CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer Class Reference

Detects and parameterizes the MMFF94 angle-bending interactions of a molecular graph. More...

Inheritance diagram for CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer:

Public Member Functions
None	__init__ ()
	Constructs an MMFF94AngleBendingInteractionParameterizer instance using the default MMFF94 parameter tables.
None	__init__ (MMFF94AngleBendingInteractionParameterizer parameterizer)
	Initializes a copy of the MMFF94AngleBendingInteractionParameterizer instance parameterizer. More...
None	__init__ (Chem.MolecularGraph molgraph, MMFF94AngleBendingInteractionList 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 (InteractionFilterFunction3 func)
	Sets the filter function used to skip atom triplets during parameterization. More...
None	setAtomTypeFunction (MMFF94NumericAtomTypeFunction func)
	Sets the function used to look up the MMFF94 numeric atom type of an atom. More...
None	setBondTypeIndexFunction (MMFF94BondTypeIndexFunction func)
	Sets the function used to look up the MMFF94 bond type index of a bond. More...
None	setAromaticRingSetFunction (MMFF94RingSetFunction func)
	Sets the function used to obtain the set of MMFF94 aromatic rings of the input molecular graph. More...
None	setAngleBendingParameterTable (MMFF94AngleBendingParameterTable table)
	Sets the primary table providing angle type-specific angle-bending parameters. More...
None	setBondStretchingParameterTable (MMFF94BondStretchingParameterTable table)
	Sets the primary bond-stretching parameter table (used to retrieve reference bond lengths in the empirical rule fallback). More...
None	setBondStretchingRuleParameterTable (MMFF94BondStretchingRuleParameterTable table)
	Sets the fallback bond-stretching rule parameter table (used in the empirical rule fallback). More...
None	setAtomTypePropertyTable (MMFF94AtomTypePropertyTable table)
	Sets the table providing MMFF94 numeric atom type property data (used by the empirical rule fallback). More...
None	setParameterAtomTypeMap (MMFF94PrimaryToParameterAtomTypeMap map)
	Sets the map used to translate primary atom types into their corresponding parameter atom types. More...
MMFF94AngleBendingInteractionParameterizer	assign (MMFF94AngleBendingInteractionParameterizer parameterizer)
	Replaces the current state of self with a copy of the state of the MMFF94AngleBendingInteractionParameterizer instance parameterizer. More...
None	parameterize (Chem.MolecularGraph molgraph, MMFF94AngleBendingInteractionList ia_list, bool strict)
	Perceives the MMFF94 angle-bending interactions for molgraph and outputs the corresponding parameter data into ia_list. More...

Properties
	objectID = property(getObjectID)

Detailed Description

Detects and parameterizes the MMFF94 angle-bending interactions of a molecular graph.

For every non-filtered atom triplet (i-j-k) consisting of a central atom j and two of its neighbors the parameterizer determines the MMFF94 angle type index (0-8, accounting for ring membership and double bond character), looks up the matching MMFF94 angle-bending parameters, falls back to the empirical rule when no exact entry is found and emits an MMFF94AngleBendingInteraction instance.

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.__init__

(

MMFF94AngleBendingInteractionParameterizer

parameterizer

)

Initializes a copy of the MMFF94AngleBendingInteractionParameterizer instance parameterizer.

Parameters

parameterizer

The MMFF94AngleBendingInteractionParameterizer instance to copy.

__init__() [2/2]

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.__init__	(	Chem.MolecularGraph	molgraph,
		MMFF94AngleBendingInteractionList	ia_list,
		bool	strict
	)

Constructs the parameterizer and processes the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to parameterize the angle-bending interactions.
ia_list	Output list receiving the generated MMFF94AngleBendingInteraction 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.MMFF94AngleBendingInteractionParameterizer.getObjectID

(

)

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

Different Python MMFF94AngleBendingInteractionParameterizer 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 MMFF94AngleBendingInteractionParameterizer 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.MMFF94AngleBendingInteractionParameterizer.setFilterFunction

(

InteractionFilterFunction3

func

)

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

Parameters

func	The new three-atom filter function (when it returns False, the triplet is skipped).

setAtomTypeFunction()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.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.

setBondTypeIndexFunction()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setBondTypeIndexFunction

(

MMFF94BondTypeIndexFunction

func

)

Sets the function used to look up the MMFF94 bond type index of a bond.

Parameters

func	The new bond type index lookup function.

setAromaticRingSetFunction()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setAromaticRingSetFunction

(

MMFF94RingSetFunction

func

)

Sets the function used to obtain the set of MMFF94 aromatic rings of the input molecular graph.

Parameters

func	The new aromatic ring set retrieval function.

setAngleBendingParameterTable()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setAngleBendingParameterTable

(

MMFF94AngleBendingParameterTable

table

)

Sets the primary table providing angle type-specific angle-bending parameters.

Parameters

table

The new angle-bending parameter table.

setBondStretchingParameterTable()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setBondStretchingParameterTable

(

MMFF94BondStretchingParameterTable

table

)

Sets the primary bond-stretching parameter table (used to retrieve reference bond lengths in the empirical rule fallback).

Parameters

table

The new bond-stretching parameter table.

setBondStretchingRuleParameterTable()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setBondStretchingRuleParameterTable

(

MMFF94BondStretchingRuleParameterTable

table

)

Sets the fallback bond-stretching rule parameter table (used in the empirical rule fallback).

Parameters

table

The new bond-stretching rule parameter table.

setAtomTypePropertyTable()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setAtomTypePropertyTable

(

MMFF94AtomTypePropertyTable

table

)

Sets the table providing MMFF94 numeric atom type property data (used by the empirical rule fallback).

Parameters

table

The new atom type property table.

setParameterAtomTypeMap()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.setParameterAtomTypeMap

(

MMFF94PrimaryToParameterAtomTypeMap

map

)

Sets the map used to translate primary atom types into their corresponding parameter atom types.

Parameters

map	The new primary-to-parameter atom type map.

assign()

MMFF94AngleBendingInteractionParameterizer CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.assign

(

MMFF94AngleBendingInteractionParameterizer

parameterizer

)

Replaces the current state of self with a copy of the state of the MMFF94AngleBendingInteractionParameterizer instance parameterizer.

Parameters

parameterizer

The MMFF94AngleBendingInteractionParameterizer instance to copy.

Returns

self

parameterize()

None CDPL.ForceField.MMFF94AngleBendingInteractionParameterizer.parameterize	(	Chem.MolecularGraph	molgraph,
		MMFF94AngleBendingInteractionList	ia_list,
		bool	strict
	)

Perceives the MMFF94 angle-bending interactions for molgraph and outputs the corresponding parameter data into ia_list.

Parameters

molgraph	The molecular graph for which to parameterize the angle-bending interactions.
ia_list	Output list receiving the generated MMFF94AngleBendingInteraction instances.
strict	If True, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.