Lookup table mapping (torsion type, terminal-atom-1 type, center-atom-1 type, center-atom-2 type, terminal-atom-2 type) quintuples to the three MMFF94 torsion-energy Fourier-series parameters (V1, V2, V3). More...

#include <MMFF94TorsionParameterTable.hpp>

Classes
class	Entry
	A single torsion parameter record. More...

Public Types
typedef std::shared_ptr< MMFF94TorsionParameterTable >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94TorsionParameterTable` 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
	MMFF94TorsionParameterTable ()
	Constructs an empty `MMFF94TorsionParameterTable` instance. More...

void	addEntry (unsigned int tor_type_idx, unsigned int term_atom1_type, unsigned int ctr_atom1_type, unsigned int ctr_atom2_type, unsigned int term_atom2_type, double tor_param1, double tor_param2, double tor_param3)
	Adds (or overwrites) the entry for the given (torsion type, terminal-atom 1, center-atom 1, center-atom 2, terminal-atom 2) quintuple. More...

const Entry &	getEntry (unsigned int tor_type_idx, unsigned int term_atom1_type, unsigned int ctr_atom1_type, unsigned int ctr_atom2_type, unsigned int term_atom2_type) const
	Returns the entry for the given (torsion type, terminal-atom 1, center-atom 1, center-atom 2, terminal-atom 2) quintuple. 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 tor_type_idx, unsigned int term_atom1_type, unsigned int ctr_atom1_type, unsigned int ctr_atom2_type, unsigned int term_atom2_type)
	Removes the entry for the given (torsion type, terminal-atom 1, center-atom 1, center-atom 2, terminal-atom 2) quintuple. 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 (unsigned int param_set)
	Loads the built-in default torsion parameter entries for the specified MMFF94 parameter set. More...

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

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

Detailed Description

Lookup table mapping (torsion type, terminal-atom-1 type, center-atom-1 type, center-atom-2 type, terminal-atom-2 type) quintuples to the three MMFF94 torsion-energy Fourier-series parameters (V1, V2, V3).

The table maintains separate process-wide defaults per MMFF94 parameter set (see Util::MMFF94ParameterSet).

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94TorsionParameterTable> CDPL::ForceField::MMFF94TorsionParameterTable::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94TorsionParameterTable instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const DataStorage::value_type&)>, DataStorage::const_iterator> CDPL::ForceField::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::EntryIterator

A mutable iterator over the entries of the table.

Constructor & Destructor Documentation

◆ MMFF94TorsionParameterTable()

CDPL::ForceField::MMFF94TorsionParameterTable::MMFF94TorsionParameterTable ( )

Constructs an empty MMFF94TorsionParameterTable instance.

Member Function Documentation

◆ addEntry()

void CDPL::ForceField::MMFF94TorsionParameterTable::addEntry	(	unsigned int	tor_type_idx,
		unsigned int	term_atom1_type,
		unsigned int	ctr_atom1_type,
		unsigned int	ctr_atom2_type,
		unsigned int	term_atom2_type,
		double	tor_param1,
		double	tor_param2,
		double	tor_param3
	)

Adds (or overwrites) the entry for the given (torsion type, terminal-atom 1, center-atom 1, center-atom 2, terminal-atom 2) quintuple.

Parameters

tor_type_idx	The MMFF94 torsion type index.
term_atom1_type	The numeric MMFF94 atom type of the first terminal atom.
ctr_atom1_type	The numeric MMFF94 atom type of the first center atom.
ctr_atom2_type	The numeric MMFF94 atom type of the second center atom.
term_atom2_type	The numeric MMFF94 atom type of the second terminal atom.
tor_param1	The torsion-energy parameter `V1`.
tor_param2	The torsion-energy parameter `V2`.
tor_param3	The torsion-energy parameter `V3`.

◆ getEntry()

const Entry& CDPL::ForceField::MMFF94TorsionParameterTable::getEntry	(	unsigned int	tor_type_idx,
		unsigned int	term_atom1_type,
		unsigned int	ctr_atom1_type,
		unsigned int	ctr_atom2_type,
		unsigned int	term_atom2_type
	)		const

Returns the entry for the given (torsion type, terminal-atom 1, center-atom 1, center-atom 2, terminal-atom 2) quintuple.

Parameters

tor_type_idx	The MMFF94 torsion type index.
term_atom1_type	The numeric MMFF94 atom type of the first terminal atom.
ctr_atom1_type	The numeric MMFF94 atom type of the first center atom.
ctr_atom2_type	The numeric MMFF94 atom type of the second center atom.
term_atom2_type	The numeric MMFF94 atom type of the second terminal 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::MMFF94TorsionParameterTable::getNumEntries ( ) const

Returns the number of entries in the table.

Returns: The entry count.

◆ clear()

void CDPL::ForceField::MMFF94TorsionParameterTable::clear ( )

Removes all entries from the table.

◆ removeEntry() [1/2]

bool CDPL::ForceField::MMFF94TorsionParameterTable::removeEntry	(	unsigned int	tor_type_idx,
		unsigned int	term_atom1_type,
		unsigned int	ctr_atom1_type,
		unsigned int	ctr_atom2_type,
		unsigned int	term_atom2_type
	)

Removes the entry for the given (torsion type, terminal-atom 1, center-atom 1, center-atom 2, terminal-atom 2) quintuple.

Parameters

tor_type_idx	The MMFF94 torsion type index.
term_atom1_type	The numeric MMFF94 atom type of the first terminal atom.
ctr_atom1_type	The numeric MMFF94 atom type of the first center atom.
ctr_atom2_type	The numeric MMFF94 atom type of the second center atom.
term_atom2_type	The numeric MMFF94 atom type of the second terminal atom.

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

◆ removeEntry() [2/2]

EntryIterator CDPL::ForceField::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::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::MMFF94TorsionParameterTable::load ( std::istream & is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ loadDefaults()

void CDPL::ForceField::MMFF94TorsionParameterTable::loadDefaults ( unsigned int param_set )

Loads the built-in default torsion parameter entries for the specified MMFF94 parameter set.

Parameters

param_set The Util::MMFF94ParameterSet identifier selecting which built-in defaults to load.

◆ set()

static void CDPL::ForceField::MMFF94TorsionParameterTable::set	(	const SharedPointer &	table,
		unsigned int	param_set
	)

static

Replaces the process-wide default table for param_set by table.

Parameters

table	The new default table (a `nullptr` resets to the built-in default).
param_set	The Util::MMFF94ParameterSet identifier selecting which default slot to replace.

◆ get()

static const SharedPointer& CDPL::ForceField::MMFF94TorsionParameterTable::get ( unsigned int param_set )

static

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

Parameters

param_set The Util::MMFF94ParameterSet identifier selecting which default slot to return.

Returns: A const reference to the selected default-table shared pointer.

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

MMFF94TorsionParameterTable.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

◆ EntryIterator

Constructor & Destructor Documentation

◆ MMFF94TorsionParameterTable()

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()