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Molassembler
1.0.0
Molecule graph and conformer library
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Molassembler
1.0.0
Molecule graph and conformer library
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Wrapper class to make working with RDL in C++ more pleasant. More...
#include <Cycles.h>
Data Structures | |
| class | AllCyclesIterator |
| Iterator for all relevant cycles of the graph. More... | |
| class | UrfIdsCycleIterator |
| Iterator for cycles of specific universal ring families. More... | |
Public Member Functions | |
Special member functions | |
| Cycles (const Graph &sourceGraph, bool ignoreEtaBonds=true) | |
| Constructor from outer graph. More... | |
| Cycles (const PrivateGraph &innerGraph, bool ignoreEtaBonds=true) | |
Information | |
| unsigned | numCycleFamilies () const |
| Returns the number of unique ring families (URFs) More... | |
| unsigned | numCycleFamilies (AtomIndex index) const |
| Returns the number of unique ring families (URFs) an index is involved in. More... | |
| unsigned | numCycleFamilies (const BondIndex &bond) const |
| Returns the number of unique ring families (URFs) a bond is in. More... | |
| unsigned | numRelevantCycles () const |
| Returns the number of relevant cycles (RCs) More... | |
| unsigned | numRelevantCycles (AtomIndex index) const |
| Returns the number of relevant cycles (RCs) More... | |
| unsigned | numRelevantCycles (const BondIndex &index) const |
| Returns the number of relevant cycles (RCs) a bond is in. More... | |
| RDL_data * | dataPtr () const |
| Provide access to calculated data. | |
Iterators | |
| AllCyclesIterator | begin () const |
| AllCyclesIterator | end () const |
Ranges | |
| IteratorRange < UrfIdsCycleIterator > | containing (AtomIndex atom) const |
| Range of relevant cycles containing an atom. More... | |
| IteratorRange < UrfIdsCycleIterator > | containing (const BondIndex &bond) const |
| Range of relevant cycles containing a bond. More... | |
| IteratorRange < UrfIdsCycleIterator > | containing (const std::vector< BondIndex > &bonds) const |
| Range of relevant cycles containing several bonds. More... | |
Operators | |
| bool | operator== (const Cycles &other) const |
| Must be copy of another to compare equal. Constructed from same graph does not suffice. | |
| bool | operator!= (const Cycles &other) const |
| Must be copy of another to compare equal. Constructed from same graph does not suffice. | |
Private Attributes | |
| std::shared_ptr< RdlDataPtrs > | rdlPtr_ |
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std::unordered_map< BondIndex, std::vector< unsigned > , boost::hash< BondIndex > > | urfMap_ |
Wrapper class to make working with RDL in C++ more pleasant.
Calculated data from a graph is movable, copyable and assignable in all the usual ways, and is therefore suited for caching. Equality comparison of this type and its nested types follows same-base, not equal-base logic of comparison due to management of the C pointer types and the associated allocated memory using shared_ptrs.
| Scine::Molassembler::Cycles::Cycles | ( | const Graph & | sourceGraph, |
| bool | ignoreEtaBonds = true |
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Constructor from outer graph.
Complexity Approximately linear in the number of bonds in cycles
| Scine::Molassembler::Cycles::Cycles | ( | const PrivateGraph & | innerGraph, |
| bool | ignoreEtaBonds = true |
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
| IteratorRange<UrfIdsCycleIterator> Scine::Molassembler::Cycles::containing | ( | AtomIndex | atom | ) | const |
Range of relevant cycles containing an atom.
Complexity \(O(U)\) where \(U\) is the number of unique ring families of the molecule
| IteratorRange<UrfIdsCycleIterator> Scine::Molassembler::Cycles::containing | ( | const BondIndex & | bond | ) | const |
Range of relevant cycles containing a bond.
Complexity \(\Theta(1)\)
| IteratorRange<UrfIdsCycleIterator> Scine::Molassembler::Cycles::containing | ( | const std::vector< BondIndex > & | bonds | ) | const |
Range of relevant cycles containing several bonds.
Complexity \(\Theta(B)\) where \(B\) is the number of bonds in the parameters
| unsigned Scine::Molassembler::Cycles::numCycleFamilies | ( | ) | const |
Returns the number of unique ring families (URFs)
Complexity \(\Theta(1)\)
| unsigned Scine::Molassembler::Cycles::numCycleFamilies | ( | AtomIndex | index | ) | const |
Returns the number of unique ring families (URFs) an index is involved in.
Complexity \(\Theta(U)\) where \(U\) is the number of unique ring families in the molecule
| unsigned Scine::Molassembler::Cycles::numCycleFamilies | ( | const BondIndex & | bond | ) | const |
Returns the number of unique ring families (URFs) a bond is in.
Complexity \(\Theta(U)\) where \(U\) is the number of unique ring families in the molecule
| unsigned Scine::Molassembler::Cycles::numRelevantCycles | ( | ) | const |
Returns the number of relevant cycles (RCs)
Complexity \(\Theta(1)\)
| unsigned Scine::Molassembler::Cycles::numRelevantCycles | ( | AtomIndex | index | ) | const |
Returns the number of relevant cycles (RCs)
Complexity \(\Theta(U)\) where \(U\) is the number of unique ring families in the molecule
| unsigned Scine::Molassembler::Cycles::numRelevantCycles | ( | const BondIndex & | index | ) | const |
Returns the number of relevant cycles (RCs) a bond is in.
Complexity \(\Theta(U)\) where \(U\) is the number of unique ring families in the molecule