Data structure for the storage and lookup of MMFF94 stretch-bend interaction parameters. More...

#include <MMFF94StretchBendParameterTable.hpp>

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

Public Types
typedef std::shared_ptr< MMFF94StretchBendParameterTable >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94StretchBendParameterTable` 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
	MMFF94StretchBendParameterTable ()
	Constructs an empty `MMFF94StretchBendParameterTable` instance. More...

void	addEntry (unsigned int sb_type_idx, unsigned int term_atom1_type, unsigned int ctr_atom_type, unsigned int term_atom2_type, double ijk_force_const, double kji_force_const)
	Adds a new (or overwrites an existing) entry for the given query and parameter values. More...

const Entry &	getEntry (unsigned int sb_type_idx, unsigned int term_atom1_type, unsigned int ctr_atom_type, unsigned int term_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 sb_type_idx, unsigned int term_atom1_type, unsigned int ctr_atom_type, unsigned int term_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 stretch-bend parameter 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 stretch-bend interaction parameters.

Two directional force constants are stored per entry: IJK couples the bond i-j to the angle i-j-k, and KJI couples the bond j-k to the same angle.

See also: [MMFF94]

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94StretchBendParameterTable> CDPL::ForceField::MMFF94StretchBendParameterTable::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94StretchBendParameterTable instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const DataStorage::value_type&)>, DataStorage::const_iterator> CDPL::ForceField::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::EntryIterator

A mutable iterator over the entries of the table.

Constructor & Destructor Documentation

◆ MMFF94StretchBendParameterTable()

CDPL::ForceField::MMFF94StretchBendParameterTable::MMFF94StretchBendParameterTable ( )

Constructs an empty MMFF94StretchBendParameterTable instance.

Member Function Documentation

◆ addEntry()

void CDPL::ForceField::MMFF94StretchBendParameterTable::addEntry	(	unsigned int	sb_type_idx,
		unsigned int	term_atom1_type,
		unsigned int	ctr_atom_type,
		unsigned int	term_atom2_type,
		double	ijk_force_const,
		double	kji_force_const
	)

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

Parameters

sb_type_idx	The MMFF94 stretch-bend type index.
term_atom1_type	The numeric MMFF94 atom type of the first terminal atom.
ctr_atom_type	The numeric MMFF94 atom type of the center atom.
term_atom2_type	The numeric MMFF94 atom type 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::MMFF94StretchBendParameterTable::getEntry	(	unsigned int	sb_type_idx,
		unsigned int	term_atom1_type,
		unsigned int	ctr_atom_type,
		unsigned int	term_atom2_type
	)		const

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

Parameters

sb_type_idx	The MMFF94 stretch-bend type index.
term_atom1_type	The numeric MMFF94 atom type of the first terminal atom.
ctr_atom_type	The numeric MMFF94 atom type of the 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 if no matching entry exists.

◆ getNumEntries()

std::size_t CDPL::ForceField::MMFF94StretchBendParameterTable::getNumEntries ( ) const

Returns the number of entries in the table.

Returns: The entry count.

◆ clear()

void CDPL::ForceField::MMFF94StretchBendParameterTable::clear ( )

Removes all entries from the table.

◆ removeEntry() [1/2]

bool CDPL::ForceField::MMFF94StretchBendParameterTable::removeEntry	(	unsigned int	sb_type_idx,
		unsigned int	term_atom1_type,
		unsigned int	ctr_atom_type,
		unsigned int	term_atom2_type
	)

Removes the entry matching the specified query values.

Parameters

sb_type_idx	The MMFF94 stretch-bend type index.
term_atom1_type	The numeric MMFF94 atom type of the first terminal atom.
ctr_atom_type	The numeric MMFF94 atom type of the 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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::load ( std::istream & is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ loadDefaults()

void CDPL::ForceField::MMFF94StretchBendParameterTable::loadDefaults ( )

Loads the built-in default MMFF94 stretch-bend parameter entries.

◆ set()

static void CDPL::ForceField::MMFF94StretchBendParameterTable::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::MMFF94StretchBendParameterTable::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:

MMFF94StretchBendParameterTable.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

◆ EntryIterator

Constructor & Destructor Documentation

◆ MMFF94StretchBendParameterTable()

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()