Data structure for the storage and lookup of MMFF94 bond charge increments. More...

#include <MMFF94BondChargeIncrementTable.hpp>

Classes
class	Entry
	Data structure for the storage of values associated with a single table entry. More...

Public Types
typedef std::shared_ptr< MMFF94BondChargeIncrementTable >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94BondChargeIncrementTable` instances. More...

typedef boost::transform_iterator< std::function< const Entry &(const DataStorage::value_type &)>, DataStorage::const_iterator >	ConstEntryIterator
	A constant iterator over the entries of the table. More...

typedef boost::transform_iterator< std::function< Entry &(DataStorage::value_type &)>, DataStorage::iterator >	EntryIterator
	A mutable iterator over the entries of the table. More...

Public Member Functions
	MMFF94BondChargeIncrementTable ()
	Constructs an empty `MMFF94BondChargeIncrementTable` instance. More...

void	addEntry (unsigned int bond_type_idx, unsigned int atom1_type, unsigned int atom2_type, double bond_chg_inc)
	Adds a new (or overwrites an existing) entry for the given query values and charge increment. More...

const Entry &	getEntry (unsigned int bond_type_idx, unsigned int atom1_type, unsigned int atom2_type) const
	Returns a reference to the entry matching the specified query values. More...

std::size_t	getNumEntries () const
	Returns the number of entries in the table. More...

void	clear ()
	Removes all entries from the table. More...

bool	removeEntry (unsigned int bond_type_idx, unsigned int atom1_type, unsigned int atom2_type)
	Removes the entry matching the specified query values. More...

EntryIterator	removeEntry (const EntryIterator &it)
	Removes the entry pointed to by the iterator it. More...

ConstEntryIterator	getEntriesBegin () const
	Returns a constant iterator pointing to the beginning of the entry list. More...

ConstEntryIterator	getEntriesEnd () const
	Returns a constant iterator pointing one past the last entry. More...

EntryIterator	getEntriesBegin ()
	Returns a mutable iterator pointing to the beginning of the entry list. More...

EntryIterator	getEntriesEnd ()
	Returns a mutable iterator pointing one past the last entry. More...

ConstEntryIterator	begin () const
	Returns a constant iterator pointing to the beginning of the entry list (alias of getEntriesBegin()). More...

ConstEntryIterator	end () const
	Returns a constant iterator pointing one past the last entry (alias of getEntriesEnd()). More...

EntryIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the entry list (alias of getEntriesBegin()). More...

EntryIterator	end ()
	Returns a mutable iterator pointing one past the last entry (alias of getEntriesEnd()). More...

void	load (std::istream &is)
	Loads table entries from the input stream is. More...

void	loadDefaults ()
	Loads the built-in default MMFF94 bond charge increment entries. More...

Static Public Member Functions
static void	set (const SharedPointer &table)
	Replaces the process-wide default table by table. More...

static const SharedPointer &	get ()
	Returns the process-wide default table (lazily initialized on first call). More...

Detailed Description

Data structure for the storage and lookup of MMFF94 bond charge increments.

The charge increment is applied to the first atom (and its negative to the second atom) when partitioning partial atomic charges along bonded pairs in the MMFF94 charge model.

See also: [MMFF94]

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94BondChargeIncrementTable> CDPL::ForceField::MMFF94BondChargeIncrementTable::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94BondChargeIncrementTable instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const DataStorage::value_type&)>, DataStorage::const_iterator> CDPL::ForceField::MMFF94BondChargeIncrementTable::ConstEntryIterator

A constant iterator over the entries of the table.

◆ EntryIterator

typedef boost::transform_iterator<std::function<Entry&(DataStorage::value_type&)>, DataStorage::iterator> CDPL::ForceField::MMFF94BondChargeIncrementTable::EntryIterator

A mutable iterator over the entries of the table.

Constructor & Destructor Documentation

◆ MMFF94BondChargeIncrementTable()

CDPL::ForceField::MMFF94BondChargeIncrementTable::MMFF94BondChargeIncrementTable ( )

Constructs an empty MMFF94BondChargeIncrementTable instance.

Member Function Documentation

◆ addEntry()

void CDPL::ForceField::MMFF94BondChargeIncrementTable::addEntry	(	unsigned int	bond_type_idx,
		unsigned int	atom1_type,
		unsigned int	atom2_type,
		double	bond_chg_inc
	)

Adds a new (or overwrites an existing) entry for the given query values and charge increment.

Parameters

bond_type_idx	The MMFF94 bond type index.
atom1_type	The numeric MMFF94 atom type of the first bonded atom.
atom2_type	The numeric MMFF94 atom type of the second bonded atom.
bond_chg_inc	The bond charge increment value.

