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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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Calculates the total MMFF94 force field energy for a set of atom 3D coordinates. More...
Inheritance diagram for CDPL.ForceField.MMFF94EnergyCalculator:Public Member Functions | |
| None | __init__ () |
| Constructs the calculator without an associated ForceField.MMFF94InteractionData instance. More... | |
| None | __init__ (MMFF94EnergyCalculator calc) |
Contructs a copy of the MMFF94EnergyCalculator instance calc. More... | |
| None | __init__ (MMFF94InteractionData ia_data) |
| Constructs the calculator and associates it with the supplied ForceField.MMFF94InteractionData instance. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| MMFF94EnergyCalculator | assign (MMFF94EnergyCalculator calc) |
Replaces the current state with a copy of the state of the MMFF94EnergyCalculator instance calc. More... | |
| None | setEnabledInteractionTypes (int types) |
| Enables/disables specific MMFF94 interaction-type contributions. More... | |
| int | getEnabledInteractionTypes () |
| Returns the currently enabled interaction-type contributions. More... | |
| None | setup (MMFF94InteractionData ia_data) |
| Associates the calculator with the supplied ForceField.MMFF94InteractionData instance. More... | |
| float | getTotalEnergy () |
| Returns the total MMFF94 energy computed by the most recent __call__() call. More... | |
| float | getBondStretchingEnergy () |
| Returns the bond-stretching energy contribution computed by the most recent __call__() call. More... | |
| float | getAngleBendingEnergy () |
| Returns the angle-bending energy contribution computed by the most recent __call__() call. More... | |
| float | getStretchBendEnergy () |
| Returns the stretch-bend coupling energy contribution computed by the most recent __call__() call. More... | |
| float | getOutOfPlaneBendingEnergy () |
| Returns the out-of-plane bending energy contribution computed by the most recent __call__() call. More... | |
| float | getTorsionEnergy () |
| Returns the torsion energy contribution computed by the most recent __call__() call. More... | |
| float | getElectrostaticEnergy () |
| Returns the electrostatic energy contribution computed by the most recent __call__() call. More... | |
| float | getVanDerWaalsEnergy () |
| Returns the Van der Waals energy contribution computed by the most recent __call__() call. More... | |
| float | __call__ (Math.Vector3DArray coords) |
| Computes the total MMFF94 energy of the conformation specified by coords. More... | |
Properties | |
| objectID = property(getObjectID) | |
| enabledInteractionTypes = property(getEnabledInteractionTypes, setEnabledInteractionTypes) | |
| totalEnergy = property(getTotalEnergy) | |
| bondStretchingEnergy = property(getBondStretchingEnergy) | |
| angleBendingEnergy = property(getAngleBendingEnergy) | |
| stretchBendEnergy = property(getStretchBendEnergy) | |
| outOfPlaneBendingEnergy = property(getOutOfPlaneBendingEnergy) | |
| torsionEnergy = property(getTorsionEnergy) | |
| electrostaticEnergy = property(getElectrostaticEnergy) | |
| vanDerWaalsEnergy = property(getVanDerWaalsEnergy) | |
Calculates the total MMFF94 force field energy for a set of atom 3D coordinates.
The calculator takes a ForceField.MMFF94InteractionData instance (typically produced by ForceField.MMFF94InteractionParameterizer) and computes the bond-stretching, angle-bending, stretch-bend, out-of-plane bending, torsion, electrostatic and Van der Waals energy contributions for a supplied set of atom 3D coordinates. The per-component energies are retained and made available via the dedicated accessors, the calculated sum is returned by __call__() and getTotalEnergy().
| None CDPL.ForceField.MMFF94EnergyCalculator.__init__ | ( | ) |
Constructs the calculator without an associated ForceField.MMFF94InteractionData instance.
__call__() will return zero until setup() has been called.
| None CDPL.ForceField.MMFF94EnergyCalculator.__init__ | ( | MMFF94EnergyCalculator | calc | ) |
Contructs a copy of the MMFF94EnergyCalculator instance calc.
| calc | The MMFF94EnergyCalculator instance to copy. |
| None CDPL.ForceField.MMFF94EnergyCalculator.__init__ | ( | MMFF94InteractionData | ia_data | ) |
Constructs the calculator and associates it with the supplied ForceField.MMFF94InteractionData instance.
| ia_data | The MMFF94 interaction data to use for energy calculation. |
| int CDPL.ForceField.MMFF94EnergyCalculator.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94EnergyCalculator 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 MMFF94EnergyCalculator 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().
| MMFF94EnergyCalculator CDPL.ForceField.MMFF94EnergyCalculator.assign | ( | MMFF94EnergyCalculator | calc | ) |
Replaces the current state with a copy of the state of the MMFF94EnergyCalculator instance calc.
| calc | The MMFF94EnergyCalculator instance to copy. |
| None CDPL.ForceField.MMFF94EnergyCalculator.setEnabledInteractionTypes | ( | int | types | ) |
Enables/disables specific MMFF94 interaction-type contributions.
| types | Bitwise-OR combination of ForceField.InteractionType flags. |
| int CDPL.ForceField.MMFF94EnergyCalculator.getEnabledInteractionTypes | ( | ) |
Returns the currently enabled interaction-type contributions.
| None CDPL.ForceField.MMFF94EnergyCalculator.setup | ( | MMFF94InteractionData | ia_data | ) |
Associates the calculator with the supplied ForceField.MMFF94InteractionData instance.
| ia_data | The new MMFF94 interaction data to use for energy calculation. |
| float CDPL.ForceField.MMFF94EnergyCalculator.getTotalEnergy | ( | ) |
Returns the total MMFF94 energy computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getBondStretchingEnergy | ( | ) |
Returns the bond-stretching energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getAngleBendingEnergy | ( | ) |
Returns the angle-bending energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getStretchBendEnergy | ( | ) |
Returns the stretch-bend coupling energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getOutOfPlaneBendingEnergy | ( | ) |
Returns the out-of-plane bending energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getTorsionEnergy | ( | ) |
Returns the torsion energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getElectrostaticEnergy | ( | ) |
Returns the electrostatic energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.getVanDerWaalsEnergy | ( | ) |
Returns the Van der Waals energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94EnergyCalculator.__call__ | ( | Math.Vector3DArray | coords | ) |
Computes the total MMFF94 energy of the conformation specified by coords.
The per-component energies are stored internally and can be retrieved via the dedicated accessors.
| coords | The atom 3D coordinates. |
1.9.1