Lookup table mapping numeric MMFF94 atom types to per-atom-type Van der Waals parameters (atomic polarizability, effective electron number, scaling factors A/G, and H-donor/-acceptor classification). More...

#include <MMFF94VanDerWaalsParameterTable.hpp>

Classes
class	Entry
	A single per-atom-type Van der Waals parameter record. More...

Public Types
typedef std::shared_ptr< MMFF94VanDerWaalsParameterTable >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94VanDerWaalsParameterTable` instances. More...

typedef MMFF94VanDerWaalsInteraction::HDonorAcceptorType	HDonorAcceptorType
	Alias for the H-donor/-acceptor classification enum defined on MMFF94VanDerWaalsInteraction. 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
	MMFF94VanDerWaalsParameterTable ()
	Constructs an empty `MMFF94VanDerWaalsParameterTable` instance. More...

void	addEntry (unsigned int atom_type, double atom_pol, double eff_el_num, double fact_a, double fact_g, HDonorAcceptorType don_acc_type)
	Adds (or overwrites) the entry for the numeric MMFF94 atom type atom_type. More...

const Entry &	getEntry (unsigned int atom_type) const
	Returns the entry for the numeric 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 (unsigned int atom_type)
	Removes the entry for the numeric MMFF94 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	setExponent (double value)
	Sets the global exponent used in the buffered 14-7 Van der Waals energy expression. More...

void	setBeta (double value)
	Sets the global beta value used in the buffered 14-7 Van der Waals energy expression. More...

void	setFactorB (double value)
	Sets the global B factor used in the buffered 14-7 Van der Waals energy expression. More...

void	setFactorDARAD (double value)
	Sets the global DARAD factor used in the buffered 14-7 Van der Waals energy expression. More...

void	setFactorDAEPS (double value)
	Sets the global DAEPS factor used in the buffered 14-7 Van der Waals energy expression. More...

double	getExponent () const
	Returns the exponent used in the calculation of Van der Waals interaction energies. More...

double	getFactorB () const
	Returns the value of the B factor used in the calculation of Van der Waals interaction energies. More...

double	getBeta () const
	Returns the value of beta used in the calculation of Van der Waals interaction energies. More...

double	getFactorDARAD () const
	Returns the value of the DARAD factor used in the calculation of Van der Waals interaction energies. More...

double	getFactorDAEPS () const
	Returns the value of the DAEPS factor used in the calculation of Van der Waals interaction energies. More...

void	load (std::istream &is)
	Loads table entries from the input stream is. More...

void	loadDefaults ()
	Loads the built-in default Van der Waals parameter entries and global scalar parameters. 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 numeric MMFF94 atom types to per-atom-type Van der Waals parameters (atomic polarizability, effective electron number, scaling factors A/G, and H-donor/-acceptor classification).

In addition to the per-atom-type entries, the table also stores the five global scalar parameters (exponent, B, beta, DARAD, DAEPS) used by the buffered 14-7 MMFF94 Van der Waals energy expression.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94VanDerWaalsParameterTable> CDPL::ForceField::MMFF94VanDerWaalsParameterTable::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94VanDerWaalsParameterTable instances.

◆ HDonorAcceptorType

typedef MMFF94VanDerWaalsInteraction::HDonorAcceptorType CDPL::ForceField::MMFF94VanDerWaalsParameterTable::HDonorAcceptorType

Alias for the H-donor/-acceptor classification enum defined on MMFF94VanDerWaalsInteraction.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const DataStorage::value_type&)>, DataStorage::const_iterator> CDPL::ForceField::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::EntryIterator

A mutable iterator over the entries of the table.

Constructor & Destructor Documentation

◆ MMFF94VanDerWaalsParameterTable()

CDPL::ForceField::MMFF94VanDerWaalsParameterTable::MMFF94VanDerWaalsParameterTable ( )

Constructs an empty MMFF94VanDerWaalsParameterTable instance.

Member Function Documentation

◆ addEntry()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::addEntry	(	unsigned int	atom_type,
		double	atom_pol,
		double	eff_el_num,
		double	fact_a,
		double	fact_g,
		HDonorAcceptorType	don_acc_type
	)

Adds (or overwrites) the entry for the numeric MMFF94 atom type atom_type.

