MolecularDiffusion.runmodes.analyze.xtb_electronic

XTB Electronic Property Computation using morfeus.

Provides functions to compute electronic properties for XYZ files using the morfeus XTB interface, with support for batch processing and multiple output formats (CSV, JSON, ASE database).

Attributes

ATOMIC_LEVEL_GROUPS

MOLECULAR_LEVEL_GROUPS

PROPERTY_GROUPS

logger

Functions

batch_xtb_electronic(→ pandas.DataFrame)

Batch compute XTB electronic properties for XYZ files in a directory.

compute_xtb_electronic(→ dict[str, Any])

Compute XTB electronic properties for a single XYZ file.

Module Contents

MolecularDiffusion.runmodes.analyze.xtb_electronic.batch_xtb_electronic(input_dir: str, output_path: str | None = None, output_format: str = 'csv', method: int | str = 2, charge: int = 0, n_unpaired: int = 0, solvent: str | None = None, properties: list[str] | None = None, corrected: bool = True, timeout: int = 120, n_jobs: int = 1) → pandas.DataFrame

Batch compute XTB electronic properties for XYZ files in a directory.

Parameters:

  • input_dir – Directory containing XYZ files

  • output_path – Output file path (without extension for ‘all’ format)

  • output_format – Output format (“csv”, “json”, “ase”, or “all”)

  • method – XTB method (1=GFN1, 2=GFN2, “ptb”=PTB)

  • charge – Molecular charge

  • n_unpaired – Number of unpaired electrons

  • solvent – Solvent name for implicit solvation

  • properties – List of property groups to compute

  • corrected – Whether to apply empirical IP/EA correction

  • timeout – Timeout per molecule in seconds

  • n_jobs – Number of parallel jobs

Returns:

DataFrame with results

MolecularDiffusion.runmodes.analyze.xtb_electronic.compute_xtb_electronic(xyz_path: str, method: int | str = 2, charge: int = 0, n_unpaired: int = 0, solvent: str | None = None, properties: list[str] | None = None, corrected: bool = True) → dict[str, Any]

Compute XTB electronic properties for a single XYZ file.

Parameters:

  • xyz_path – Path to XYZ file

  • method – XTB method (1=GFN1, 2=GFN2, “ptb”=PTB)

  • charge – Molecular charge

  • n_unpaired – Number of unpaired electrons

  • solvent – Solvent name for implicit solvation (e.g., “water”, “thf”)

  • properties – List of property groups to compute. If None, computes “energy”

  • corrected – Whether to apply empirical IP/EA correction

Returns:

Dictionary containing computed properties and metadata

MolecularDiffusion.runmodes.analyze.xtb_electronic.ATOMIC_LEVEL_GROUPS
MolecularDiffusion.runmodes.analyze.xtb_electronic.MOLECULAR_LEVEL_GROUPS
MolecularDiffusion.runmodes.analyze.xtb_electronic.PROPERTY_GROUPS
MolecularDiffusion.runmodes.analyze.xtb_electronic.logger