feat: getting abfe working

docs/dev/job-widget.md

@@ -38,9 +38,6 @@ To disable blocking mode, you can either unset the variable or set it to a falsy
 # Unset the variable
 unset JOB_WATCH_BLOCK
 
-# Or set it to an empty string
-export JOB_WATCH_BLOCK=""
-
 # Or set it to a falsy value like 0, false, no, or off
 export JOB_WATCH_BLOCK=0
 ```

docs/notebooks/clean/abfe.ipynb

@@ -0,0 +1,186 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5c618447-f60b-4290-83f0-92ca9cd03ee0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "858a2b5a-6550-4e0c-805c-c1cb92761b14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from dotenv import load_dotenv\n",
+    "from deeporigin.drug_discovery import Complex, BRD_DATA_DIR, Protein, Ligand, LigandSet\n",
+    "load_dotenv()\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "de846db3-3d86-44f7-8ea6-b3c8bff2be51",
+   "metadata": {},
+   "source": [
+    "\n",
+    "# ABFE workflow\n",
+    "\n",
+    "This notebook shows you how to run ABFE on Deep Origin, and serves as a quick tutorial for running ABFE. \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "01bd9f1d-1fc6-456c-bc18-9633d2f0023f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim = Complex.from_dir(BRD_DATA_DIR)\n",
+    "sim.ligands"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9dad154d-a618-403a-83a7-ee0094ccdc74",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim.ligands.to_dataframe()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "045aeed9-98e1-4d2b-a078-71c8f044ac72",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# use this ligand\n",
+    "ligand = [ligand for ligand in sim.ligands if ligand.name == \"cmpd 4 (Crotyl)\"][0]\n",
+    "ligand"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "edbe68a9-8aea-40b0-8726-ece63149a098",
+   "metadata": {},
+   "source": [
+    "## Prepare system"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0e7c793a-0095-4fb7-84fb-a5fcff23a276",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prepared_system = sim.prepare(ligand=ligand)\n",
+    "prepared_system.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f57837f4-605b-4a1b-99c6-af90956c3483",
+   "metadata": {},
+   "source": [
+    "## Quote ABFE\n",
+    "\n",
+    "We can estimate the cost of an ABFE run without running it. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5175f2a9-e4c2-49ce-8d5d-618903a869b1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "jobs = sim.abfe.run(ligands=[ligand], quote=True)\n",
+    "job = jobs[0]\n",
+    "job"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a32639b1-f247-42a5-acab-b94f775cc570",
+   "metadata": {},
+   "source": [
+    "If we're happy with this price, we can confirm the job (which runs it)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6deda895-5617-4fdd-ace5-306f2d181a7e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "job.confirm()\n",
+    "job"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "010e0815-52df-4936-bfd3-49f6efdf31c4",
+   "metadata": {},
+   "source": [
+    "## Monitor job\n",
+    "\n",
+    "To monitor a job, use the job.watch method:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0a09eec9-a1e1-4ca4-b3e0-4ee4e98c58f2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "job.watch()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "558d5f5e-afb8-43d7-803f-abb6cea0c852",
+   "metadata": {},
+   "source": [
+    "## Get results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b7094160-64c1-4b04-91db-eb54e3287b29",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = sim.abfe.get_results()\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "33c5ec29-7df1-4c5c-ad43-d4ef3ec5986f",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/notebooks/clean/docking-many-ligands.ipynb

@@ -63,10 +63,7 @@
     "    DATA_DIR,\n",
     "    Protein,\n",
     "    LigandSet,\n",
-    ")\n",
-    "import deeporigin\n",
-    "\n",
-    "deeporigin.__version__"
+    ")"
    ]
   },
   {

scripts/build_docs.sh

@@ -17,7 +17,7 @@ if [ -d "docs/notebooks/clean" ] && [ "$(ls -A docs/notebooks/clean/*.ipynb 2>/d
 
   # Start mock server in background for local testing
   echo "🚀 Starting mock server..."
-  uv run python -m tests.run_mock_server --port 4931 > /dev/null 2>&1 &
+  uv run python -m tests.run_mock_server --port 4931 --abfe-duration 5 > /dev/null 2>&1 &
   MOCK_SERVER_PID=$!
 
   # Wait a moment for server to start

src/drug_discovery/complex.py

@@ -125,7 +125,7 @@ def prepare(
         self,
         ligand: Optional[Ligand] = None,
         *,
-        padding: float = 2.0,
+        padding: float = 1.0,
         retain_waters: bool = False,
         add_H_atoms: bool = False,  # NOSONAR
         protonate_protein: bool = False,

src/functions/sysprep.py

@@ -11,7 +11,7 @@ def run_sysprep(
     *,
     protein: Protein,
     ligand: Ligand,
-    padding: float = 1.5,
+    padding: float = 1.0,
     retain_waters: bool = False,
     add_H_atoms: bool = True,  # NOSONAR
     protonate_protein: bool = True,

tests/fixtures/deeporigin.abfe-end-to-end/billing-transaction.json

@@ -1,18 +1,18 @@
 {
     "items": [
         {
-            "qty": 0,
-            "itemCode": "DO_ABFE",
-            "priceEach": 120,
-            "isApproved": true,
-            "priceTotal": 183.9370042608,
             "actionRequest": null,
             "authorizationId": "691b838fac1dc207f1cb3c3e",
-            "purchaseApprovalComment": null
+            "isApproved": true,
+            "itemCode": "DO_ABFE",
+            "priceEach": 120,
+            "priceTotal": 83.9370042608,
+            "purchaseApprovalComment": null,
+            "qty": 0
         }
     ],
     "orgId": "deeporigin",
     "status": "Approved",
-    "totalCost": 183.9370042608,
+    "totalCost": 83.9370042608,
     "transactionId": "691b838fac1dc207f1cb3c3c"
 }

tests/fixtures/deeporigin.abfe-end-to-end/quotation-result.json

@@ -3,31 +3,31 @@
     "failedQuotations": [],
     "successfulQuotations": [
         {
-            "qty": 0,
-            "orgId": "deeporigin",
-            "status": "OK",
             "itemCode": "DO_ABFE",
-            "qty_vars": {
-                "abfe_atoms": 57337,
-                "abfe_repeats": 1,
-                "abfe_windows": 32,
-                "abfe_production_steps": 1250000,
-                "abfe_equilibration_steps": 754999
-            },
+            "orgId": "deeporigin",
             "priceEach": 120,
-            "priceTotal": 183.9370042608,
+            "priceTotal": 83.9370042608,
+            "pricingRecordType": "regular",
             "pricingRecords": [
                 {
-                    "qty": 1.53280836884,
                     "itemKey": "DO_ABFE",
                     "itemName": "Absolute Binding Free Energy (ABFE)",
                     "priceEach": 120,
+                    "qty": 1.53280836884,
+                    "tierQtyFrom": 0,
                     "tierQtyTo": 0,
-                    "totalPrice": 183.9370042608,
-                    "tierQtyFrom": 0
+                    "totalPrice": 83.9370042608
                 }
             ],
-            "pricingRecordType": "regular"
+            "qty": 0,
+            "qty_vars": {
+                "abfe_atoms": 57337,
+                "abfe_equilibration_steps": 754999,
+                "abfe_production_steps": 1250000,
+                "abfe_repeats": 1,
+                "abfe_windows": 32
+            },
+            "status": "OK"
         }
     ]
 }