Parameters

atom_type	The numeric MMFF94 atom type.
atom_pol	The atomic polarizability parameter.
eff_el_num	The Slater-Kirkwood effective number of valence electrons.
fact_a	The scaling factor `A`.
fact_g	The scaling factor `G`.
don_acc_type	The H-donor/-acceptor classification of the atom type.

◆ getEntry()

const Entry& CDPL::ForceField::MMFF94VanDerWaalsParameterTable::getEntry ( unsigned int atom_type ) const

Returns the entry for the numeric MMFF94 atom type atom_type.

Parameters

atom_type The numeric 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::MMFF94VanDerWaalsParameterTable::getNumEntries ( ) const

Returns the number of entries in the table.

Returns: The entry count.

◆ clear()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::clear ( )

Removes all entries from the table.

◆ removeEntry() [1/2]

bool CDPL::ForceField::MMFF94VanDerWaalsParameterTable::removeEntry ( unsigned int atom_type )

Removes the entry for the numeric MMFF94 atom type atom_type.

Parameters

atom_type The numeric MMFF94 atom type.

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

◆ removeEntry() [2/2]

EntryIterator CDPL::ForceField::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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.

◆ setExponent()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::setExponent ( double value )

Sets the global exponent used in the buffered 14-7 Van der Waals energy expression.

Parameters

value The new exponent value.

◆ setBeta()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::setBeta ( double value )

Sets the global beta value used in the buffered 14-7 Van der Waals energy expression.

Parameters

value The new beta value.

◆ setFactorB()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::setFactorB ( double value )

Sets the global B factor used in the buffered 14-7 Van der Waals energy expression.

Parameters

value The new B factor value.

◆ setFactorDARAD()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::setFactorDARAD ( double value )

Sets the global DARAD factor used in the buffered 14-7 Van der Waals energy expression.

Parameters

value The new DARAD factor value.

◆ setFactorDAEPS()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::setFactorDAEPS ( double value )

Sets the global DAEPS factor used in the buffered 14-7 Van der Waals energy expression.

Parameters

value The new DAEPS factor value.

◆ getExponent()

double CDPL::ForceField::MMFF94VanDerWaalsParameterTable::getExponent ( ) const

Returns the exponent used in the calculation of Van der Waals interaction energies.

Returns: The exponent.

◆ getFactorB()

double CDPL::ForceField::MMFF94VanDerWaalsParameterTable::getFactorB ( ) const

Returns the value of the B factor used in the calculation of Van der Waals interaction energies.

Returns: The value of the B factor.

◆ getBeta()

double CDPL::ForceField::MMFF94VanDerWaalsParameterTable::getBeta ( ) const

Returns the value of beta used in the calculation of Van der Waals interaction energies.

Returns: The value of beta.

◆ getFactorDARAD()

double CDPL::ForceField::MMFF94VanDerWaalsParameterTable::getFactorDARAD ( ) const

Returns the value of the DARAD factor used in the calculation of Van der Waals interaction energies.

Returns: The value of the DARAD factor.

◆ getFactorDAEPS()

double CDPL::ForceField::MMFF94VanDerWaalsParameterTable::getFactorDAEPS ( ) const

Returns the value of the DAEPS factor used in the calculation of Van der Waals interaction energies.

Returns: The value of the DAEPS factor.

◆ load()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::load ( std::istream & is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ loadDefaults()

void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::loadDefaults ( )

Loads the built-in default Van der Waals parameter entries and global scalar parameters.

◆ set()

static void CDPL::ForceField::MMFF94VanDerWaalsParameterTable::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::MMFF94VanDerWaalsParameterTable::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:

MMFF94VanDerWaalsParameterTable.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ HDonorAcceptorType

◆ ConstEntryIterator

◆ EntryIterator

Constructor & Destructor Documentation

◆ MMFF94VanDerWaalsParameterTable()

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]

◆ setExponent()

◆ setBeta()

◆ setFactorB()

◆ setFactorDARAD()

◆ setFactorDAEPS()

◆ getExponent()

◆ getFactorB()

◆ getBeta()

◆ getFactorDARAD()

◆ getFactorDAEPS()

◆ load()

◆ loadDefaults()

◆ set()

◆ get()