Hierarchies of particles

Manipulate particles representing molecules at multiple levels. More...

Detailed Description

Manipulate particles representing molecules at multiple levels.

Classes
class	IMP::atom::Atom
	A decorator for a particle representing an atom. More...
class	IMP::core::ChildrenRefiner
	Return the hierarchy children of a particle. More...
class	IMP::core::Hierarchy
	A decorator for helping deal with a generalized hierarchy. More...
struct	IMP::core::HierarchyCounter
	A simple functor to count the number of particles in a hierarchy. More...
class	IMP::core::HierarchyVisitor
	A visitor for traversal of a hierarchy. More...
class	IMP::core::LeavesRefiner
	Return the hierarchy leaves under a particle. More...
class	IMP::core::ModifierVisitor
	A visitor which applies a modifier to each Particle in a hierarchy. More...
class	IMP::atom::Residue
	A decorator for a residue. More...

Functions
template<class HD , class F >
HD	IMP::core::find_breadth_first (HD h, F f)
	Find the first node which matches some criteria. More...
template<class H , class Out , class F >
Out	IMP::core::gather (H h, F f, Out out)
	Gather all the particles in the hierarchy that meet some criteria. More...
template<class H , class Out , class K , class V >
Out	IMP::core::gather_by_attribute (H h, K k, V v, Out out)
	Gather all the particles in the hierarchy which match on an attribute. More...
template<class H , class Out , class K0 , class V0 , class K1 , class V1 >
Out	IMP::core::gather_by_attributes (H h, K0 k0, V0 v0, K1 k1, V1 v1, Out out)
	Gather all the particles in the hierarchy which match on two attributes. More...
template<class H , class Out , class F >
Out	IMP::core::gather_slice (H h, F f, Out out)
	Gather all the uppermost particles in the hierarchy that meet some criteria. More...
template<class ND >
std::ostream &	IMP::core::show (Hierarchy h, std::ostream &out=std::cout)
	Print the hierarchy using a given decorator to display each node. More...
template<class HD , class F >
F	IMP::core::visit_breadth_first (HD d, F f)
	Apply the visitor to each particle, breadth first. More...
template<class HD , class F >
F	IMP::core::visit_breadth_first_with_data (HD d, F f, typename F::result_type data)
	Apply functor F to each particle, traversing the hierarchy breadth first. More...
template<class HD , class F >
F	IMP::core::visit_depth_first (HD d, F &f)
	Apply functor F to each particle, traversing the hierarchy depth first. More...
template<class HD , class F >
F	IMP::core::visit_depth_first_with_data (HD d, F f, typename F::result_type data)
	Apply functor F to each particle, traversing the hierarchy depth first. More...

Function Documentation

template<class HD , class F >

HD IMP::core::find_breadth_first	(	HD	h,
		F	f
	)

Find the first node which matches some criteria.

See Also

Hierarchy

Definition at line 521 of file core/Hierarchy.h.

template<class H , class Out , class F >

Out IMP::core::gather	(	H	h,
		F	f,
		Out	out
	)

Gather all the particles in the hierarchy that meet some criteria.

Gather all the particles in the hierarchy for which f() returns true and appends them to out

Parameters

h	hierarchy root
f	boolean function / functor that returns true on desired particles
out	a output iterator for appending the result

Returns

the output iterator

See Also

Hierarchy

Definition at line 472 of file core/Hierarchy.h.

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template<class H , class Out , class K , class V >

Out IMP::core::gather_by_attribute	(	H	h,
		K	k,
		V	v,
		Out	out
	)

Gather all the particles in the hierarchy which match on an attribute.

See Also

Hierarchy

Definition at line 497 of file core/Hierarchy.h.

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template<class H , class Out , class K0 , class V0 , class K1 , class V1 >

Out IMP::core::gather_by_attributes	(	H	h,
		K0	k0,
		V0	v0,
		K1	k1,
		V1	v1,
		Out	out
	)

Gather all the particles in the hierarchy which match on two attributes.

See Also

Hierarchy

Definition at line 509 of file core/Hierarchy.h.

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template<class H , class Out , class F >

Out IMP::core::gather_slice	(	H	h,
		F	f,
		Out	out
	)

Gather all the uppermost particles in the hierarchy that meet some criteria.

Descent in the tree terminates when a node is gathered so that none of its children are explored.

See Also

Hierarchy

Definition at line 486 of file core/Hierarchy.h.

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template<class ND >

std::ostream& IMP::core::show	(	Hierarchy	h,
		std::ostream &	out = std::cout
	)

Print the hierarchy using a given decorator to display each node.

See Also

Hierarchy

Definition at line 423 of file core/Hierarchy.h.

template<class HD , class F >

F IMP::core::visit_breadth_first	(	HD	d,
		F	f
	)

Apply the visitor to each particle, breadth first.

Parameters

[in]	d	The Hierarchy for the tree in question
[in]	f	The visitor to be applied. This is passed by reference. A branch of the traversal stops when f returns false.

See Also

Hierarchy

Definition at line 311 of file core/Hierarchy.h.

template<class HD , class F >

F IMP::core::visit_breadth_first_with_data	(	HD	d,
		F	f,
		typename F::result_type	data
	)

Apply functor F to each particle, traversing the hierarchy breadth first.

This method allows data to be associated with each visited node. The data of the parent is passed to each invocation of the child.

Parameters

[in]	d	The Hierarchy for the tree in question
[in]	f	The functor to be applied F must define a type Data which is returned by each call. The result of the parent call is passed as the second argument to the operator() of the child. e.g. struct DepthVisitor { typedef int result_type; result_type operator()(Particle *p, int i) const { if (p==nullptr) return 0; else return i+1; } };
[in]	data	The data to be used for d (since it has no relevant parent)

Returns

A copy of the functor passed in. Use this if you care about the functor state.

See Also

Hierarchy

Definition at line 377 of file core/Hierarchy.h.

template<class HD , class F >

F IMP::core::visit_depth_first	(	HD	d,
		F &	f
	)

Apply functor F to each particle, traversing the hierarchy depth first.

See visit_breadth_first() for documentation.

See Also

Hierarchy

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

template<class HD , class F >

F IMP::core::visit_depth_first_with_data	(	HD	d,
		F	f,
		typename F::result_type	data
	)

Apply functor F to each particle, traversing the hierarchy depth first.

See visit_breadth_first() for documentation.

See Also

Hierarchy

Definition at line 401 of file core/Hierarchy.h.