Detailed Description

These functions and classes aid in manipulating 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::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.
Hierarchy	create_fragment (const Hierarchies &ps)
	Create a fragment containing the specified nodes.
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.
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.
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.
Hierarchy	get_residue (Hierarchy mhd, unsigned int index)
	Get the residue with the specified index.
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.
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.
template<class HD , class F >
F	IMP::core::visit_breadth_first (HD d, F f)
	Apply the visitor to each particle, breadth first.
template<class HD , class F >
F	visit_breadth_first (HD d, F f)
	Apply the visitor to each particle, breadth first.
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.
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.
template<class HD , class F >
F	visit_depth_first (HD d, F f)
	Apply functor F to each particle, traversing the hierarchy depth first.
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.
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.
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.

Function Documentation

Hierarchy create_fragment ( const Hierarchies & ps )

Create a fragment containing the specified nodes.

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 )

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.

template<class HD , class F >

HD 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
	)

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 F >

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

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 K , class V >

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

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 K0 , class V0 , class K1 , class V1 >

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

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.

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

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.

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
	)

Get the residue with the specified 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
	)

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.

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.

The last argument limits how deep will be printed out.

template<class ND >

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

The last argument limits how deep will be printed out.

template<class HD , class F >

F 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.

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.

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.

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.

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.

template<class HD , class F >

F visit_depth_first	(	HD	d,
		F	f
	)

See breadth_first_traversal() for documentation.

template<class HD , class F >

F visit_depth_first	(	HD	d,
		F	f
	)

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

See breadth_first_traversal() for documentation.

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.

See breadth_first_traversal for documentation.

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.

Detailed Description

Classes

Functions

Function Documentation