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

Inheritance diagram for CDPL.ForceField.MMFF94VanDerWaalsParameterTable:

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

Public Member Functions
None	__init__ ()
	Constructs an empty `MMFF94VanDerWaalsParameterTable` instance.

None	__init__ (MMFF94VanDerWaalsParameterTable table)
	Initializes a copy of the `MMFF94VanDerWaalsParameterTable` instance table. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

None	addEntry (int atom_type, float atom_pol, float eff_el_num, float fact_a, float fact_g, HDonorAcceptorType don_acc_type)
	Adds a new (or overwrites an existing) entry for the numeric MMFF94 atom type atom_type that stores the given parameter values. More...

bool	removeEntry (int atom_type)
	Removes the entry for the numeric MMFF94 atom type atom_type. More...

Entry	getEntry (int atom_type)
	Returns the entry for the numeric MMFF94 atom type atom_type. More...

None	clear ()
	Removes all entries from the table.

int	getNumEntries ()
	Returns the number of entries in the table. More...

list	getEntries ()

None	load (Base.IStream is)
	Loads table entries from the input stream is. More...

None	loadDefaults ()
	Loads the built-in default MMFF94 Van der Waals parameter entries and global scalar parameters.

MMFF94VanDerWaalsParameterTable	assign (MMFF94VanDerWaalsParameterTable table)
	Replaces the current state of self with a copy of the state of the `MMFF94VanDerWaalsParameterTable` instance table. More...

None	setExponent (float value)
	Sets the global exponent used in the buffered 14-7 Van der Waals energy expression. More...

None	setBeta (float value)
	Sets the global beta value used in the buffered 14-7 Van der Waals energy expression. More...

None	setFactorB (float value)
	Sets the global B factor used in the buffered 14-7 Van der Waals energy expression. More...

None	setFactorDARAD (float value)
	Sets the global DARAD factor used in the buffered 14-7 Van der Waals energy expression. More...

None	setFactorDAEPS (float value)
	Sets the global DAEPS factor used in the buffered 14-7 Van der Waals energy expression. More...

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

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

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

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

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

Static Public Member Functions
None	set (MMFF94VanDerWaalsParameterTable table)
	Replaces the process-wide default table by table. More...

MMFF94VanDerWaalsParameterTable	get ()
	Returns the process-wide default table (lazily initialized on first call). More...

Properties
	objectID = property(getObjectID)

	numEntries = property(getNumEntries)

	entries = property(getEntries)

	exponent = property(getExponent, setExponent)

	beta = property(getBeta, setBeta)

	factorB = property(getFactorB, setFactorB)

	factorDARAD = property(getFactorDARAD, setFactorDARAD)

	factorDAEPS = property(getFactorDAEPS, setFactorDAEPS)

Detailed Description

Data structure for the storage and lookup of MMFF94 interaction parameters.

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.

Constructor & Destructor Documentation

◆ init()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.__init__ ( MMFF94VanDerWaalsParameterTable table )

Initializes a copy of the MMFF94VanDerWaalsParameterTable instance table.

Parameters

table The MMFF94VanDerWaalsParameterTable instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python MMFF94VanDerWaalsParameterTable instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two MMFF94VanDerWaalsParameterTable instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ addEntry()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.addEntry	(	int	atom_type,
		float	atom_pol,
		float	eff_el_num,
		float	fact_a,
		float	fact_g,
		HDonorAcceptorType	don_acc_type
	)

Adds a new (or overwrites an existing) entry for the numeric MMFF94 atom type atom_type that stores the given parameter values.

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.

◆ removeEntry()

bool CDPL.ForceField.MMFF94VanDerWaalsParameterTable.removeEntry ( 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.

◆ getEntry()

Entry CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getEntry ( int atom_type )

Returns the entry for the numeric MMFF94 atom type atom_type.

Parameters

atom_type The numeric MMFF94 atom type.

Returns: A reference to the matching entry or to an uninitialized entry if no matching entry exists.

◆ getNumEntries()

int CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getNumEntries ( )

Returns the number of entries in the table.

Returns: The entry count.

◆ getEntries()

list CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getEntries ( )

Returns

◆ load()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.load ( Base.IStream is )

Loads table entries from the input stream is.

Parameters

is	The input stream to read from.

◆ assign()

MMFF94VanDerWaalsParameterTable CDPL.ForceField.MMFF94VanDerWaalsParameterTable.assign ( MMFF94VanDerWaalsParameterTable table )

Replaces the current state of self with a copy of the state of the MMFF94VanDerWaalsParameterTable instance table.

Parameters

table The MMFF94VanDerWaalsParameterTable instance to copy.

Returns: self

◆ setExponent()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.setExponent ( float value )

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

Parameters

value The new exponent value.

◆ setBeta()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.setBeta ( float value )

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

Parameters

value The new beta value.

◆ setFactorB()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.setFactorB ( float 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()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.setFactorDARAD ( float 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()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.setFactorDAEPS ( float 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()

float CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getExponent ( )

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

Returns: The exponent.

◆ getFactorB()

float CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getFactorB ( )

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()

float CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getBeta ( )

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

Returns: The value of beta.

◆ getFactorDARAD()

float CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getFactorDARAD ( )

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()

float CDPL.ForceField.MMFF94VanDerWaalsParameterTable.getFactorDAEPS ( )

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

Returns: The value of the DAEPS factor.

◆ set()

None CDPL.ForceField.MMFF94VanDerWaalsParameterTable.set ( MMFF94VanDerWaalsParameterTable 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()

MMFF94VanDerWaalsParameterTable CDPL.ForceField.MMFF94VanDerWaalsParameterTable.get ( )

static

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

Returns: A shared reference to the default table.

Classes

Public Member Functions

Static Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ addEntry()

◆ removeEntry()

◆ getEntry()

◆ getNumEntries()

◆ getEntries()

◆ load()

◆ assign()

◆ setExponent()

◆ setBeta()

◆ setFactorB()

◆ setFactorDARAD()

◆ setFactorDAEPS()

◆ getExponent()

◆ getFactorB()

◆ getBeta()

◆ getFactorDARAD()

◆ getFactorDAEPS()

◆ set()

◆ get()

◆ init()