schrodinger.livedesign.pymol_convert module

PyMOL conversion utilities for LiveDesign.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.livedesign.pymol_convert.run_pymol_script(pml_script: str) → None

Run a PyMOL script command using subprocess.

Parameters:

pml_script – PyMOL script to execute

Raises:

• RuntimeError – if PyMOL cannot be located

• subprocess.CalledProcessError – if PyMOL execution fails

schrodinger.livedesign.pymol_convert.pse_to_mols(pse_block: str) → List[Mol]

Convert a PyMOL session file (.pse) to RDKit molecules via Maestro format.

A single PSE file can contain multiple molecules/objects. This function extracts all of them.

Parameters:

pse_block – PSE file contents as string (binary data encoded as string)

Returns:

List of RDKit molecules

schrodinger.livedesign.pymol_convert.mols_to_pse(mols: List[Mol]) → str

Convert RDKit molecules to a PyMOL session file (.pse) via Maestro format.

All molecules are stored in a single PSE file, which can contain multiple objects.

Parameters:

mols – List of RDKit molecules

Returns:

PSE file contents as string (binary data encoded as string)