Chemical Data Processing Library C++ API - Version 1.1.1
Public Types | Public Member Functions | List of all members
CDPL::ForceField::MMFF94AromaticSSSRSubset Class Reference

Implements the extraction of all rings in the SSSR of a molecular graph that are aromatic according to MMFF94 conventions. More...

#include <MMFF94AromaticSSSRSubset.hpp>

+ Inheritance diagram for CDPL::ForceField::MMFF94AromaticSSSRSubset:

Public Types

typedef std::shared_ptr< MMFF94AromaticSSSRSubsetSharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94AromaticSSSRSubset instances. More...
 
- Public Types inherited from CDPL::Chem::FragmentList
typedef std::shared_ptr< FragmentListSharedPointer
 
- Public Types inherited from CDPL::Util::IndirectArray< Fragment >
typedef Array< typename ValueType::SharedPointer > BaseType
 The type of the public Array<PointerType> base class storing the pointer elements. More...
 
typedef Fragment ElementType
 The type of the object that is obtained after dereferenciation of a stored pointer element. More...
 
typedef std::shared_ptr< IndirectArraySharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated IndirectArray instances. More...
 
typedef boost::transform_iterator< DerefFunc, typename BaseType::ConstElementIterator, const Fragment & > ConstElementIterator
 A constant random access iterator used to iterate over the pointed-to objects. More...
 
typedef boost::transform_iterator< DerefFunc, typename BaseType::ConstReverseElementIterator, const Fragment & > ConstReverseElementIterator
 A constant random access iterator used to iterate over the pointed-to objects in reverse order. More...
 
typedef boost::transform_iterator< DerefFunc, typename BaseType::ElementIterator, Fragment & > ElementIterator
 A mutable random access iterator used to iterate over the pointed-to objects. More...
 
typedef boost::transform_iterator< DerefFunc, typename BaseType::ReverseElementIterator, Fragment & > ReverseElementIterator
 A mutable random access iterator used to iterate over the pointed-to objects in reverse order. More...
 
- Public Types inherited from CDPL::Util::Array< typename ValueType::SharedPointer >
typedef std::vector< typename ValueType::SharedPointer > StorageType
 
typedef std::shared_ptr< ArraySharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated Array instances. More...
 
typedef typename ValueType::SharedPointer ElementType
 The type of objects stored by the array. More...
 
typedef std::size_t SizeType
 The type of objects stored by the array. More...
 
typedef Array BaseType
 Specifies for derived classes the type of the Array base class. More...
 
typedef StorageType::const_iterator ConstElementIterator
 A constant random access iterator used to iterate over the elements of the array. More...
 
typedef StorageType::const_reverse_iterator ConstReverseElementIterator
 A constant random access iterator used to iterate over the elements of the array in reverse order. More...
 
typedef StorageType::iterator ElementIterator
 A mutable random access iterator used to iterate over the elements of the array. More...
 
typedef StorageType::reverse_iterator ReverseElementIterator
 A mutable random access iterator used to iterate over the elements of the array in reverse order. More...
 

Public Member Functions

 MMFF94AromaticSSSRSubset ()
 Constructs an empty MMFF94AromaticSSSRSubset instance. More...
 
 MMFF94AromaticSSSRSubset (const Chem::MolecularGraph &molgraph)
 Construct a MMFF94AromaticSSSRSubset instance that contains all aromatic rings of the SSSR of the molecular graph molgraph. More...
 
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...
 
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...
 
- Public Member Functions inherited from CDPL::Util::IndirectArray< Fragment >
 IndirectArray ()
 Creates an empty array. More...
 
 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...
 
 IndirectArray (const InputIter &first, const InputIter &last)
 Creates and initializes the array with copies of the pointers in the range [first, last). More...
 
virtual ~IndirectArray ()
 Virtual destructor. More...
 
ElementIterator insertElement (const ElementIterator &it, const typename ValueType::SharedPointer &ptr)
 Inserts a new element before the location specified by the iterator it. More...
 
void insertElement (std::size_t idx, const Fragment &value=Fragment())
 Inserts a new element before the location specified by the index idx. More...
 
ElementIterator insertElement (const ElementIterator &it, const Fragment &value=Fragment())
 Inserts a new element before the location specified by the iterator it. More...
 
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...
 
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...
 
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...
 
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...
 
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...
 
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...
 
ElementIterator removeElement (const ElementIterator &it)
 Removes the element at the position specified by the iterator it. More...
 
void removeElement (std::size_t idx)
 Removes the element at the position specified by the index idx. More...
 