◆ getEntry()

const Entry& CDPL::ForceField::MMFF94BondChargeIncrementTable::getEntry	(	unsigned int	bond_type_idx,
		unsigned int	atom1_type,
		unsigned int	atom2_type
	)		const

Returns a reference to the entry matching the specified query values.

Parameters

bond_type_idx	The MMFF94 bond type index.
atom1_type	The numeric MMFF94 atom type of the first bonded atom.
atom2_type	The numeric MMFF94 atom type of the second bonded atom.

Returns: A const reference to the matching entry or to an uninitialized entry if no matching entry exists.

◆ getNumEntries()

std::size_t CDPL::ForceField::MMFF94BondChargeIncrementTable::getNumEntries ( ) const

Returns the number of entries in the table.

Returns: The entry count.

◆ clear()

void CDPL::ForceField::MMFF94BondChargeIncrementTable::clear ( )

Removes all entries from the table.

◆ removeEntry() [1/2]

bool CDPL::ForceField::MMFF94BondChargeIncrementTable::removeEntry	(	unsigned int	bond_type_idx,
		unsigned int	atom1_type,
		unsigned int	atom2_type
	)

Removes the entry matching the specified query values.

Parameters

bond_type_idx	The MMFF94 bond type index.
atom1_type	The numeric MMFF94 atom type of the first bonded atom.
atom2_type	The numeric MMFF94 atom type of the second bonded atom.

Returns: true if a matching entry was removed, and false if no such entry existed.

◆ removeEntry() [2/2]

EntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::removeEntry ( const EntryIterator & it )

Removes the entry pointed to by the iterator it.

Parameters

it	An iterator pointing to the entry to remove.

Returns: An iterator pointing to the entry immediately following the removed one.

◆ getEntriesBegin() [1/2]

ConstEntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::getEntriesBegin ( ) const

Returns a constant iterator pointing to the beginning of the entry list.

Returns: A constant iterator to the first entry.

◆ getEntriesEnd() [1/2]

ConstEntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::getEntriesEnd ( ) const

Returns a constant iterator pointing one past the last entry.

Returns: A constant iterator to the end of the entry list.

◆ getEntriesBegin() [2/2]

EntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::getEntriesBegin ( )

Returns a mutable iterator pointing to the beginning of the entry list.

Returns: A mutable iterator to the first entry.

◆ getEntriesEnd() [2/2]

EntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::getEntriesEnd ( )

Returns a mutable iterator pointing one past the last entry.

Returns: A mutable iterator to the end of the entry list.

◆ begin() [1/2]

ConstEntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::begin ( ) const

Returns a constant iterator pointing to the beginning of the entry list (alias of getEntriesBegin()).

Returns: A constant iterator to the first entry.

◆ end() [1/2]

ConstEntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::end ( ) const

Returns a constant iterator pointing one past the last entry (alias of getEntriesEnd()).

Returns: A constant iterator to the end of the entry list.

◆ begin() [2/2]

EntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::begin ( )

Returns a mutable iterator pointing to the beginning of the entry list (alias of getEntriesBegin()).

Returns: A mutable iterator to the first entry.

◆ end() [2/2]

EntryIterator CDPL::ForceField::MMFF94BondChargeIncrementTable::end ( )

Returns a mutable iterator pointing one past the last entry (alias of getEntriesEnd()).

Returns: A mutable iterator to the end of the entry list.

◆ load()

void CDPL::ForceField::MMFF94BondChargeIncrementTable::load ( std::istream & is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ loadDefaults()

void CDPL::ForceField::MMFF94BondChargeIncrementTable::loadDefaults ( )

Loads the built-in default MMFF94 bond charge increment entries.

◆ set()

static void CDPL::ForceField::MMFF94BondChargeIncrementTable::set ( const SharedPointer & table )

static

Replaces the process-wide default table by table.

Parameters

table The new default table (nullptr resets to the built-in default).

◆ get()

static const SharedPointer& CDPL::ForceField::MMFF94BondChargeIncrementTable::get ( )

static

Returns the process-wide default table (lazily initialized on first call).

Returns: A shared pointer to the default table.

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

MMFF94BondChargeIncrementTable.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

◆ EntryIterator

Constructor & Destructor Documentation

◆ MMFF94BondChargeIncrementTable()

Member Function Documentation

◆ addEntry()

◆ getEntry()

◆ getNumEntries()

◆ clear()

◆ removeEntry() [1/2]

◆ removeEntry() [2/2]

◆ getEntriesBegin() [1/2]

◆ getEntriesEnd() [1/2]

◆ getEntriesBegin() [2/2]

◆ getEntriesEnd() [2/2]

◆ begin() [1/2]

◆ end() [1/2]

◆ begin() [2/2]

◆ end() [2/2]

◆ load()

◆ loadDefaults()

◆ set()

◆ get()