Implements the extraction of all rings in the SSSR of a molecular graph that are aromatic according to MMFF94 conventions.
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| MMFF94AromaticSSSRSubset () |
| Constructs an empty MMFF94AromaticSSSRSubset instance. More...
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| MMFF94AromaticSSSRSubset (const Chem::MolecularGraph &molgraph) |
| Construct a MMFF94AromaticSSSRSubset instance that contains all aromatic rings of the SSSR of the molecular graph molgraph. More...
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void | extract (const Chem::MolecularGraph &molgraph) |
| Replaces the current set of rings by the aromatic rings in the SSSR of the molecular graph molgraph. More...
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void | extract (const Chem::MolecularGraph &molgraph, const Chem::FragmentList &sssr) |
| Replaces the current set of rings by the aromatic rings in the SSSR of the molecular graph molgraph. More...
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| IndirectArray () |
| Creates an empty array. More...
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| IndirectArray (std::size_t num_elem, const typename ValueType::SharedPointer &ptr=typename ValueType::SharedPointer()) |
| Creates and initializes the array with num_elem copies of ptr. More...
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| IndirectArray (const InputIter &first, const InputIter &last) |
| Creates and initializes the array with copies of the pointers in the range [first, last). More...
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virtual | ~IndirectArray () |
| Virtual destructor. More...
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ElementIterator | insertElement (const ElementIterator &it, const typename ValueType::SharedPointer &ptr) |
| Inserts a new element before the location specified by the iterator it. More...
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void | insertElement (std::size_t idx, const Fragment &value=Fragment()) |
| Inserts a new element before the location specified by the index idx. More...
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ElementIterator | insertElement (const ElementIterator &it, const Fragment &value=Fragment()) |
| Inserts a new element before the location specified by the iterator it. More...
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void | insertElements (const ElementIterator &it, std::size_t num_elem, const typename ValueType::SharedPointer &ptr) |
| Inserts num_elem copies of ptr before the location specified by the iterator it. More...
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void | insertElements (const ElementIterator &it, const InputIter &first, const InputIter &last) |
| Inserts the range of pointers [first, last) before the location specified by the iterator it. More...
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void | insertElements (std::size_t idx, std::size_t num_elem, const Fragment &value=Fragment()) |
| Inserts num_elem copies of value before the location specified by the index idx. More...
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void | insertElements (const ElementIterator &it, std::size_t num_elem, const Fragment &value=Fragment()) |
| Inserts num_elem copies of value before the location specified by the iterator it. More...
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void | insertElements (std::size_t idx, const InputIter &first, const InputIter &last) |
| Inserts the range of elements [first, last) before the location specified by the index idx. More...
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void | insertElements (const ElementIterator &it, const InputIter &first, const InputIter &last) |
| Inserts the range of elements [first, last) before the location specified by the iterator it. More...
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ElementIterator | removeElement (const ElementIterator &it) |
| Removes the element at the position specified by the iterator it. More...
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void | removeElement (std::size_t idx) |
| Removes the element at the position specified by the index idx. More...
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ElementIterator | removeElement (const ElementIterator &it) |
| Removes the element at the position specified by the iterator it. More...
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ElementIterator | removeElements (const ElementIterator &first, const ElementIterator &last) |
| Removes the elements pointed to by the iterators in the range [first, last). More...
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ElementIterator | removeElements (const ElementIterator &first, const ElementIterator &last) |
| Removes the elements pointed to by the iterators in the range [first, last). More...
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const Fragment & | getFirstElement () const |
| Returns a const reference to the object pointed to by the first element of the array. More...
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Fragment & | getFirstElement () |
| Returns a non-const reference to the object pointed to by the first element of the array. More...
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const Fragment & | getLastElement () const |
| Returns a const reference to the object pointed to by the last element of the array. More...
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Fragment & | getLastElement () |
| Returns a non-const reference to the object pointed to by the last element of the array. More...
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ConstElementIterator | getElementsBegin () const |
| Returns a constant iterator over the pointed-to objects that points to the beginning of the array. More...
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ElementIterator | getElementsBegin () |
| Returns a mutable iterator over the pointed-to objects that points to the beginning of the array. More...
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ConstElementIterator | getElementsEnd () const |
| Returns a constant iterator over the pointed-to objects that points to the end of the array. More...
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ElementIterator | getElementsEnd () |
| Returns a mutable iterator over the pointed-to objects that points to the end of the array. More...
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ConstElementIterator | begin () const |
| Returns a constant iterator over the pointed-to objects that points to the beginning of the array. More...
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ElementIterator | begin () |
| Returns a mutable iterator over the pointed-to objects that points to the beginning of the array. More...
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ConstElementIterator | end () const |
| Returns a constant iterator over the pointed-to objects that points to the end of the array. More...
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ElementIterator | end () |
| Returns a mutable iterator over the pointed-to objects that points to the end of the array. More...
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ConstReverseElementIterator | getElementsReverseBegin () const |
| Returns a constant iterator over the pointed-to objects that points to the beginning of the reversed array. More...
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ReverseElementIterator | getElementsReverseBegin () |
| Returns a mutable iterator over the pointed-to objects that points to the beginning of the reversed array. More...
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ConstReverseElementIterator | getElementsReverseEnd () const |
| Returns a constant iterator over the pointed-to objects that points to the end of the reversed array. More...
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ReverseElementIterator | getElementsReverseEnd () |
| Returns a mutable iterator over the pointed-to objects that points to the end of the reversed array. More...
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const Fragment & | getElement (std::size_t idx) const |
| Returns a const reference to the object pointed-to by the pointer element at index idx. More...
