Data Structures | |
| 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 hierarchy. More... | |
| class | IMP::atom::Hierarchy |
| The standard decorator for manipulating molecular structures. More... | |
| class | IMP::core::HierarchyCounter |
| A simple functor to count the number of particles in a hierarchy. More... | |
| struct | IMP::core::HierarchyPrinter< PD > |
| A simple visitor which pretty-prints the 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 | |
| template<class HD , class F > | |
| HD | IMP::core::Hierarchy::breadth_first_find (HD h, F f) |
| Find the first node which matches some criteria. | |
| template<class HD , class F > | |
| HD | IMP::core::breadth_first_find (HD h, F f) |
| Find the first node which matches some criteria. | |
| template<class HD , class F > | |
| F | IMP::core::Hierarchy::breadth_first_traversal (HD d, F f) |
| Apply the visitor to each particle, breadth first. | |
| template<class HD , class F > | |
| F | IMP::core::breadth_first_traversal (HD d, F f) |
| Apply the visitor to each particle, breadth first. | |
| template<class HD , class F > | |
| F | IMP::core::Hierarchy::breadth_first_traversal_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 | IMP::core::breadth_first_traversal_with_data (HD d, F f, typename F::result_type i) |
| Apply functor F to each particle, traversing the hierarchy breadth first. | |
| Hierarchy | IMP::atom::Hierarchy::create_fragment (const HierarchiesTemp &ps) |
| Create a fragment containing the specified nodes. | |
| Hierarchy | IMP::atom::create_fragment (const HierarchiesTemp &ps) |
| Create a fragment containing the specified nodes. | |
| template<class HD , class F > | |
| F | IMP::core::Hierarchy::depth_first_traversal (HD d, F f) |
| Apply functor F to each particle, traversing the hierarchy depth first. | |
| template<class HD , class F > | |
| F | IMP::core::depth_first_traversal (HD d, F f) |
| Apply functor F to each particle, traversing the hierarchy depth first. | |
| template<class HD , class F > | |
| F | IMP::core::Hierarchy::depth_first_traversal_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 | IMP::core::depth_first_traversal_with_data (HD d, F f, typename F::result_type i) |
| Apply functor F to each particle, traversing the hierarchy depth first. | |
| template<class Out , class F > | |
| Out | IMP::core::Hierarchy::gather (Hierarchy h, F f, Out out) |
| Gather all the particles in the hierarchy which meet some criteria. | |
| template<class Out , class F > | |
| Out | IMP::core::gather (Hierarchy h, F f, Out out) |
| Gather all the particles in the hierarchy which meet some criteria. | |
| template<class Out , class K , class V > | |
| Out | IMP::core::Hierarchy::gather_by_attribute (Hierarchy h, K k, V v, Out out) |
| Gather all the particles in the hierarchy which match on an attribute. | |
| template<class Out , class K , class V > | |
| Out | IMP::core::gather_by_attribute (Hierarchy h, K k, V v, Out out) |
| Gather all the particles in the hierarchy which match on an attribute. | |
| template<class Out , class K0 , class V0 , class K1 , class V1 > | |
| Out | IMP::core::Hierarchy::gather_by_attributes (Hierarchy 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 Out , class K0 , class V0 , class K1 , class V1 > | |
| Out | IMP::core::gather_by_attributes (Hierarchy h, K0 k0, V0 v0, K1 k1, V1 v1, Out out) |
| Gather all the particles in the hierarchy which match on two attributes. | |
| HierarchiesTemp | IMP::atom::Hierarchy::get_by_type (Hierarchy mhd, GetByType t) |
| HierarchiesTemp | IMP::atom::get_by_type (Hierarchy mhd, GetByType t) |
| Hierarchy | IMP::atom::Hierarchy::get_residue (Hierarchy mhd, unsigned int index) |
| Get the residue with the specified index. | |
| Hierarchy | IMP::atom::get_residue (Hierarchy mhd, unsigned int index) |
| Get the residue with the specified index. | |
| template<class ND > | |
| std::ostream & | IMP::core::Hierarchy::show (Hierarchy h, std::ostream &out=std::cout, unsigned int max_depth=std::numeric_limits< unsigned int >::max()) |
| Print the hierarchy using a given decorator as to display each node. | |
| template<class ND > | |
| std::ostream & | IMP::core::show (Hierarchy h, std::ostream &out=std::cout, unsigned int max_depth=std::numeric_limits< unsigned int >::max()) |
| Print the hierarchy using a given decorator as to display each node. | |
| F breadth_first_traversal | ( | HD | d, | |
| F | f | |||
| ) | [related, inherited] |
Apply the visitor to each particle, breadth first.
