Lookup table mapping symbolic MMFF94 atom types to their formal-charge definitions used by the MMFF94 charge model. More...

#include <MMFF94FormalAtomChargeDefinitionTable.hpp>

Classes
class	Entry
	A single formal-charge definition. More...

Public Types
typedef std::shared_ptr< MMFF94FormalAtomChargeDefinitionTable >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94FormalAtomChargeDefinitionTable` 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
	MMFF94FormalAtomChargeDefinitionTable ()
	Constructs an empty `MMFF94FormalAtomChargeDefinitionTable` instance. More...

void	addEntry (const std::string &atom_type, std::size_t ass_mode, double charge, const std::string &nbr_types)
	Adds (or overwrites) the formal-charge definition for the symbolic atom type atom_type. More...

const Entry &	getEntry (const std::string &atom_type) const
	Returns the entry for the symbolic MMFF94 atom type atom_type. 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 (const std::string &atom_type)
	Removes the entry for the symbolic atom type atom_type. 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 formal-charge definitions. 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 symbolic MMFF94 atom types to their formal-charge definitions used by the MMFF94 charge model.

Each entry specifies a formal charge plus an assignment-mode flag that controls how the charge is distributed across the atom and its neighbours of selected types.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94FormalAtomChargeDefinitionTable> CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94FormalAtomChargeDefinitionTable instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const DataStorage::value_type&)>, DataStorage::const_iterator> CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::EntryIterator

A mutable iterator over the entries of the table.

Constructor & Destructor Documentation

◆ MMFF94FormalAtomChargeDefinitionTable()

CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::MMFF94FormalAtomChargeDefinitionTable ( )

Constructs an empty MMFF94FormalAtomChargeDefinitionTable instance.

Member Function Documentation

◆ addEntry()

void CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::addEntry	(	const std::string &	atom_type,
		std::size_t	ass_mode,
		double	charge,
		const std::string &	nbr_types
	)

Adds (or overwrites) the formal-charge definition for the symbolic atom type atom_type.

Parameters

atom_type	The symbolic MMFF94 atom type.
ass_mode	The charge-assignment mode flag.
charge	The formal charge value.
nbr_types	A whitespace-separated list of neighbour atom types used by the assignment.

◆ getEntry()

const Entry& CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::getEntry ( const std::string & atom_type ) const

Returns the entry for the symbolic MMFF94 atom type atom_type.

Parameters

atom_type The symbolic MMFF94 atom type.

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::MMFF94FormalAtomChargeDefinitionTable::getNumEntries ( ) const

Returns the number of entries in the table.

Returns: The entry count.

◆ clear()

void CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::clear ( )

Removes all entries from the table.

◆ removeEntry() [1/2]

bool CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::removeEntry ( const std::string & atom_type )

Removes the entry for the symbolic atom type atom_type.

Parameters

atom_type The symbolic MMFF94 atom type.

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

◆ removeEntry() [2/2]

EntryIterator CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::load ( std::istream & is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ loadDefaults()

void CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::loadDefaults ( )

Loads the built-in default formal-charge definitions.

◆ set()

static void CDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::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::MMFF94FormalAtomChargeDefinitionTable::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:

MMFF94FormalAtomChargeDefinitionTable.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

◆ EntryIterator

Constructor & Destructor Documentation

◆ MMFF94FormalAtomChargeDefinitionTable()

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()