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Fragment & | getElement (std::size_t idx) |
| Returns a non-const reference to the object pointed-to by the pointer element at index idx. More...
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const Fragment & | operator[] (std::size_t idx) const |
| Returns a const reference to the object pointed-to by the pointer element at index idx. More...
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Fragment & | operator[] (std::size_t idx) |
| Returns a non-const reference to the object pointed-to by the pointer element at index idx. More...
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| Array () |
| Creates an empty array. More...
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| Array (std::size_t num_elem, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Creates and initializes the array with num_elem copies of value. More...
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| Array (const InputIter &first, const InputIter &last) |
| Creates and initializes the array with copies of the elements in the range [first, last). More...
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virtual | ~Array () |
| Virtual destructor. More...
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StorageType & | getData () |
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const StorageType & | getData () const |
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BaseType & | getBase () |
| Returns a non-const reference to itself. More...
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const BaseType & | getBase () const |
| Returns a const reference to itself. More...
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std::size_t | getSize () const |
| Returns the number of elements stored in the array. More...
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std::size_t | size () const |
| Returns the number of elements stored in the array. More...
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bool | isEmpty () const |
| Tells whether the array is empty (getSize() == 0). More...
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void | resize (std::size_t num_elem, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Inserts or erases elements at the end so that the size becomes num_elem. More...
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void | reserve (std::size_t num_elem) |
| Preallocates memory for (at least) num_elem elements. More...
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std::size_t | getCapacity () const |
| Returns the number of elements for which memory has been allocated. More...
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void | clear () |
| Erases all elements. More...
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void | swap (Array &array) |
| Swaps the contents with array. More...
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void | assign (std::size_t num_elem, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| This function fills the array with num_elem copies of the given value. More...
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void | assign (const InputIter &first, const InputIter &last) |
| This function fills a vector with copies of the elements in the range [first, last). More...
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void | addElement (const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Inserts a new element at the end of the array. More...
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void | insertElement (std::size_t idx, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Inserts a new element before the location specified by the index idx. More...
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ElementIterator | insertElement (const ElementIterator &it, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Inserts a new element before the location specified by the iterator it. More...
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void | insertElements (std::size_t idx, std::size_t num_elem, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Inserts num_elem copies of value before the location specified by the index idx. More...
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void | insertElements (const ElementIterator &it, std::size_t num_elem, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Inserts num_elem copies of value before the location specified by the iterator it. More...
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void | insertElements (std::size_t idx, const InputIter &first, const InputIter &last) |
| Inserts the range of elements [first, last) before the location specified by the index idx. More...
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void | insertElements (const ElementIterator &it, const InputIter &first, const InputIter &last) |
| Inserts the range of elements [first, last) before the location specified by the iterator it. More...
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void | popLastElement () |
| Removes the last element of the array. More...
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void | removeElement (std::size_t idx) |
| Removes the element at the position specified by the index idx. More...
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ElementIterator | removeElement (const ElementIterator &it) |
| Removes the element at the position specified by the iterator it. More...
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ElementIterator | removeElements (const ElementIterator &first, const ElementIterator &last) |
| Removes the elements pointed to by the iterators in the range [first, last). More...
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const typename ValueType::SharedPointer & | getFirstElement () const |
| Returns a const reference to the first element of the array. More...
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typename ValueType::SharedPointer & | getFirstElement () |
| Returns a non-const reference to the first element of the array. More...
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const typename ValueType::SharedPointer & | getLastElement () const |
| Returns a const reference to the last element of the array. More...
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typename ValueType::SharedPointer & | getLastElement () |
| Returns a non-const reference to the last element of the array. More...
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ConstElementIterator | getElementsBegin () const |
| Returns a constant iterator pointing to the beginning of the array. More...
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ElementIterator | getElementsBegin () |
| Returns a mutable iterator pointing to the beginning of the array. More...
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ConstElementIterator | getElementsEnd () const |
| Returns a constant iterator pointing to the end of the array. More...
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ElementIterator | getElementsEnd () |
| Returns a mutable iterator pointing to the end of the array. More...
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ConstElementIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the array. More...
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ElementIterator | begin () |
| Returns a mutable iterator pointing to the beginning of the array. More...
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ConstElementIterator | end () const |
| Returns a constant iterator pointing to the end of the array. More...
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ElementIterator | end () |
| Returns a mutable iterator pointing to the end of the array. More...
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ConstReverseElementIterator | getElementsReverseBegin () const |
| Returns a constant iterator pointing to the beginning of the reversed array. More...
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ReverseElementIterator | getElementsReverseBegin () |
| Returns a mutable iterator pointing to the beginning of the reversed array. More...
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ConstReverseElementIterator | getElementsReverseEnd () const |
| Returns a constant iterator pointing to the end of the reversed array. More...
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ReverseElementIterator | getElementsReverseEnd () |
| Returns a mutable iterator pointing to the end of the reversed array. More...
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const typename ValueType::SharedPointer & | getElement (std::size_t idx) const |
| Returns a const reference to the element at index idx. More...
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typename ValueType::SharedPointer & | getElement (std::size_t idx) |
| Returns a non-const reference to the element at index idx. More...
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void | setElement (std::size_t idx, const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer()) |
| Assigns a new value to the element specified by the index idx. More...
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const typename ValueType::SharedPointer & | operator[] (std::size_t idx) const |
| Returns a const reference to the element at index idx. More...
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typename ValueType::SharedPointer & | operator[] (std::size_t idx) |
| Returns a non-const reference to the element at index idx. More...
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