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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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Detects and parameterizes the MMFF94 electrostatic interactions of a molecular graph. More...
Inheritance diagram for CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer:Public Member Functions | |
| None | __init__ () |
Constructs an MMFF94ElectrostaticInteractionParameterizer instance with default settings. | |
| None | __init__ (MMFF94ElectrostaticInteractionParameterizer parameterizer) |
Initializes a copy of the MMFF94ElectrostaticInteractionParameterizer instance parameterizer. More... | |
| None | __init__ (Chem.MolecularGraph molgraph, MMFF94ElectrostaticInteractionList 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 | setAtomChargeFunction (MMFF94AtomChargeFunction func) |
| Sets the function used to look up the MMFF94 partial charge 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 | setDielectricConstant (float de_const) |
| Sets the dielectric constant used by the MMFF94 electrostatic potential. More... | |
| None | setDistanceExponent (float dist_expo) |
| Sets the exponent of the MMFF94 distance-dependent electrostatic potential. More... | |
| MMFF94ElectrostaticInteractionParameterizer | assign (MMFF94ElectrostaticInteractionParameterizer parameterizer) |
Replaces the current state of self with a copy of the state of the MMFF94ElectrostaticInteractionParameterizer instance parameterizer. More... | |
| None | parameterize (Chem.MolecularGraph molgraph, MMFF94ElectrostaticInteractionList ia_list, bool strict) |
| Perceives the MMFF94 electrostatic interactions for molgraph and outputs the corresponding parameter data into ia_list. More... | |
Static Public Attributes | |
| float | DEF_DISTANCE_EXPONENT = 1.0 |
| Default value of the distance exponent in the MMFF94 electrostatic potential (1.0 — Coulomb form). | |
| float | DEF_DIELECTRIC_CONSTANT = 1.0 |
| Default value of the dielectric constant (1.0 — gas-phase). | |
| float | DIELECTRIC_CONSTANT_WATER = 80.0 |
| Convenience constant: dielectric constant of bulk water at room temperature (80.0). | |
Properties | |
| objectID = property(getObjectID) | |
Detects and parameterizes the MMFF94 electrostatic interactions of a molecular graph.
For every pair of atoms that is at least 1,4-separated (1,4-pairs use a scaling factor of 0.75; 1,5 and farther pairs use 1.0) the parameterizer emits an MMFF94ElectrostaticInteraction instance storing the partial charges, the configured dielectric constant and the configured distance exponent.
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.__init__ | ( | MMFF94ElectrostaticInteractionParameterizer | parameterizer | ) |
Initializes a copy of the MMFF94ElectrostaticInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94ElectrostaticInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.__init__ | ( | Chem.MolecularGraph | molgraph, |
| MMFF94ElectrostaticInteractionList | ia_list, | ||
| bool | strict | ||
| ) |
Constructs the parameterizer and processes the molecular graph molgraph.
| molgraph | The molecular graph for which to parameterize the electrostatic interactions. |
| ia_list | Output list receiving the generated MMFF94ElectrostaticInteraction instances. |
| strict | If True, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used. |
| int CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94ElectrostaticInteractionParameterizer 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 MMFF94ElectrostaticInteractionParameterizer 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.ForceField.MMFF94ElectrostaticInteractionParameterizer.setFilterFunction | ( | Chem.BoolAtom2Functor | func | ) |
Sets the filter function used to skip atom pairs during parameterization.
| func | The new filter function (when it returns False for an atom pair, the pair is skipped). |
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.setAtomChargeFunction | ( | MMFF94AtomChargeFunction | func | ) |
Sets the function used to look up the MMFF94 partial charge of an atom.
| func | The new atom charge lookup function. |
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.setTopologicalDistanceFunction | ( | TopologicalAtomDistanceFunction | func | ) |
Sets the function used to determine the topological distance between two atoms (number of bonds along the shortest path).
| func | The new topological distance function. |
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.setDielectricConstant | ( | float | de_const | ) |
Sets the dielectric constant used by the MMFF94 electrostatic potential.
| de_const | The new dielectric constant. |
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.setDistanceExponent | ( | float | dist_expo | ) |
Sets the exponent of the MMFF94 distance-dependent electrostatic potential.
| dist_expo | The new distance exponent. |
| MMFF94ElectrostaticInteractionParameterizer CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.assign | ( | MMFF94ElectrostaticInteractionParameterizer | parameterizer | ) |
Replaces the current state of self with a copy of the state of the MMFF94ElectrostaticInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94ElectrostaticInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94ElectrostaticInteractionParameterizer.parameterize | ( | Chem.MolecularGraph | molgraph, |
| MMFF94ElectrostaticInteractionList | ia_list, | ||
| bool | strict | ||
| ) |
Perceives the MMFF94 electrostatic interactions for molgraph and outputs the corresponding parameter data into ia_list.
| molgraph | The molecular graph for which to parameterize the electrostatic interactions. |
| ia_list | Output list receiving the generated MMFF94ElectrostaticInteraction instances. |
| strict | If True, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used. |
1.9.1