IMP.pmi.output.RMFHierarchyHandler Class Reference

class to allow more advanced handling of RMF files. More...

Inheritance diagram for IMP.pmi.output.RMFHierarchyHandler:

Detailed Description

class to allow more advanced handling of RMF files.

It is both a container and a IMP.atom.Hierarchy.

• it is iterable (while loading the corresponding frame)
• Item brackets [] load the corresponding frame
• slice create an iterator
• can relink to another RMF file

Note

This class is only available in Python.

Definition at line 960 of file output.py.

Public Member Functions
def	__init__
def	link_to_rmf
	Link to another RMF file. More...
Public Member Functions inherited from IMP::atom::Hierarchy
	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

Additional Inherited Members
Public Types inherited from IMP::core::Hierarchy
typedef HierarchyTraits	DecoratorTraits
Static Public Member Functions inherited from IMP::atom::Hierarchy
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 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())
Protected Member Functions inherited from IMP::Decorator
	Decorator (Model *m, ParticleIndex pi)
	Decorator (ParticleAdaptor p)
Related Functions inherited from IMP::atom::Hierarchy
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...

Constructor & Destructor Documentation

def IMP.pmi.output.RMFHierarchyHandler.__init__	(		self,
			model,
			rmf_file_name
	)

Parameters

model	the IMP.Model()
rmf_file_name	str, path of the rmf file

Definition at line 968 of file output.py.

Member Function Documentation

def IMP.pmi.output.RMFHierarchyHandler.link_to_rmf	(		self,
			rmf_file_name
	)

Link to another RMF file.

Definition at line 986 of file output.py.

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

• output.py