Add topology writing functionality and MMFF94S handling

[joserdf]

No description provided.

[Copilot]

Pull Request Overview

This PR introduces functionality to apply MMFF94S parameters to receptors and generate a corresponding topology file.

• Adds a new module (receptor_mmff94s.py) to load MMFF94S data and write topology in mmCIF format.
• Injects MMFF atom types and partial charges into the mmCIF data structure.
• Calls write_topology in main.py after modeller operations to produce a _topology.cif file.

Reviewed Changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 2 comments.

File	Description
docktprep/receptor_mmff94s.py	New functions to load MMFF94S parameters and write topology data into mmCIF files.
docktprep/main.py	Invokes write_topology after receptor processing.

Comments suppressed due to low confidence (3)

docktprep/receptor_mmff94s.py:22

• [nitpick] The parameter name file shadows the built-in Python name; consider renaming it to something like output_path for clarity.

def write_topology(receptor: Receptor, file: str):

docktprep/receptor_mmff94s.py:22

• [nitpick] The file parameter is not described in the docstring; please add an Args: entry to clarify what this argument represents and its expected format.

def write_topology(receptor: Receptor, file: str):

docktprep/main.py:30

• [nitpick] Topology generation is invoked unconditionally; consider adding a CLI flag (e.g., --write-topology) to let users opt in or out.

    write_topology(receptor, args.output)

[Copilot]

[nitpick] Using file.split(".")[0] can mis-handle filenames with multiple dots or no extension; consider using os.path.splitext(output_path)[0] to derive the base name.

Suggested change

	with open(file.split(".")[0] + "_topology.cif", "w") as f:
	with open(os.path.splitext(file)[0] + "_topology.cif", "w") as f:

[Copilot]

[nitpick] Loading the pickle via a hard-coded relative path may break in deployed packages; consider using importlib.resources or pkg_resources to access bundled data.

Suggested change

	with open("docktprep/mmff94s_dict.pkl", "rb") as f:
	with importlib.resources.open_binary("docktprep", "mmff94s_dict.pkl") as f: