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::atom::Hierarchy
	The standard decorator for manipulating molecular structures. 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 which applies a singleton modifier to each Particle in a hierarchy. More...

class	IMP::atom::Residue
	A decorator for a residue. More...

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

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

template<class HD , class F >
HD	IMP::core::find_breadth_first (HD h, F f)
	Find the first node which matches some criteria.

template<class HD , class F >
HD	find_breadth_first (HD h, F f)
	Find the first node which matches some criteria.

template<class H , class Out , class F >
Out	IMP::core::gather (H h, F f, Out out)
	Gather all the particles in the hierarchy which meet some criteria.

template<class H , class Out , class F >
Out	gather (H h, F f, Out out)
	Gather all the particles in the hierarchy which meet some criteria.

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.

template<class H , class Out , class K , class V >
Out	gather_by_attribute (H h, K k, V v, Out out)
	Gather all the particles in the hierarchy which match on an attribute.

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.

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

template<class H , class Out , class F >
Out	IMP::core::gather_slice (H h, F f, Out out)
	Gather all the particles in the hierarchy which meet some criteria. More...

template<class H , class Out , class F >
Out	gather_slice (H h, F f, Out out)
	Gather all the particles in the hierarchy which meet some criteria. More...

Hierarchies	IMP::atom::get_by_type (Hierarchy mhd, GetByType t)

Hierarchies	get_by_type (Hierarchy mhd, GetByType t)

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

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

template<class ND >
std::ostream &	IMP::core::show (Hierarchy h, std::ostream &out=std::cout)
	Print the hierarchy using a given decorator as to display each node. More...

template<class ND >
std::ostream &	show (Hierarchy h, std::ostream &out=std::cout)
	Print the hierarchy using a given decorator as 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	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 i)
	Apply functor F to each particle, traversing the hierarchy breadth first. More...

template<class HD , class F >
F	visit_breadth_first_with_data (HD d, F f, typename F::result_type i)
	Apply functor F to each particle, traversing the hierarchy breadth first. More...

template<class HD , class F >
F	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 (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 i)
	Apply functor F to each particle, traversing the hierarchy depth first. More...

template<class HD , class F >
F	visit_depth_first_with_data (HD d, F f, typename F::result_type i)
	Apply functor F to each particle, traversing the hierarchy depth first. More...

Detailed Description

These functions and classes aid in manipulating particles representing molecules at multiple levels.

Function Documentation

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.

Hierarchy create_fragment ( const Hierarchies & ps )

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.

template<class H , class Out , class F >

Out gather_slice	(	H	h,
		F	f,
		Out	out
	)

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

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

Here is the call graph for this function:

template<class H , class Out , class F >

Out gather_slice	(	H	h,
		F	f,
		Out	out
	)

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

Hierarchies get_by_type	(	Hierarchy	mhd,
		GetByType	t
	)

Gather all the molecular particles of a certain level in the molecular hierarchy.

Hierarchies get_by_type	(	Hierarchy	mhd,
		GetByType	t
	)

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_residue	(	Hierarchy	mhd,
		unsigned int	index
	)

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.

template<class ND >

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

The last argument limits how deep will be printed out.

Definition at line 441 of file core/Hierarchy.h.

template<class ND >

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

Definition at line 441 of file core/Hierarchy.h.

template<class HD , class F >

F visit_breadth_first	(	HD	d,
		F	f
	)

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.

Definition at line 318 of file core/Hierarchy.h.

template<class HD , class F >

F visit_breadth_first	(	HD	d,
		F	f
	)

[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.

Definition at line 318 of file core/Hierarchy.h.

template<class HD , class F >

F visit_breadth_first_with_data	(	HD	d,
		F	f,
		typename F::result_type	i
	)

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]	i	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.

Definition at line 388 of file core/Hierarchy.h.

template<class HD , class F >

F visit_breadth_first_with_data	(	HD	d,
		F	f,
		typename F::result_type	i
	)

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]	i	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.

Definition at line 388 of file core/Hierarchy.h.

template<class HD , class F >

F visit_depth_first	(	HD	d,
		F	f
	)

Definition at line 343 of file core/Hierarchy.h.

template<class HD , class F >

F visit_depth_first	(	HD	d,
		F	f
	)

See breadth_first_traversal() for documentation.

Definition at line 343 of file core/Hierarchy.h.

template<class HD , class F >

F visit_depth_first_with_data	(	HD	d,
		F	f,
		typename F::result_type	i
	)

See breadth_first_traversal for documentation.

Definition at line 413 of file core/Hierarchy.h.

template<class HD , class F >

F visit_depth_first_with_data	(	HD	d,
		F	f,
		typename F::result_type	i
	)

Definition at line 413 of file core/Hierarchy.h.

Classes

Functions

Detailed Description

Function Documentation