ElementIterator removeElement (const ElementIterator &it)
 Removes the element at the position specified by the iterator it. More...
 
ElementIterator removeElements (const ElementIterator &first, const ElementIterator &last)
 Removes the elements pointed to by the iterators in the range [first, last). More...
 
ElementIterator removeElements (const ElementIterator &first, const ElementIterator &last)
 Removes the elements pointed to by the iterators in the range [first, last). More...
 
const Fragment & getFirstElement () const
 Returns a const reference to the object pointed to by the first element of the array. More...
 
Fragment & getFirstElement ()
 Returns a non-const reference to the object pointed to by the first element of the array. More...
 
const Fragment & getLastElement () const
 Returns a const reference to the object pointed to by the last element of the array. More...
 
Fragment & getLastElement ()
 Returns a non-const reference to the object pointed to by the last element of the array. More...
 
ConstElementIterator getElementsBegin () const
 Returns a constant iterator over the pointed-to objects that points to the beginning of the array. More...
 
ElementIterator getElementsBegin ()
 Returns a mutable iterator over the pointed-to objects that points to the beginning of the array. More...
 
ConstElementIterator getElementsEnd () const
 Returns a constant iterator over the pointed-to objects that points to the end of the array. More...
 
ElementIterator getElementsEnd ()
 Returns a mutable iterator over the pointed-to objects that points to the end of the array. More...
 
ConstElementIterator begin () const
 Returns a constant iterator over the pointed-to objects that points to the beginning of the array. More...
 
ElementIterator begin ()
 Returns a mutable iterator over the pointed-to objects that points to the beginning of the array. More...
 
ConstElementIterator end () const
 Returns a constant iterator over the pointed-to objects that points to the end of the array. More...
 
ElementIterator end ()
 Returns a mutable iterator over the pointed-to objects that points to the end of the array. More...
 
ConstReverseElementIterator getElementsReverseBegin () const
 Returns a constant iterator over the pointed-to objects that points to the beginning of the reversed array. More...
 
ReverseElementIterator getElementsReverseBegin ()
 Returns a mutable iterator over the pointed-to objects that points to the beginning of the reversed array. More...
 
ConstReverseElementIterator getElementsReverseEnd () const
 Returns a constant iterator over the pointed-to objects that points to the end of the reversed array. More...
 
ReverseElementIterator getElementsReverseEnd ()
 Returns a mutable iterator over the pointed-to objects that points to the end of the reversed array. More...
 
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...
 
Fragment & getElement (std::size_t idx)
 Returns a non-const reference to the object pointed-to by the pointer element at index idx. More...
 
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...
 
Fragment & operator[] (std::size_t idx)
 Returns a non-const reference to the object pointed-to by the pointer element at index idx. More...
 
- Public Member Functions inherited from CDPL::Util::Array< typename ValueType::SharedPointer >
 Array ()
 Creates an empty array. More...
 
 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...
 
 Array (const InputIter &first, const InputIter &last)
 Creates and initializes the array with copies of the elements in the range [first, last). More...
 
virtual ~Array ()
 Virtual destructor. More...
 
StorageTypegetData ()
 
const StorageTypegetData () const
 
BaseTypegetBase ()
 Returns a non-const reference to itself. More...
 
const BaseTypegetBase () const
 Returns a const reference to itself. More...
 
std::size_t getSize () const
 Returns the number of elements stored in the array. More...
 
std::size_t size () const
 Returns the number of elements stored in the array. More...
 
bool isEmpty () const
 Tells whether the array is empty (getSize() == 0). More...
 
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...
 
void reserve (std::size_t num_elem)
 Preallocates memory for (at least) num_elem elements. More...
 
std::size_t getCapacity () const
 Returns the number of elements for which memory has been allocated. More...
 
void clear ()
 Erases all elements. More...
 
void swap (Array &array)
 Swaps the contents with array. More...
 
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...
 
void assign (const InputIter &first, const InputIter &last)
 This function fills a vector with copies of the elements in the range [first, last). More...
 
void addElement (const typename ValueType::SharedPointer &value=typename ValueType::SharedPointer())
 Inserts a new element at the end of the array. More...
 
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...
 
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...
 
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...
 
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...
 
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...
 
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...
 
void popLastElement ()
 Removes the last element of the array. More...
 
void removeElement (std::size_t idx)
 Removes the element at the position specified by the index idx. More...
 