| [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. |
| F breadth_first_traversal | ( | HD | d, | |
| F | f | |||
| ) |
Apply the visitor to each particle, breadth first.
| [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. |
| F breadth_first_traversal_with_data | ( | HD | d, | |
| F | f, | |||
| typename F::result_type | i | |||
| ) | [related, inherited] |
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.
| [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==NULL) return 0; else return i+1; } }; |
| [in] | i | The data to be used for d (since it has no relevant parent) |
| F breadth_first_traversal_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.
| [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==NULL) return 0; else return i+1; } }; |
| [in] | i | The data to be used for d (since it has no relevant parent) |
| Hierarchy create_fragment | ( | const HierarchiesTemp & | ps | ) | [related, inherited] |
Create a fragment containing the specified nodes.
A particle representing the frament 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 frament.
| ValueException | If all the particles do not have the same parent. |
| Hierarchy create_fragment | ( | const HierarchiesTemp & | ps | ) |
Create a fragment containing the specified nodes.
A particle representing the frament 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 frament.
| ValueException | If all the particles do not have the same parent. |
| F depth_first_traversal | ( | HD | d, | |
| F | f | |||
| ) | [related, inherited] |
Apply functor F to each particle, traversing the hierarchy depth first.
See breadth_first_traversal() for documentation.
| F depth_first_traversal | ( | HD | d, | |
| F | f | |||
| ) |
Apply functor F to each particle, traversing the hierarchy depth first.
See breadth_first_traversal() for documentation.
| F depth_first_traversal_with_data | ( | HD | d, | |
| F | f, | |||
| typename F::result_type | i | |||
| ) | [related, inherited] |
Apply functor F to each particle, traversing the hierarchy depth first.
See breadth_first_traversal for documentation.
| F depth_first_traversal_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.
| HierarchiesTemp get_by_type | ( | Hierarchy | mhd, | |
| GetByType | t | |||
| ) | [related, inherited] |
Gather all the molecular particles of a certain level in the molecular hierarchy
| HierarchiesTemp get_by_type | ( | Hierarchy | mhd, | |
| GetByType | t | |||
| ) |
Gather all the molecular particles of a certain level in the molecular hierarchy
| Hierarchy get_residue | ( | Hierarchy | mhd, | |
| unsigned int | index | |||
| ) | [related, inherited] |
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.
| ValueException | if mhd's type is not one of CHAIN, PROTEIN, NUCLEOTIDE |
| 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.
| ValueException | if mhd's type is not one of CHAIN, PROTEIN, NUCLEOTIDE |
| std::ostream & show | ( | Hierarchy | h, | |
| std::ostream & | out = std::cout, |
|||
| unsigned int | max_depth = std::numeric_limits<unsigned int>::max() | |||
| ) | [related, inherited] |
Print the hierarchy using a given decorator as to display each node.
The last argument limits how deep will be printed out.
| std::ostream & show | ( | Hierarchy | h, | |
| std::ostream & | out = std::cout, |
|||
| unsigned int | max_depth = std::numeric_limits<unsigned int>::max() | |||
| ) |
Print the hierarchy using a given decorator as to display each node.
The last argument limits how deep will be printed out.
