rdkit.ForceField.rdForceField module

Exposes the ForceField class

class rdkit.ForceField.rdForceField.ForceField

Bases: object

A force field

AddDistanceConstraint(self, idx1: int, idx2: int, minLen: float, maxLen: float, forceConstant: float) → None

Adds a distance constraint to the UFF force field (deprecated, use UFFAddDistanceConstraint instead).

AddExtraPoint(self, x: float, y: float, z: float, fixed: bool = True) → int

Adds an extra point, this can be useful for adding constraints.

AddFixedPoint(self, idx: int) → None

Adds a fixed point to the force field.

CalcEnergy(self, pos: object | None = None) → float

Returns the energy (in kcal/mol) of the current arrangement or of the supplied coordinate list (if non-empty)

CalcGrad(self, pos: object | None = None) → tuple

Returns a tuple filled with the per-coordinate gradients of the current arrangement or of the supplied coordinate list (if non-empty)

Dimension(self) → int

Returns the dimension of the ForceField

GetExtraPointPos(self, idx: int) → tuple

returns the location of an extra point as a tuple

Initialize(self) → None

initializes the force field (call this before minimizing)

MMFFAddAngleConstraint(self, idx1: int, idx2: int, idx3: int, relative: bool, minAngleDeg: float, maxAngleDeg: float, forceConstant: float) → None

Adds an angle constraint to the MMFF force field; if relative == True, then minAngleDeg and maxAngleDeg are intended as relative to the current angle.

MMFFAddDistanceConstraint(self, idx1: int, idx2: int, relative: bool, minLen: float, maxLen: float, forceConstant: float) → None

Adds a distance constraint to the MMFF force field; if relative == True, then minLen and maxLen are intended as relative to the current distance.

MMFFAddPositionConstraint(self, idx: int, maxDispl: float, forceConstant: float) → None

Adds a position constraint to the MMFF force field.

MMFFAddTorsionConstraint(self, idx1: int, idx2: int, idx3: int, idx4: int, relative: bool, minDihedralDeg: float, maxDihedralDeg: float, forceConstant: float) → None

Adds a dihedral angle constraint to the MMFF force field; if relative == True, then minDihedralDeg and maxDihedralDeg are intended as relative to the current dihedral angle.

Minimize(self, maxIts: int = 200, forceTol: float = 0.0001, energyTol: float = 1e-06) → int

Runs some minimization iterations.

Returns 0 if the minimization succeeded.

MinimizeTrajectory(self, snapshotFreq: int, maxIts: int = 200, forceTol: float = 0.0001, energyTol: float = 1e-06) → tuple

Runs some minimization iterations, recording the minimization trajectory every snapshotFreq steps.

Returns a (int, []) tuple; the int is 0 if the minimization succeeded, while the list contains Snapshot objects.

NumPoints(self) → int

Returns the number of points the ForceField is handling

Positions(self) → tuple

Returns a tuple filled with the coordinates of the points the ForceField is handling

UFFAddAngleConstraint(self, idx1: int, idx2: int, idx3: int, relative: bool, minAngleDeg: float, maxAngleDeg: float, forceConstant: float) → None

Adds an angle constraint to the UFF force field; if relative == True, then minAngleDeg and maxAngleDeg are intended as relative to the current angle.

UFFAddDistanceConstraint(self, idx1: int, idx2: int, relative: bool, minLen: float, maxLen: float, forceConstant: float) → None

Adds a distance constraint to the UFF force field; if relative == True, then minLen and maxLen are intended as relative to the current distance.

UFFAddPositionConstraint(self, idx: int, maxDispl: float, forceConstant: float) → None

Adds a position constraint to the UFF force field.

UFFAddTorsionConstraint(self, idx1: int, idx2: int, idx3: int, idx4: int, relative: bool, minDihedralDeg: float, maxDihedralDeg: float, forceConstant: float) → None

Adds a dihedral angle constraint to the UFF force field; if relative == True, then minDihedralDeg and maxDihedralDeg are intended as relative to the current dihedral angle.

class rdkit.ForceField.rdForceField.MMFFMolProperties(self, mol: rdkit.Chem.rdchem.Mol, mmffVariant: str = 'MMFF94', verbosity: int = MMFFVerbosity.MMFF_VERBOSITY_NONE)

Bases: object

MMFF molecular properties

GetMMFFAngleBendParams(self, mol: rdkit.Chem.rdchem.Mol, idx1: int, idx2: int, idx3: int) → object

Retrieves MMFF angle bend parameters for atoms with indexes idx1, idx2, idx3 as a (angleType, ka, theta0) tuple, or None if no parameters could be found

GetMMFFAngleTerm(self) → bool

Returns whether the angle term is included in the MMFF equation.

GetMMFFAtomType(self, idx: int) → int

Retrieves MMFF atom type for atom with index idx

GetMMFFBondStretchParams(self, mol: rdkit.Chem.rdchem.Mol, idx1: int, idx2: int) → object

Retrieves MMFF bond stretch parameters for atoms with indexes idx1, idx2 as a (bondType, kb, r0) tuple, or None if no parameters could be found

GetMMFFBondTerm(self) → bool

Returns whether the bond term is included in the MMFF equation.