ElementIterator removeElement (const ElementIterator &it)
 Removes the element at the position specified by the iterator it. More...
 
ElementIterator removeElements (const ElementIterator &first, const ElementIterator &last)
 Removes the elements pointed to by the iterators in the range [first, last). More...
 
const typename ValueType::SharedPointer & getFirstElement () const
 Returns a const reference to the first element of the array. More...
 
typename ValueType::SharedPointer & getFirstElement ()
 Returns a non-const reference to the first element of the array. More...
 
const typename ValueType::SharedPointer & getLastElement () const
 Returns a const reference to the last element of the array. More...
 
typename ValueType::SharedPointer & getLastElement ()
 Returns a non-const reference to the last element of the array. More...
 
ConstElementIterator getElementsBegin () const
 Returns a constant iterator pointing to the beginning of the array. More...
 
ElementIterator getElementsBegin ()
 Returns a mutable iterator pointing to the beginning of the array. More...
 
ConstElementIterator getElementsEnd () const
 Returns a constant iterator pointing to the end of the array. More...
 
ElementIterator getElementsEnd ()
 Returns a mutable iterator pointing to the end of the array. More...
 
ConstElementIterator begin () const
 Returns a constant iterator pointing to the beginning of the array. More...
 
ElementIterator begin ()
 Returns a mutable iterator pointing to the beginning of the array. More...
 
ConstElementIterator end () const
 Returns a constant iterator pointing to the end of the array. More...
 
ElementIterator end ()
 Returns a mutable iterator pointing to the end of the array. More...
 
ConstReverseElementIterator getElementsReverseBegin () const
 Returns a constant iterator pointing to the beginning of the reversed array. More...
 
ReverseElementIterator getElementsReverseBegin ()
 Returns a mutable iterator pointing to the beginning of the reversed array. More...
 
ConstReverseElementIterator getElementsReverseEnd () const
 Returns a constant iterator pointing to the end of the reversed array. More...
 
ReverseElementIterator getElementsReverseEnd ()
 Returns a mutable iterator pointing to the end of the reversed array. More...
 
const typename ValueType::SharedPointer & getElement (std::size_t idx) const
 Returns a const reference to the element at index idx. More...
 
typename ValueType::SharedPointer & getElement (std::size_t idx)
 Returns a non-const reference to the element at index idx. More...
 
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...
 
const typename ValueType::SharedPointer & operator[] (std::size_t idx) const
 Returns a const reference to the element at index idx. More...
 
typename ValueType::SharedPointer & operator[] (std::size_t idx)
 Returns a non-const reference to the element at index idx. More...
 

Additional Inherited Members

- Protected Member Functions inherited from CDPL::Util::Array< typename ValueType::SharedPointer >
void checkIfNonEmpty () const
 
void checkIndex (std::size_t idx, bool allow_end) const
 
void checkIterator (const ElementIterator &it, bool allow_end)
 
void checkIterator (const ConstElementIterator &it, bool allow_end) const
 

Detailed Description

Implements the extraction of all rings in the SSSR of a molecular graph that are aromatic according to MMFF94 conventions.

Member Typedef Documentation

◆ SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94AromaticSSSRSubset instances.

Constructor & Destructor Documentation

◆ MMFF94AromaticSSSRSubset() [1/2]

CDPL::ForceField::MMFF94AromaticSSSRSubset::MMFF94AromaticSSSRSubset ( )
inline

Constructs an empty MMFF94AromaticSSSRSubset instance.

◆ MMFF94AromaticSSSRSubset() [2/2]

CDPL::ForceField::MMFF94AromaticSSSRSubset::MMFF94AromaticSSSRSubset ( const Chem::MolecularGraph molgraph)

Construct a MMFF94AromaticSSSRSubset instance that contains all aromatic rings of the SSSR of the molecular graph molgraph.

Parameters
molgraphThe molecular graph for which to extract the aromatic rings.

Member Function Documentation

◆ extract() [1/2]

void CDPL::ForceField::MMFF94AromaticSSSRSubset::extract ( const Chem::MolecularGraph molgraph)

Replaces the current set of rings by the aromatic rings in the SSSR of the molecular graph molgraph.

Parameters
molgraphThe molecular graph for which to extract the aromatic rings.

◆ extract() [2/2]

void CDPL::ForceField::MMFF94AromaticSSSRSubset::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.

Parameters
molgraphThe molecular graph for which to extract the aromatic rings.
sssrThe SSSR of the molecular graph molgraph.

The documentation for this class was generated from the following file: