IMP
2.0.1
The Integrative Modeling Platform
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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... | |
These functions and classes aid in manipulating particles representing molecules at multiple levels.
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.
ValueException | If all the particles do not have the same parent. |
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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.
ValueException | If all the particles do not have the same parent. |
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.
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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.
Hierarchies get_by_type | ( | Hierarchy | mhd, |
GetByType | t | ||
) |
Gather all the molecular particles of a certain level in the molecular hierarchy.
Gather all the molecular particles of a certain level in the molecular hierarchy.
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.
ValueException | if mhd's type is not one of CHAIN, PROTEIN, NUCLEOTIDE |
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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 |
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) |
The last argument limits how deep will be printed out.
Definition at line 441 of file core/Hierarchy.h.
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The last argument limits how deep will be printed out.
Definition at line 441 of file core/Hierarchy.h.
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.
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[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.
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.
[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) |
Definition at line 388 of file core/Hierarchy.h.
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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==nullptr) return 0; else return i+1; } }; |
[in] | i | The data to be used for d (since it has no relevant parent) |
Definition at line 388 of file core/Hierarchy.h.
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See breadth_first_traversal() for documentation.
Definition at line 343 of file core/Hierarchy.h.
F visit_depth_first | ( | HD | d, |
F | f | ||
) |
See breadth_first_traversal() for documentation.
Definition at line 343 of file core/Hierarchy.h.
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.
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See breadth_first_traversal for documentation.
Definition at line 413 of file core/Hierarchy.h.