chemaxon.calculations.conformer

class ConformerForceField(enum.IntEnum):

The supported types of force fields for the conformer generation calculation.

DREIDING = <ConformerForceField.DREIDING: 0>

DREIDING force field, a generic force field for molecular mechanics simulations.

MMFF94 = <ConformerForceField.MMFF94: 1>

Merck Molecular force field, a widely used force field for small molecules.

class ConformerEnergyUnit(enum.IntEnum):

The supported types of energy units for the conformer generation calculation.

KCAL_PER_MOL = <ConformerEnergyUnit.KCAL_PER_MOL: 0>

kcal/mol, a common unit for energy in molecular mechanics simulations. Note that 1 kcal/mol is approximately equal to 4.184 kJ/mol.

KJ_PER_MOL = <ConformerEnergyUnit.KJ_PER_MOL: 1>

kJ/mol, a common unit for energy in molecular mechanics simulations.

class ConformerOptimization(enum.IntEnum):

The supported types of optimization limits for the conformer generation calculation.

VERY_LOOSE = <ConformerOptimization.VERY_LOOSE: 0>

Very loose optimization limit, allowing for a larger number of conformers to be generated with less strict energy minimization.

NORMAL = <ConformerOptimization.NORMAL: 1>

Normal optimization limit, providing a balance between the number of conformers generated and the quality of energy minimization.

STRICT = <ConformerOptimization.STRICT: 2>

Strict optimization limit, resulting in fewer conformers being generated but with more rigorous energy minimization.

VERY_STRICT = <ConformerOptimization.VERY_STRICT: 3>

Very strict optimization limit, producing a small number of conformers with very rigorous energy minimization.

class ConformerOptions:

Class representing the options for a conformer generation calculation.

force_field: ConformerForceField = <ConformerForceField.DREIDING: 0>

Force field to use for conformer generation. Default is ConformerForceField.DREIDING.

energy_unit: ConformerEnergyUnit = <ConformerEnergyUnit.KCAL_PER_MOL: 0>

Unit for energy values. Default is ConformerEnergyUnit.KCAL_PER_MOL.

optimization_limit: ConformerOptimization = <ConformerOptimization.NORMAL: 1>

Optimization limit. Default is ConformerOptimization.NORMAL.

max_number_of_conformers: int = 100

Maximum number of conformers to generate. Default is 100.

diversity_limit: float = 0.1

Diversity limit for conformer selection. Default is 0.1.

time_limit: int = 900

Time limit for conformer generation in seconds. Default is 900.

calculate_lowest_energy_conformer: bool = False

If True, calculate the lowest energy conformer. Default is False.

prehydrogenize: bool = False

If True, pre-hydrogenize the molecule. Default is False.

hyperfine: bool = False

If True, include hyperfine structure. Default is False.

multi_fragment_optimization: bool = False

If True, optimize multi-fragment molecules with MMFF94. Default is False.

class ConformerResult:

Class representing the result of a conformer generation calculation.

ConformerResult(result: chemaxon.calculations.conformer._CConformerResult)
length: int

Number of conformers.

conformers: list[chemaxon.molecule.Molecule]

Conformers as list of Molecule objects.

energies: list[float]

Energies of the conformers as list of floats.

def conformers( mol: chemaxon.molecule.Molecule, options: ConformerOptions = <ConformerOptions object>) -> list[tuple[chemaxon.molecule.Molecule, float]]:

Calculate conformers for a molecule. Conformational isomerism is a form of isomerism that describes the phenomenon of molecules with the same structural formula having different 3D structure. Conformations are transformed into each other by rotations along rotatable bonds. Different conformations might have different energies.

Link: https://docs.chemaxon.com/latest/calculators_conformer-plugin.html

Parameters
  • mol: Molecule - The molecule for which to calculate conformers.
  • options: ConformerOptions - The options for the conformer generation calculation.
Returns

list[(Molecule, float)] - The list of conformers and their energies, sorted by energy in ascending order.