Skip to content

Commit 704488a

Browse files
IAlibayIAlibay
committed
Clean up notebook and delete extra files
1 parent 0fc2050 commit 704488a

3 files changed

Lines changed: 165 additions & 106 deletions

File tree

‎abfe_tutorial/abfe_analysis.ipynb‎

Lines changed: 36 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -33,23 +33,23 @@
3333
"name": "stdout",
3434
"output_type": "stream",
3535
"text": [
36-
"--2025-10-21 10:38:07-- https://zenodo.org/records/17348229/files/abfe_results.zip\n",
37-
"Resolving zenodo.org (zenodo.org)... 2001:1458:d00:25::100:372, 2001:1458:d00:24::100:f6, 2001:1458:d00:61::100:2f3, ...\n",
38-
"Connecting to zenodo.org (zenodo.org)|2001:1458:d00:25::100:372|:443... connected.\n",
36+
"--2025-10-21 11:53:17-- https://zenodo.org/records/17348229/files/abfe_results.zip\n",
37+
"Resolving zenodo.org (zenodo.org)... 188.185.45.92, 188.185.43.25, 188.185.48.194, ...\n",
38+
"Connecting to zenodo.org (zenodo.org)|188.185.45.92|:443... connected.\n",
3939
"HTTP request sent, awaiting response... 200 OK\n",
4040
"Length: 1005319 (982K) [application/octet-stream]\n",
4141
"Saving to: ‘abfe_results.zip’\n",
4242
"\n",
43-
"abfe_results.zip 100%[===================>] 981.76K 391KB/s in 2.5s \n",
43+
"abfe_results.zip 100%[===================>] 981.76K 718KB/s in 1.4s \n",
4444
"\n",
45-
"2025-10-21 10:38:19 (391 KB/s) - ‘abfe_results.zip’ saved [1005319/1005319]\n",
45+
"2025-10-21 11:53:20 (718 KB/s) - ‘abfe_results.zip’ saved [1005319/1005319]\n",
4646
"\n",
4747
"Archive: abfe_results.zip\n",
48-
" creating: abfe_results\n",
49-
" creating: abfe_results/results_2\n",
48+
" creating: abfe_results/\n",
49+
" creating: abfe_results/results_2/\n",
5050
" inflating: abfe_results/toluene_results.json \n",
51-
" creating: abfe_results/results_1\n",
52-
" creating: abfe_results/results_0\n",
51+
" creating: abfe_results/results_1/\n",
52+
" creating: abfe_results/results_0/\n",
5353
" inflating: abfe_results/results_2/1.json \n",
5454
" inflating: abfe_results/results_1/1.json \n",
5555
" inflating: abfe_results/results_0/1.json \n"
@@ -72,7 +72,7 @@
7272
},
7373
{
7474
"cell_type": "code",
75-
"execution_count": 1,
75+
"execution_count": 2,
7676
"id": "7fbf1482-25ca-427b-a881-af88a983461c",
7777
"metadata": {},
7878
"outputs": [],
@@ -107,7 +107,7 @@
107107
},
108108
{
109109
"cell_type": "code",
110-
"execution_count": 2,
110+
"execution_count": 3,
111111
"id": "04ccdedd-84e3-4ccc-ae42-4f3772acb115",
112112
"metadata": {},
113113
"outputs": [],
@@ -153,7 +153,7 @@
153153
},
154154
{
155155
"cell_type": "code",
156-
"execution_count": 3,
156+
"execution_count": 4,
157157
"id": "3733c540-de62-45a0-ba66-268397a38b49",
158158
"metadata": {},
159159
"outputs": [],
@@ -211,7 +211,7 @@
211211
},
212212
{
213213
"cell_type": "code",
214-
"execution_count": 4,
214+
"execution_count": 5,
215215
"id": "08afcbcf-34a8-4450-a967-eb4ed5800ee1",
216216
"metadata": {},
217217
"outputs": [],
@@ -245,7 +245,7 @@
245245
},
246246
{
247247
"cell_type": "code",
248-
"execution_count": 5,
248+
