CDPL::Biomol::ResidueList Class Reference

Implements the extraction of residues in biological macromolecules. More...

#include <ResidueList.hpp>

Inheritance diagram for CDPL::Biomol::ResidueList:

Public Types
typedef std::shared_ptr< ResidueList >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated ResidueList instances. More...
Public Types inherited from CDPL::Chem::FragmentList
typedef std::shared_ptr< FragmentList >	SharedPointer
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< IndirectArray >	SharedPointer
	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< Array >	SharedPointer
	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
	ResidueList ()
	Constructs an empty ResidueList instance. More...
	ResidueList (const Chem::MolecularGraph &molgraph, unsigned int flags=AtomPropertyFlag::DEFAULT)
	Constructs a ResidueList instance that contains the residues of the molecular graph molgraph. More...
void	extract (const Chem::MolecularGraph &molgraph, unsigned int flags=AtomPropertyFlag::DEFAULT)
	Replaces the current list of residues by the residues in 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...
StorageType &	getData ()
const StorageType &	getData () const
BaseType &	getBase ()
	Returns a non-const reference to itself. More...
const BaseType &	getBase () 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 residues in biological macromolecules.

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<ResidueList> CDPL::Biomol::ResidueList::SharedPointer

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

Constructor & Destructor Documentation

ResidueList() [1/2]

CDPL::Biomol::ResidueList::ResidueList ( )

inline

Constructs an empty ResidueList instance.

ResidueList() [2/2]

CDPL::Biomol::ResidueList::ResidueList	(	const Chem::MolecularGraph &	molgraph,
		unsigned int	flags = AtomPropertyFlag::DEFAULT
	)

Constructs a ResidueList instance that contains the residues of the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to extract the residues.
flags	The set of atom properties uniquely identifying a residue.

Member Function Documentation

extract()

void CDPL::Biomol::ResidueList::extract	(	const Chem::MolecularGraph &	molgraph,
		unsigned int	flags = AtomPropertyFlag::DEFAULT
	)

Replaces the current list of residues by the residues in the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to extract the residues.
flags	The set of atom properties uniquely identifying a residue.

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

• ResidueList.hpp