feat: bumped version of ABFE (#233)

Author: sg-s

notebooks/abfe.py

@@ -34,7 +34,6 @@ def _():
 @app.cell
 def _():
     sim = Complex.from_dir(EXAMPLE_DATA_DIR)
-    sim.connect()
     return (sim,)
 
 
@@ -44,6 +43,26 @@ def _(sim):
     return
 
 
+@app.cell(hide_code=True)
+def _():
+    mo.md(
+        r"""
+    ## System preparation
+
+    Before we start a ABFE run, we can prepare the system using `sim.prepare`. Doing so shows a preview of the prepared system. 
+
+
+    """
+    )
+    return
+
+
+@app.cell
+def _(sim):
+    sim.prepare(ligand=sim.ligands[0])
+    return
+
+
 @app.cell(hide_code=True)
 def _():
     mo.md(
@@ -64,9 +83,11 @@ def _():
 
 
 @app.cell
-def _():
-    # sim.abfe.run_end_to_end(ligand_ids=["Ligands-1"])
-    return
+def _(sim):
+    sim.abfe.set_test_run()
+    jobs = sim.abfe.run_end_to_end(ligands=[sim.ligands[0]])
+    this_job = jobs[0]
+    return (this_job,)
 
 
 @app.cell(hide_code=True)
@@ -82,9 +103,8 @@ def _():
 
 
 @app.cell
-def _(sim):
-    job = sim.abfe.jobs[0]
-    job
+def _(this_job):
+    this_job
     return
 
 
@@ -101,8 +121,8 @@ def _():
 
 
 @app.cell
-def _():
-    # job.cancel()
+def _(this_job):
+    this_job.cancel()
     return
 
 

src/drug_discovery/abfe.py

@@ -28,7 +28,7 @@ class ABFE(WorkflowStep):
     Objects instantiated here are meant to be used within the Complex class."""
 
     """tool version to use for ABFE"""
-    tool_version = "0.2.6"
+    tool_version = "0.2.7"
     _tool_key = "deeporigin.abfe-end-to-end"  # Tool key for ABFE jobs
 
     _max_atom_count: int = 100_000

src/drug_discovery/structures/ligand.py

@@ -53,7 +53,6 @@
 ligand.visualize()
 """
 
-# from deeporigin.drug_discovery.utilities.props import predict_properties, protonate
 from dataclasses import dataclass, field
 import os
 from pathlib import Path
@@ -979,9 +978,9 @@ def show_ligands(ligands: list[Ligand]):
     # re‑index your DataFrame
     df = df[new_order]
 
-    from deeporigin.utils.notebook import _in_marimo
+    from deeporigin.utils.notebook import get_notebook_environment
 
-    if _in_marimo():
+    if get_notebook_environment() == "marimo":
         import marimo as mo
 
         return mo.plain(df)