Lookup table mapping (bond type, atom-type 1, atom-type 2) triples to MMFF94 bond charge increments. More...

#include <MMFF94BondChargeIncrementTable.hpp>

Classes
class	Entry
	A single bond charge increment table record. 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 (or overwrites) the entry for the given (bond type, atom type 1, atom type 2) triple. More...

const Entry &	getEntry (unsigned int bond_type_idx, unsigned int atom1_type, unsigned int atom2_type) const
	Returns the entry for the given (bond type, atom type 1, atom type 2) triple. 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 for the given (bond type, atom type 1, atom type 2) triple. 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 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

Lookup table mapping (bond type, atom-type 1, atom-type 2) triples to MMFF94 bond charge increments.

The charge increment is applied to atom 1 (and its negative to atom 2) when partitioning partial atomic charges along bonded pairs in the MMFF94 charge model.

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 (or overwrites) the entry for the given (bond type, atom type 1, atom type 2) triple.

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 the entry for the given (bond type, atom type 1, atom type 2) triple.

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 (whose operator bool() returns false) if no match 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 for the given (bond type, atom type 1, atom type 2) triple.

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 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 (a 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 const reference to the default-table shared pointer.

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()