if the particle can be cast to the decorator. More...
 

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...
 
Restraintcreate_excluded_volume_restraint (const Hierarchies &hs, double resolution=-1)
 
Hierarchy create_fragment (const Hierarchies &ps)
 Create a fragment containing the specified nodes. More...
 
Hierarchy create_protein (Model *m, std::string name, double resolution, int number_of_residues, int first_residue_index=0, double volume=-1)
 Create a coarse grained molecule. More...
 
void destroy (Hierarchy d)
 Delete the Hierarchy. More...
 
Atom get_atom (Residue rd, AtomType at)
 Return a particle atom from the residue. More...
 
algebra::Sphere3D get_bounding_sphere (const Hierarchy &h)
 
Hierarchies get_by_type (Hierarchy mhd, GetByType t)
 
HierarchyTree get_hierarchy_tree (Hierarchy h)
 
Hierarchies get_leaves (const Selection &h)
 
Hierarchies get_leaves (Hierarchy h)
 
Hierarchies get_leaves (const Hierarchies &h)
 
Residue get_residue (Atom d, bool nothrow=false)
 Return the Residue containing this atom. More...
 
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 setup_as_approximation (Hierarchy h)
 
void show (Hierarchy h, std::ostream &out=std::cout)
 Print out a molecular hierarchy.
 

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() return 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
 

PDB Reading

The read PDB methods produce a hierarchy that looks as follows:

  • One Atom per ATOM or HETATM record in the PDB.
  • All Atom particles have a parent which is a Residue.
  • All Residue particles have a parent which is a Chain.

Waters are currently dropped if they are ATOM records. This can be fixed.

The read_pdb() functions should successfully parse all valid pdb files. It can produce warnings on files which are not valid. It will attempt to read such files, but all bets are off.

When reading PDBs, PDBSelector objects can be used to choose to only process certain record types. See the class documentation for more information. When no PDB selector is supplied for reading, the NonWaterPDBSelector is used.

Set the IMP::LogLevel to VERBOSE to see details of parse errors.

Hierarchy read_pdb (base::TextInput input, Model *model, PDBSelector *selector, bool select_first_model=true)
 

Additional Inherited Members

- Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits DecoratorTraits
 
typedef Decorator DecoratorTraitsBase
 
- Protected Member Functions inherited from IMP::kernel::Decorator
 Decorator (Model *m, ParticleIndex pi)
 
 Decorator (Particle *p)
 

Detailed Description

IMP represents molecular structures using the Hierachy 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 significant. 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 hierarchy are from the same model
  • all Atoms has a Residue for as 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 in of a particle appear in order of their AtomType

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

Definition at line 209 of file atom/Hierarchy.h.

Member Function Documentation

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

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 292 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 298 of file atom/Hierarchy.h.

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

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 322 of file atom/Hierarchy.h.

static bool IMP::atom::Hierarchy::particle_is_instance ( Particle p)
static

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

Definition at line 274 of file atom/Hierarchy.h.

static Hierarchy IMP::atom::Hierarchy::setup_particle ( Model m,
ParticleIndex  pi,
const ParticlesTemp &  children = ParticlesTemp() 
)
static

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

Definition at line 252 of file atom/Hierarchy.h.

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Friends And Related Function Documentation

Hierarchy create_clone ( Hierarchy  d)
related

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

Hierarchy create_clone_one ( Hierarchy  d)
related

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

Restraint * create_excluded_volume_restraint ( const Hierarchies &  hs,
double  resolution = -1 
)
related

Create an excluded volume restraint for the included molecules. If a value is provided for resolution, then something less than the full resolution representation will be used.

If one or more of the selections is a rigid body, this will be used to accelerate the computation.

Hierarchy create_protein ( Model m,
std::string  name,
double  resolution,
int  number_of_residues,
int  first_residue_index = 0,
double  volume = -1 
)
related

The coarse grained model is created with a number of spheres based on the resolution and the volume. If the volume is not provided it is estimated based on the number of residues. The protein is created as a molecular hierarchy rooted at p. The leaves are Domain particles with appropriate residue indexes stored and are XYZR particles.

Volume is, as usual, in cubic anstroms.

Currently the function creates a set of balls with radii no greater than resolution which overlap by 20% and have a volume of their union equal to the passed volume.

The coordinates of the balls defining the protein are optimized by default, and have garbage coordinate values.

Warning: create_protein has not been well tested yet
Use with caution and please report any bugs found.
Warning: create_protein has not been stabilized and is likely to change without notice.
void destroy ( Hierarchy  d)
related

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.

Atom get_atom ( Residue  rd,
AtomType  at 
)
related

The residue must be part of a molecular hierarchy.

algebra::Sphere3D get_bounding_sphere ( const Hierarchy h)
related

See get_bounding_box() for more details.

HierarchyTree get_hierarchy_tree ( Hierarchy  h)
related

Get a graph for the passed Hierarchy. This can be used, for example, to graphically display the hierarchy in 2D.

Hierarchies get_leaves ( const Selection h)
related
Hierarchies get_leaves ( Hierarchy  h)
related

Definition at line 425 of file atom/Hierarchy.h.

Hierarchies get_leaves ( const Hierarchies &  h)
related

Definition at line 430 of file atom/Hierarchy.h.

Residue get_residue ( Atom  d,
bool  nothrow = false 
)
related

The atom must be part of a molecular hierarchy.

Exceptions
ValueExceptionif no residue is found, unless nothrow is true.
Hierarchy get_root ( Hierarchy  h)
related

Definition at line 417 of file atom/Hierarchy.h.

void setup_as_approximation ( Hierarchy  h)
related

Set the mass, radius, residues, and coordinates to approximate the passed particle based on the leaves of h.


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