CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer Class Reference

Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph. More...

Inheritance diagram for CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer:

Public Member Functions
None	__init__ ()
	Constructs an MMFF94VanDerWaalsInteractionParameterizer instance using the default MMFF94 parameter tables.
None	__init__ (MMFF94VanDerWaalsInteractionParameterizer parameterizer)
	Initializes a copy of the MMFF94VanDerWaalsInteractionParameterizer instance parameterizer. More...
None	__init__ (Chem.MolecularGraph molgraph, MMFF94VanDerWaalsInteractionList ia_list, bool strict)
	Constructs the parameterizer and processes the molecular graph molgraph. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setFilterFunction (Chem.BoolAtom2Functor func)
	Sets the filter function used to skip atom pairs during parameterization. More...
None	setAtomTypeFunction (MMFF94NumericAtomTypeFunction func)
	Sets the function used to look up the MMFF94 numeric atom type of an atom. More...
None	setTopologicalDistanceFunction (TopologicalAtomDistanceFunction func)
	Sets the function used to determine the topological distance between two atoms (number of bonds along the shortest path). More...
None	setVanDerWaalsParameterTable (MMFF94VanDerWaalsParameterTable table)
	Sets the table providing MMFF94 numeric atom type Van der Waals parameters and donor/acceptor classifications. More...
MMFF94VanDerWaalsInteractionParameterizer	assign (MMFF94VanDerWaalsInteractionParameterizer parameterizer)
	Replaces the current state of self with a copy of the state of the MMFF94VanDerWaalsInteractionParameterizer instance parameterizer. More...
None	parameterize (Chem.MolecularGraph molgraph, MMFF94VanDerWaalsInteractionList ia_list, bool strict)
	Perceives the MMFF94 Van der Waals interactions for molgraph and outputs the corresponding parameter data into ia_list. More...

Properties
	objectID = property(getObjectID)

Detailed Description

Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph.

For every pair of atoms separated by at least three bonds the parameterizer looks up the per-atom type Van der Waals parameters and the donor/acceptor classification from the supplied parameter table, applies the MMFF94 combining rules and emits an MMFF94VanDerWaalsInteraction instance.

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.__init__

(

MMFF94VanDerWaalsInteractionParameterizer

parameterizer

)

Initializes a copy of the MMFF94VanDerWaalsInteractionParameterizer instance parameterizer.

Parameters

parameterizer

The MMFF94VanDerWaalsInteractionParameterizer instance to copy.

__init__() [2/2]

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.__init__	(	Chem.MolecularGraph	molgraph,
		MMFF94VanDerWaalsInteractionList	ia_list,
		bool	strict
	)

Constructs the parameterizer and processes the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to parameterize the Van der Waals interactions.
ia_list	Output list receiving the generated MMFF94VanDerWaalsInteraction instances.
strict	If True, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

Member Function Documentation

getObjectID()

int CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.getObjectID

(

)

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

Different Python MMFF94VanDerWaalsInteractionParameterizer 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 MMFF94VanDerWaalsInteractionParameterizer 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.

setFilterFunction()

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.setFilterFunction

(

Chem.BoolAtom2Functor

func

)

Sets the filter function used to skip atom pairs during parameterization.

Parameters

func	The new filter function (when it returns False for an atom pair, the pair is skipped).

setAtomTypeFunction()

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.setAtomTypeFunction

(

MMFF94NumericAtomTypeFunction

func

)

Sets the function used to look up the MMFF94 numeric atom type of an atom.

Parameters

func	The new numeric atom type lookup function.

setTopologicalDistanceFunction()

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.setTopologicalDistanceFunction

(

TopologicalAtomDistanceFunction

func

)

Sets the function used to determine the topological distance between two atoms (number of bonds along the shortest path).

Parameters

func	The new topological distance function.

setVanDerWaalsParameterTable()

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.setVanDerWaalsParameterTable

(

MMFF94VanDerWaalsParameterTable

table

)

Sets the table providing MMFF94 numeric atom type Van der Waals parameters and donor/acceptor classifications.

Parameters

table

The new Van der Waals parameter table.

assign()

MMFF94VanDerWaalsInteractionParameterizer CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.assign

(

MMFF94VanDerWaalsInteractionParameterizer

parameterizer

)

Replaces the current state of self with a copy of the state of the MMFF94VanDerWaalsInteractionParameterizer instance parameterizer.

Parameters

parameterizer

The MMFF94VanDerWaalsInteractionParameterizer instance to copy.

Returns

self

parameterize()

None CDPL.ForceField.MMFF94VanDerWaalsInteractionParameterizer.parameterize	(	Chem.MolecularGraph	molgraph,
		MMFF94VanDerWaalsInteractionList	ia_list,
		bool	strict
	)

Perceives the MMFF94 Van der Waals interactions for molgraph and outputs the corresponding parameter data into ia_list.

Parameters

molgraph	The molecular graph for which to parameterize the Van der Waals interactions.
ia_list	Output list receiving the generated MMFF94VanDerWaalsInteraction instances.
strict	If True, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.