CDPL.ForceField.MMFF94BondTyper Class Reference

Inheritance diagram for CDPL.ForceField.MMFF94BondTyper:

Public Member Functions
None	__init__ ()
	Initializes the MMFF94BondTyper instance.
None	__init__ (MMFF94BondTyper typer)
	Initializes a copy of the MMFF94BondTyper instance typer. More...
None	__init__ (Chem.MolecularGraph molgraph, Util.UIArray types, bool strict)
	Initializes the MMFF94BondTyper instance. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setAtomTypeFunction (MMFF94NumericAtomTypeFunction func)
None	setAromaticRingSetFunction (MMFF94RingSetFunction func)
None	setAtomTypePropertyTable (MMFF94AtomTypePropertyTable table)
MMFF94BondTyper	assign (MMFF94BondTyper typer)
	Replaces the current state of self with a copy of the state of the MMFF94BondTyper instance typer. More...
None	perceiveTypes (Chem.MolecularGraph molgraph, Util.UIArray types, bool strict)
	Determines MMFF94 bond type indicies for the bonds of a molecular graph. More...

Properties
	objectID = property(getObjectID)

Constructor & Destructor Documentation

__init__() [1/2]

None CDPL.ForceField.MMFF94BondTyper.__init__

(

MMFF94BondTyper

typer

)

Initializes a copy of the MMFF94BondTyper instance typer.

Parameters

typer

The MMFF94BondTyper instance to copy.

__init__() [2/2]

None CDPL.ForceField.MMFF94BondTyper.__init__	(	Chem.MolecularGraph	molgraph,
		Util.UIArray	types,
		bool	strict
	)

Initializes the MMFF94BondTyper instance.

Parameters

molgraph
types
strict

Member Function Documentation

getObjectID()

int CDPL.ForceField.MMFF94BondTyper.getObjectID

(

)

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

Different Python MMFF94BondTyper 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 MMFF94BondTyper 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.

setAtomTypeFunction()

None CDPL.ForceField.MMFF94BondTyper.setAtomTypeFunction

(

MMFF94NumericAtomTypeFunction

func

)

Parameters

func

setAromaticRingSetFunction()

None CDPL.ForceField.MMFF94BondTyper.setAromaticRingSetFunction

(

MMFF94RingSetFunction

func

)

Parameters

func

setAtomTypePropertyTable()

None CDPL.ForceField.MMFF94BondTyper.setAtomTypePropertyTable

(

MMFF94AtomTypePropertyTable

table

)

Parameters

table

assign()

MMFF94BondTyper CDPL.ForceField.MMFF94BondTyper.assign

(

MMFF94BondTyper

typer

)

Replaces the current state of self with a copy of the state of the MMFF94BondTyper instance typer.

Parameters

typer

The MMFF94BondTyper instance to copy.

Returns

self

perceiveTypes()

None CDPL.ForceField.MMFF94BondTyper.perceiveTypes	(	Chem.MolecularGraph	molgraph,
		Util.UIArray	types,
		bool	strict
	)

Determines MMFF94 bond type indicies for the bonds of a molecular graph.

Specifically, an nonstandard bond type index of "1" is assigned whenever a single bond (formal bond order 1) is found a) between non-aromatic atoms i and j of types I and J for which "sbmb" entries in of "1" appear in the "MMFFPROP.PAR" file or b) between aromatic atoms belonging to different aromatic rings (as in the case of the central C-C bond in biphenyl).

Parameters

molgraph	The molecular graph for which to assign bond type indices
types	The output array storing the determined bond type indices.
strict	If True, strict parameterization will be peformed that might fail.