Some cleanup

Author: hannahbaumann

openmm_septop/septop_analysis.ipynb

@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "id": "f47af914-150a-4a57-8837-c12e14cb8802",
    "metadata": {},
    "outputs": [],
@@ -48,7 +48,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "c185164a-f1c6-483b-b013-f4d499889570",
    "metadata": {},
    "outputs": [],
@@ -93,7 +93,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "3733c540-de62-45a0-ba66-268397a38b49",
    "metadata": {},
    "outputs": [],
@@ -153,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "id": "08afcbcf-34a8-4450-a967-eb4ed5800ee1",
    "metadata": {},
    "outputs": [],
@@ -191,16 +191,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def _generate_raw(legs:dict, allow_partial=True) -> None:\n",
+    "def _generate_raw(legs:dict) -> None:\n",
     "    \"\"\"\n",
     "    Write out all legs found and their DG values, or indicate that they have failed.\n",
     "\n",
     "    Parameters\n",
     "    ----------\n",
     "    legs : dict\n",
     "        Dict of legs to write out.\n",
-    "    allow_partial : bool, optional\n",
-    "        Unused for this function, since all results will be included.\n",
     "    \"\"\"\n",
     "    data = []\n",
     "    for ligpair, results in sorted(legs.items()):\n",
@@ -230,16 +228,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def _generate_ddg(legs:dict, allow_partial:bool) -> None:\n",
+    "def _generate_ddg(legs:dict) -> None:\n",
     "    \"\"\"Compute and write out DDG values for the given legs.\n",
     "\n",
     "    Parameters\n",
     "    ----------\n",
     "    legs : dict\n",
     "        Dict of legs to write out.\n",
-    "    allow_partial : bool\n",
-    "        If ``True``, no error will be thrown for incomplete or invalid results,\n",
-    "        and DDGs will be reported for whatever valid results are found.\n",
     "    \"\"\"\n",
     "    data = []\n",
     "    for ligpair, results in sorted(legs.items()):\n",
@@ -265,22 +260,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def _generate_dg_mle(legs: dict, allow_partial: bool) -> None:\n",
+    "def _generate_dg_mle(legs: dict) -> None:\n",
     "    \"\"\"Compute and write out DG values for the given legs.\n",
     "\n",
     "    Parameters\n",
     "    ----------\n",
     "    legs : dict\n",
     "        Dict of legs to write out.\n",
-    "    allow_partial : bool\n",
-    "        If ``True``, no error will be thrown for incomplete or invalid results,\n",
-    "        and DGs will be reported for whatever valid results are found.\n",
     "    \"\"\"\n",
     "    import networkx as nx\n",
     "    import numpy as np\n",
     "    from cinnabar.stats import mle\n",
     "\n",
-    "    DDGs = _generate_ddg(legs, allow_partial=allow_partial)\n",
+    "    DDGs = _generate_ddg(legs)\n",
     "    MLEs = []\n",
     "    expected_ligs = []\n",
     "\n",
@@ -417,7 +409,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_ddg = _generate_ddg(ddgs, allow_partial=True)\n",
+    "df_ddg = _generate_ddg(ddgs)\n",
     "df_ddg.to_csv('ddg.tsv', sep=\"\\t\", lineterminator=\"\\n\", index=False)"
    ]
   },
@@ -519,7 +511,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_dg = _generate_dg_mle(ddgs, allow_partial=True)\n",
+    "df_dg = _generate_dg_mle(ddgs)\n",
     "df_dg.to_csv('dg.tsv', sep=\"\\t\", lineterminator=\"\\n\", index=False)"
    ]
   },