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Chemical Data Processing Library Python API - Version 1.4.0
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Chemical Data Processing Library Python API - Version 1.4.0
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Calculator that uses the Partial Equalization of Orbital Electronegativities (PEOE) method of Gasteiger and Marsili to compute sigma atomic charges and electronegativities of a molecular graph. More...
Inheritance diagram for CDPL.MolProp.PEOESigmaChargeCalculator:Public Member Functions | |
| None | __init__ () |
Constructs the PEOESigmaChargeCalculator instance. | |
| None | __init__ (Chem.MolecularGraph molgraph) |
Constructs the PEOESigmaChargeCalculator instance and calculates the sigma charges and electronegativities of the atoms in the molecular graph molgraph by the PEOE method. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| None | setNumIterations (int num_iter) |
| Allows to specify the number of charge shifting iterations that have to be performed. More... | |
| None | setDampingFactor (float factor) |
| Allows to specify the applied damping factor. More... | |
| int | getNumIterations () |
| Returns the number of performed charge shifting iterations. More... | |
| float | getDampingFactor () |
| Returns the applied damping factor. More... | |
| None | calculate (Chem.MolecularGraph molgraph) |
| Calculates the sigma charges and electronegativities of the atoms in the molecular graph molgraph by the PEOE method. More... | |
| float | getCharge (int idx) |
| Returns the calculated sigma charge of the atom with index idx. More... | |
| float | getElectronegativity (int idx) |
| Returns the calculated sigma electronegativity of the atom with index idx. More... | |
Static Public Attributes | |
| int | DEF_NUM_ITERATIONS = 20 |
| Default number of charge-shifting iterations. | |
| float | DEF_DAMPING_FACTOR = 0.48 |
| Default per-iteration damping factor. | |
Properties | |
| objectID = property(getObjectID) | |
| numIterations = property(getNumIterations, setNumIterations) | |
| dampingFactor = property(getDampingFactor, setDampingFactor) | |
Calculator that uses the Partial Equalization of Orbital Electronegativities (PEOE) method of Gasteiger and Marsili to compute sigma atomic charges and electronegativities of a molecular graph.
The calculation iteratively shifts partial charges between bonded atoms until the orbital electronegativities are (approximately) equalized. The number of iterations and the damping factor that controls the shift attenuation per iteration can be configured.
| None CDPL.MolProp.PEOESigmaChargeCalculator.__init__ | ( | Chem.MolecularGraph | molgraph | ) |
Constructs the PEOESigmaChargeCalculator instance and calculates the sigma charges and electronegativities of the atoms in the molecular graph molgraph by the PEOE method.
| molgraph | The molecular graph for which to perform the calculations. |
| int CDPL.MolProp.PEOESigmaChargeCalculator.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python PEOESigmaChargeCalculator 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 PEOESigmaChargeCalculator 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().
| None CDPL.MolProp.PEOESigmaChargeCalculator.setNumIterations | ( | int | num_iter | ) |
Allows to specify the number of charge shifting iterations that have to be performed.
| num_iter | The number of iterations to perform. |
| None CDPL.MolProp.PEOESigmaChargeCalculator.setDampingFactor | ( | float | factor | ) |
Allows to specify the applied damping factor.
| factor | The damping factor to apply. |
| int CDPL.MolProp.PEOESigmaChargeCalculator.getNumIterations | ( | ) |
Returns the number of performed charge shifting iterations.
| float CDPL.MolProp.PEOESigmaChargeCalculator.getDampingFactor | ( | ) |
Returns the applied damping factor.
| None CDPL.MolProp.PEOESigmaChargeCalculator.calculate | ( | Chem.MolecularGraph | molgraph | ) |
Calculates the sigma charges and electronegativities of the atoms in the molecular graph molgraph by the PEOE method.
| molgraph | The molecular graph for which to perform the calculations. |
| float CDPL.MolProp.PEOESigmaChargeCalculator.getCharge | ( | int | idx | ) |
Returns the calculated sigma charge of the atom with index idx.
| idx | The index of the atom for which to return the charge. |
| Base.IndexError | If idx is not in the range [0, NA - 1] where NA is the number of atoms of the molecular graph for which the calculations have been performed. |
| float CDPL.MolProp.PEOESigmaChargeCalculator.getElectronegativity | ( | int | idx | ) |
Returns the calculated sigma electronegativity of the atom with index idx.
| idx | The index of the atom for which to return the electronegativity. |
| Base.IndexError | If idx is not in the range [0, NA - 1] where NA is the number of atoms of the molecular graph for which the calculations have been performed. |
1.9.1