Lookup table mapping (terminal-atom-1 PTE row, center-atom PTE row, terminal-atom-2 PTE row) triples to fallback MMFF94 stretch-bend coupling force constants used when no atom-type-specific entry is available. More...

#include <MMFF94DefaultStretchBendParameterTable.hpp>

Classes
class	Entry
	A single PTE-row-based default stretch-bend parameter record. More...

Public Types
typedef std::shared_ptr< MMFF94DefaultStretchBendParameterTable >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94DefaultStretchBendParameterTable` 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
	MMFF94DefaultStretchBendParameterTable ()
	Constructs an empty `MMFF94DefaultStretchBendParameterTable` instance. More...

void	addEntry (unsigned int term_atom1_pte_row, unsigned int ctr_atom_pte_row, unsigned int term_atom2_pte_row, double ijk_force_const, double kji_force_const)
	Adds (or overwrites) the entry for the given (terminal-atom 1 PTE row, center-atom PTE row, terminal-atom 2 PTE row) triple. More...

const Entry &	getEntry (unsigned int term_atom1_pte_row, unsigned int ctr_atom_pte_row, unsigned int term_atom2_pte_row) const
	Returns the entry for the given (terminal-atom 1 PTE row, center-atom PTE row, terminal-atom 2 PTE row) 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 term_atom1_pte_row, unsigned int ctr_atom_pte_row, unsigned int term_atom2_pte_row)
	Removes the entry for the given (terminal-atom 1 PTE row, center-atom PTE row, terminal-atom 2 PTE row) 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 stretch-bend fallback 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 (terminal-atom-1 PTE row, center-atom PTE row, terminal-atom-2 PTE row) triples to fallback MMFF94 stretch-bend coupling force constants used when no atom-type-specific entry is available.

The PTE row of an atom is the row index in the periodic table of the elements. Two directional force constants are stored per entry (IJK and KJI) — see Util::MMFF94StretchBendParameterTable for the coupling semantics.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94DefaultStretchBendParameterTable> CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94DefaultStretchBendParameterTable instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const DataStorage::value_type&)>, DataStorage::const_iterator> CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::EntryIterator

A mutable iterator over the entries of the table.

Constructor & Destructor Documentation

◆ MMFF94DefaultStretchBendParameterTable()

CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::MMFF94DefaultStretchBendParameterTable ( )

Constructs an empty MMFF94DefaultStretchBendParameterTable instance.

Member Function Documentation

◆ addEntry()

void CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::addEntry	(	unsigned int	term_atom1_pte_row,
		unsigned int	ctr_atom_pte_row,
		unsigned int	term_atom2_pte_row,
		double	ijk_force_const,
		double	kji_force_const
	)

Adds (or overwrites) the entry for the given (terminal-atom 1 PTE row, center-atom PTE row, terminal-atom 2 PTE row) triple.

Parameters

term_atom1_pte_row	The PTE row of the first terminal atom.
ctr_atom_pte_row	The PTE row of the center atom.
term_atom2_pte_row	The PTE row of the second terminal atom.
ijk_force_const	The IJK stretch-bend force constant.
kji_force_const	The KJI stretch-bend force constant.

◆ getEntry()

const Entry& CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::getEntry	(	unsigned int	term_atom1_pte_row,
		unsigned int	ctr_atom_pte_row,
		unsigned int	term_atom2_pte_row
	)		const

Returns the entry for the given (terminal-atom 1 PTE row, center-atom PTE row, terminal-atom 2 PTE row) triple.

Parameters

term_atom1_pte_row	The PTE row of the first terminal atom.
ctr_atom_pte_row	The PTE row of the center atom.
term_atom2_pte_row	The PTE row 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::MMFF94DefaultStretchBendParameterTable::getNumEntries ( ) const

Returns the number of entries in the table.

Returns: The entry count.

◆ clear()

void CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::clear ( )

Removes all entries from the table.

◆ removeEntry() [1/2]

bool CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::removeEntry	(	unsigned int	term_atom1_pte_row,
		unsigned int	ctr_atom_pte_row,
		unsigned int	term_atom2_pte_row
	)

Removes the entry for the given (terminal-atom 1 PTE row, center-atom PTE row, terminal-atom 2 PTE row) triple.

Parameters

term_atom1_pte_row	The PTE row of the first terminal atom.
ctr_atom_pte_row	The PTE row of the center atom.
term_atom2_pte_row	The PTE row 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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::load ( std::istream & is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ loadDefaults()

void CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::loadDefaults ( )

Loads the built-in default stretch-bend fallback entries.

◆ set()

static void CDPL::ForceField::MMFF94DefaultStretchBendParameterTable::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::MMFF94DefaultStretchBendParameterTable::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:

MMFF94DefaultStretchBendParameterTable.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

◆ EntryIterator

Constructor & Destructor Documentation

◆ MMFF94DefaultStretchBendParameterTable()

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()