GetMMFFDielectricConstant(self) → float

Returns the currently configured MMFF dielectric constant.

GetMMFFDielectricModel(self) → int

Returns the currently configured MMFF dielectric model (1: constant; 2: distance-dependent).

GetMMFFEleTerm(self) → bool

Returns whether the electrostatic term is included in the MMFF equation.

GetMMFFFormalCharge(self, idx: int) → float

Retrieves MMFF formal charge for atom with index idx

GetMMFFOopBendParams(self, mol: rdkit.Chem.rdchem.Mol, idx1: int, idx2: int, idx3: int, idx4: int) → object

Retrieves MMFF out-of-plane bending force constant for atoms with indexes idx1, idx2, idx3, idx4 as a koop float value

GetMMFFOopTerm(self) → bool

Returns whether the out-of-plane bend term is included in the MMFF equation.

GetMMFFPartialCharge(self, idx: int) → float

Retrieves MMFF partial charge for atom with index idx

GetMMFFStretchBendParams(self, mol: rdkit.Chem.rdchem.Mol, idx1: int, idx2: int, idx3: int) → object

Retrieves MMFF stretch-bend parameters for atoms with indexes idx1, idx2, idx3 as a (stretchBendType, kbaIJK, kbaKJI) tuple, or None if no parameters could be found

GetMMFFStretchBendTerm(self) → bool

Returns whether the stretch-bend term is included in the MMFF equation.

GetMMFFTorsionParams(self, mol: rdkit.Chem.rdchem.Mol, idx1: int, idx2: int, idx3: int, idx4: int) → object

Retrieves MMFF torsion parameters for atoms with indexes idx1, idx2, idx3, idx4 as a (torsionType, V1, V2, V3) tuple, or None if no parameters could be found

GetMMFFTorsionTerm(self) → bool

Returns whether the torsional term is included in the MMFF equation.

GetMMFFVariant(self) → str

Returns the currently configured MMFF variant (“MMFF94” or “MMFF94s”).

GetMMFFVdWParams(self, idx1: int, idx2: int) → object

Retrieves MMFF van der Waals parameters for atoms with indexes idx1, idx2 as a (R_ij_starUnscaled, epsilonUnscaled, R_ij_star, epsilon) tuple, or None if no parameters could be found

GetMMFFVdWTerm(self) → bool

Returns whether the Van der Waals term is included in the MMFF equation.

SetMMFFAngleTerm(self, state: bool = True) → None

Sets the angle term to be included in the MMFF equation (defaults to True)

SetMMFFBondTerm(self, state: bool = True) → None

Sets the bond term to be included in the MMFF equation (defaults to True)

SetMMFFDielectricConstant(self, dielConst: float = 1.0) → None

Sets the DielConst MMFF property (defaults to 1.0)

SetMMFFDielectricModel(self, dielModel: int = 1) → None

Sets the DielModel MMFF property (1: constant; 2: distance-dependent; defaults to constant)

SetMMFFEleTerm(self, state: bool = True) → None

Sets the electrostatic term to be included in the MMFF equation (defaults to True)

SetMMFFOopTerm(self, state: bool = True) → None

Sets the out-of-plane bend term to be included in the MMFF equation (defaults to True)

SetMMFFStretchBendTerm(self, state: bool = True) → None

Sets the stretch-bend term to be included in the MMFF equation (defaults to True)

SetMMFFTorsionTerm(self, state: bool = True) → None

Sets the torsional term to be included in the MMFF equation (defaults to True)

SetMMFFVariant(self, mmffVariant: str = 'MMFF94') → None

Sets the MMFF variant to be used (“MMFF94” or “MMFF94s”; defaults to “MMFF94”)

SetMMFFVdWTerm(self, state: bool = True) → None

Sets the Van der Waals term to be included in the MMFF equation (defaults to True)

SetMMFFVerbosity(self, verbosity: int = 0) → None

Sets the MMFF verbosity (0: none; 1: low; 2: high; defaults to 0)

class rdkit.ForceField.rdForceField.MMFFVerbosity(*values)

Bases: Enum

MMFF_VERBOSITY_HIGH = 2

MMFF_VERBOSITY_LOW = 1

MMFF_VERBOSITY_NONE = 0

class rdkit.ForceField.rdForceField.Snapshot

Bases: object

A snapshot of atomic coordinates from a minimization trajectory

GetEnergy(self) → float

Returns the energy for this Snapshot

GetPoint2D(self, pointNum: int) → rdkit.Geometry.rdGeometry.Point2D

Returns the coordinates at pointNum as a Point2D object; requires the Trajectory dimension to be == 2

GetPoint3D(self, pointNum: int) → rdkit.Geometry.rdGeometry.Point3D

Returns the coordinates at pointNum as a Point3D object; requires the Trajectory dimension to be >= 2

SetEnergy(self, energy: float) → None

Sets the energy for this Snapshot