Merge pull request #245 from UC-Davis-molecular-computing/233-for-spe…

…ed-minimize-time-spent-creating-pintquantity-objects 233 for speed minimize time spent creating `pint.Quantity` objects
UC-Davis-molecular-computing · Oct 8, 2023 · 2ffe6ad · 2ffe6ad
2 parents 563a4a7 + c76e7f0
commit 2ffe6ad
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diff --git a/examples/many_strands_no_common_domains.py b/examples/many_strands_no_common_domains.py
@@ -8,11 +8,6 @@
 import nuad.constraints as nc  # type: ignore
 import nuad.vienna_nupack as nv  # type: ignore
 import nuad.search as ns  # type: ignore
-from nuad.constraints import NumpyFilter
-
-
-def f(x: int | float) -> float:
-    return x / 2
 
 
 # command-line arguments
@@ -51,13 +46,13 @@ def main() -> None:
     random_seed = 1
 
     # many 4-domain strands with no common domains, 4 domains each, every domain length = 10
-    # just for testing parallel processing
 
     # num_strands = 3
+    # num_strands = 5
+    # num_strands = 10
     # num_strands = 10
-    num_strands = 26
     # num_strands = 50
-    # num_strands = 100
+    num_strands = 100
     # num_strands = 355
 
     design = nc.Design()
@@ -77,7 +72,7 @@ def main() -> None:
     parallel = False
     # parallel = True
 
-    numpy_filters: List[NumpyFilter] = [
+    numpy_filters: List[nc.NumpyFilter] = [
         nc.NearestNeighborEnergyFilter(-9.3, -9.0, 52.0),
         # nc.BaseCountFilter(base='G', high_count=1),
         # nc.BaseEndFilter(bases=('C', 'G')),
@@ -157,11 +152,11 @@ def main() -> None:
     params = ns.SearchParameters(constraints=[
         # domain_nupack_ss_constraint,
         # strand_individual_ss_constraint,
-        # strand_pairs_rna_duplex_constraint,
+        strand_pairs_rna_duplex_constraint,
         # strand_pairs_rna_plex_constraint,
         # strand_pair_nupack_constraint,
         # domain_pair_nupack_constraint,
-        domain_pairs_rna_plex_constraint,
+        # domain_pairs_rna_plex_constraint,
         # domain_pairs_rna_duplex_constraint,
         # strand_base_pair_prob_constraint,
         # nc.domains_not_substrings_of_each_other_constraint(),

diff --git a/notebooks/result-allocate-time-trials.ipynb b/notebooks/result-allocate-time-trials.ipynb
@@ -87,6 +87,75 @@
     "%timeit collect_results_into_noparse_nonormalize(energies, threshold, results)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "fa645805-54fd-4e64-9940-ae0a4da5ebc8",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "image/png": 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\n",
+      "text/plain": [
+       "<Figure size 432x288 with 1 Axes>"
+      ]
+     },
+     "metadata": {
+      "needs_background": "light"
+     },
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# test search.display_report after removing pint\n",
+    "\n",
+    "import nuad.constraints as nc\n",
+    "import nuad.search as ns\n",
+    "\n",
+    "random_seed = 1\n",
+    "\n",
+    "# many 4-domain strands with no common domains, 4 domains each, every domain length = 10\n",
+    "\n",
+    "# num_strands = 3\n",
+    "# num_strands = 5\n",
+    "# num_strands = 10\n",
+    "# num_strands = 50\n",
+    "num_strands = 100\n",
+    "\n",
+    "design = nc.Design()\n",
+    "#                     si         wi         ni         ei\n",
+    "# strand i is    [----------|----------|----------|---------->\n",
+    "for i in range(num_strands):\n",
+    "    design.add_strand([f's{i}', f'w{i}', f'n{i}', f'e{i}'])\n",
+    "\n",
+    "numpy_filters = [nc.NearestNeighborEnergyFilter(-9.3, -9.0, 52.0)]\n",
+    "\n",
+    "replace_with_close_sequences = True\n",
+    "domain_pool_10 = nc.DomainPool(f'length-10_domains', 10,\n",
+    "                               numpy_filters=numpy_filters,\n",
+    "                               replace_with_close_sequences=replace_with_close_sequences,\n",
+    "                               )\n",
+    "domain_pool_11 = nc.DomainPool(f'length-11_domains', 11,\n",
+    "                               numpy_filters=numpy_filters,\n",
+    "                               replace_with_close_sequences=replace_with_close_sequences,\n",
+    "                               )\n",
+    "\n",
+    "for strand in design.strands:\n",
+    "    for domain in strand.domains[:2]:\n",
+    "        domain.pool = domain_pool_10\n",
+    "    for domain in strand.domains[2:]:\n",
+    "        domain.pool = domain_pool_11\n",
+    "\n",
+    "strand_pairs_rna_duplex_constraint = nc.rna_duplex_strand_pairs_constraint(\n",
+    "    threshold=-1.0, temperature=52, short_description='RNAduplex')\n",
+    "\n",
+    "constraints = [strand_pairs_rna_duplex_constraint]\n",
+    "\n",
+    "ns.assign_sequences_to_domains_randomly_from_pools(design=design, warn_fixed_sequences=True)\n",
+    "\n",
+    "ns.display_report(design=design, constraints=constraints)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 22,