 |
Chemical Data Processing Library Python API - Version 1.4.0
|
|
Chemical Data Processing Library Python API - Version 1.4.0
|
Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates. More...
Inheritance diagram for CDPL.ForceField.MMFF94GradientCalculator:Public Member Functions | |
| None | __init__ () |
| Constructs the calculator without an associated ForceField.MMFF94InteractionData instance. More... | |
| None | __init__ (MMFF94GradientCalculator calc) |
Contructs a copy of the MMFF94GradientCalculator instance calc. More... | |
| None | __init__ (MMFF94InteractionData ia_data, int num_atoms) |
| 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... | |
| MMFF94GradientCalculator | assign (MMFF94GradientCalculator calc) |
Replaces the current state with a copy of the state of the MMFF94GradientCalculator 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, int num_atoms) |
| Associates the calculator with the supplied ForceField.MMFF94InteractionData instance and atom count. 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... | |
| None | setFixedAtomMask (Util.BitSet mask) |
| Sets the bit mask flagging atoms whose gradient components shall be zeroed after calculation. More... | |
| None | resetFixedAtomMask () |
| Clears the fixed-atom mask so that all atoms contribute to the gradient. | |
| Util.BitSet | getFixedAtomMask () |
| Returns the bit mask flagging atoms whose gradient components are zeroed after evaluation. More... | |
| float | __call__ (Math.Vector3DArray coords) |
| Computes the total MMFF94 energy of the conformation specified by coords without calculating the gradient. More... | |
| float | __call__ (Math.Vector3DArray coords, Math.Vector3DArray grad) |
| Computes the total MMFF94 energy and the per-atom gradient 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) | |
| fixedAtomMask = property(getFixedAtomMask) | |
Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates.
The calculator takes a ForceField.MMFF94InteractionData instance and the atom count of the molecule and computes both the total MMFF94 energy and the analytical Cartesian gradient \( \partial E / \partial \mathbf{r}_i \) for each atom. The per-component energies are retained and made available via the dedicated accessors. A bit mask can be set to mark atoms whose gradient contributions are zeroed, freezing them during an energy minimization run.
| None CDPL.ForceField.MMFF94GradientCalculator.__init__ | ( | ) |
Constructs the calculator without an associated ForceField.MMFF94InteractionData instance.
__call__() will return zero until setup() has been called.
| None CDPL.ForceField.MMFF94GradientCalculator.__init__ | ( | MMFF94GradientCalculator | calc | ) |
Contructs a copy of the MMFF94GradientCalculator instance calc.
| calc | The MMFF94GradientCalculator instance to copy. |
| None CDPL.ForceField.MMFF94GradientCalculator.__init__ | ( | MMFF94InteractionData | ia_data, |
| int | num_atoms | ||
| ) |
Constructs the calculator and associates it with the supplied ForceField.MMFF94InteractionData instance.
| ia_data | The MMFF94 interaction data to use during energy/gradient calculation. |
| num_atoms | The number of atoms in the parameterized molecular graph. |
| int CDPL.ForceField.MMFF94GradientCalculator.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94GradientCalculator 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 MMFF94GradientCalculator 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().
| MMFF94GradientCalculator CDPL.ForceField.MMFF94GradientCalculator.assign | ( | MMFF94GradientCalculator | calc | ) |
Replaces the current state with a copy of the state of the MMFF94GradientCalculator instance calc.
| calc | The MMFF94GradientCalculator instance to copy. |
| None CDPL.ForceField.MMFF94GradientCalculator.setEnabledInteractionTypes | ( | int | types | ) |
Enables/disables specific MMFF94 interaction-type contributions.
| types | Bitwise-OR combination of ForceField.InteractionType flags. |
| int CDPL.ForceField.MMFF94GradientCalculator.getEnabledInteractionTypes | ( | ) |
Returns the currently enabled interaction-type contributions.
| None CDPL.ForceField.MMFF94GradientCalculator.setup | ( | MMFF94InteractionData | ia_data, |
| int | num_atoms | ||
| ) |
Associates the calculator with the supplied ForceField.MMFF94InteractionData instance and atom count.
| ia_data | The new MMFF94 interaction data to use for energy/gradient calculation. |
| num_atoms | The number of atoms in the parameterized molecular graph. |
| float CDPL.ForceField.MMFF94GradientCalculator.getTotalEnergy | ( | ) |
Returns the total MMFF94 energy computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getBondStretchingEnergy | ( | ) |
Returns the bond-stretching energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getAngleBendingEnergy | ( | ) |
Returns the angle-bending energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getStretchBendEnergy | ( | ) |
Returns the stretch-bend coupling energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getOutOfPlaneBendingEnergy | ( | ) |
Returns the out-of-plane bending energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getTorsionEnergy | ( | ) |
Returns the torsion energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getElectrostaticEnergy | ( | ) |
Returns the electrostatic energy contribution computed by the most recent __call__() call.
| float CDPL.ForceField.MMFF94GradientCalculator.getVanDerWaalsEnergy | ( | ) |
Returns the Van der Waals energy contribution computed by the most recent __call__() call.
| None CDPL.ForceField.MMFF94GradientCalculator.setFixedAtomMask | ( | Util.BitSet | mask | ) |
Sets the bit mask flagging atoms whose gradient components shall be zeroed after calculation.
| mask | The new fixed-atom bit mask (bit i set freezes atom i during minimization). |
| Util.BitSet CDPL.ForceField.MMFF94GradientCalculator.getFixedAtomMask | ( | ) |
Returns the bit mask flagging atoms whose gradient components are zeroed after evaluation.
| float CDPL.ForceField.MMFF94GradientCalculator.__call__ | ( | Math.Vector3DArray | coords | ) |
Computes the total MMFF94 energy of the conformation specified by coords without calculating the gradient.
| coords | The 3D coordinates of the molecule. |
| float CDPL.ForceField.MMFF94GradientCalculator.__call__ | ( | Math.Vector3DArray | coords, |
| Math.Vector3DArray | grad | ||
| ) |
Computes the total MMFF94 energy and the per-atom gradient of the conformation specified by coords.
Gradients of atoms marked in the fixed-atom mask (see setFixedAtomMask()) are zeroed after calculation.
| coords | The atom 3D coordinates. |
| grad | The output gradient vector. |
1.9.1