tqchem.ttconf.conformer_results¶
Classes¶
Class to store and process results of a conformer search |
Functions¶
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Escape special characters in string to make it printable as is |
Module Contents¶
- tqchem.ttconf.conformer_results.write_xyz_list(filepath: pathlib.Path | str, xyzs: list[str]) None¶
- tqchem.ttconf.conformer_results.escape_new_lines(string: str) str¶
Escape special characters in string to make it printable as is
- class tqchem.ttconf.conformer_results.ConformerResults(dataframe: pandas.DataFrame, molecular_grid: tqchem.internal_coordinates.MolecularGrid)¶
Class to store and process results of a conformer search
- dataframe¶
Dataframe containing the objective, energy, gridpoints, relaxed & aligned xyz data, and rmsd values indicating the fit of the xyz to the minimum energy xyz
- Type:
pd.DataFrame
- molgrid¶
MolecularGrid to evaluate the dihedral gridpoints to obtain the unrelaxed molecules sampled during the optimization procedure.
- Type:
- __str__: str
Return data frame string representation
- minimum_energy_xyz: str, float
Return xyz string (after gradient optimization) and energy of molecule with lowest energy
- minimum_objective_xyz: str, float
Return xyz string (after gradient optimization) and objective of molecule with lowest objective
- minimum_energy_unrelaxed_conformer: MolecularSystem, float
Return Molecular system (before gradient optimization) with lowest energy
- minimum_objective_unrelaxed_conformer: MolecularSystem, float
Return Molecular system (before gradient optimization) with lowest objective value
- sampled_unrelaxed_conformers: list[MolecularSystem]
Return list of all sampled molecular systems
- write_sampled_unrelaxed_conformers: None
Write all sampled conformers to one xyz file with energies in the comment
- minimum_energy_ensemble: list[MolecularSystem]
Molecular systems within an energy margin around the lowest energy conformer
- write_minimum_energy_ensemble: None
Write all conformers within an energy margin around the lowest energy conformer
- dataframe: _typeshed.Incomplete¶
- molgrid: _typeshed.Incomplete¶
- minimum_energy_xyz() str¶
Return xyz content of gradient optimized geometry with lowest energy
- minimum_objective_xyz() str¶
Return xyz content of gradient optimized geometry with lowest objective
- minimum_energy_unrelaxed_conformer() tqchem.internal_coordinates.MolecularSystem¶
Return Molecular system with lowest energy before gradient optimization
- minimum_objective_unrelaxed_conformer() tqchem.internal_coordinates.MolecularSystem¶
Return Molecular system with lowest objective before gradient optimization
- sampled_unrelaxed_conformers() list[tqchem.internal_coordinates.MolecularSystem]¶
Return list of all sampled unrelaxed molecular systems
- write_sampled_unrelaxed_conformers(filepath: pathlib.Path | str) None¶
Write all sampled unrelaxed conformers to one xyz file
Energy and objective (of the relaxed structures) are listed in the comment line
- minimum_energy_ensemble(energy_difference: float = 0.2, rmsd_cutoff: float = 0.1) list[str]¶
xyz strings within an energy and rmsd margin around the lowest energy conformer
The xyz strings contain the gradient optimized structures and their energy and objective value are listed in the comment line
- write_minimum_energy_ensemble(filepath: pathlib.Path | str, energy_difference: float = 0.2, rmsd_cutoff: float = 0.1) None¶
Write xyz within an energy and rmsd margin around the lowest energy conformer
The xyz strings contain the gradient optimized structures and their energy and objective value are listed in the comment line
- dataframe_to_csv(*args)¶
Convert xyz column to raw string and write dataframe to csv
Wrapper for DataFrame.to_csv which accepts the same keyword arguments