"execution_count": 6,
249249
"id": "a5d4aef3-1fab-40b4-848c-d59df8ee1441",
250250
"metadata": {},
251251
"outputs": [],
@@ -259,7 +259,7 @@
259259
},
260260
{
261261
"cell_type": "code",
262-
"execution_count": 6,
262+
"execution_count": 7,
263263
"id": "0621e3a2-7906-4661-a640-c414456f8869",
264264
"metadata": {},
265265
"outputs": [],
@@ -291,7 +291,7 @@
291291
},
292292
{
293293
"cell_type": "code",
294-
"execution_count": 7,
294+
"execution_count": 8,
295295
"id": "5821b7f7-6aed-4138-9502-44df3af52647",
296296
"metadata": {},
297297
"outputs": [],
@@ -322,7 +322,7 @@
322322
},
323323
{
324324
"cell_type": "code",
325-
"execution_count": 8,
325+
"execution_count": 9,
326326
"id": "e021b2ea-db13-4e47-a6d1-cf5229b5b494",
327327
"metadata": {},
328328
"outputs": [],
@@ -363,7 +363,7 @@
363363
},
364364
{
365365
"cell_type": "code",
366-
"execution_count": 9,
366+
"execution_count": 10,
367367
"id": "b077c4e2-373a-4314-a527-186bb4683262",
368368
"metadata": {},
369369
"outputs": [],
@@ -418,15 +418,17 @@
418418
},
419419
{
420420
"cell_type": "code",
421-
"execution_count": 10,
421+
"execution_count": 11,
422422
"id": "7bc49c0e-6fec-409c-a01c-42c35f57dcc6",
423423
"metadata": {},
424424
"outputs": [
425425
{
426426
"name": "stderr",
427427
"output_type": "stream",
428428
"text": [
429-
"/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
429+
"/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/openmoltools/utils.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
430+
" from pkg_resources import resource_filename\n",
431+
"/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
430432
"\n",
431433
"Due to the on going maintenance burden of keeping command line application\n",
432434
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
@@ -461,7 +463,7 @@
461463
},
462464
{
463465
"cell_type": "code",
464-
"execution_count": 11,
466+
"execution_count": 12,
465467
"id": "46996a74-709c-41f2-ac39-0f77fb33371e",
466468
"metadata": {},
467469
"outputs": [],
@@ -472,7 +474,7 @@
472474
},
473475
{
474476
"cell_type": "code",
475-
"execution_count": 12,
477+
"execution_count": 13,
476478
"id": "d1a6ad61-1e5a-4d8a-9067-9ed428ef145c",
477479
"metadata": {},
478480
"outputs": [
@@ -518,7 +520,7 @@
518520
"0 1 -18.36 0.98"
519521
]
520522
},
521-
"execution_count": 12,
523+
"execution_count": 13,
522524
"metadata": {},
523525
"output_type": "execute_result"
524526
}
@@ -538,7 +540,7 @@
538540
},
539541
{
540542
"cell_type": "code",
541-
"execution_count": 13,
543+
"execution_count": 14,
542544
"id": "8b2c1dd8-ffa3-4585-94a7-4a1ed1454f30",
543545
"metadata": {},
544546
"outputs": [],
@@ -549,7 +551,7 @@
549551
},
550552
{
551553
"cell_type": "code",
552-
"execution_count": 14,
554+
"execution_count": 15,
553555
"id": "08b72901-9c71-460b-b5da-9fb4a35e07f7",
554556
"metadata": {},
555557
"outputs": [
@@ -661,22 +663,14 @@
661663
"8 standard_state_correction 1 -9.0 0.0"
662664
]
663665
},
664-
"execution_count": 14,
666+
"execution_count": 15,
665667
"metadata": {},
666668
"output_type": "execute_result"
667669
}
668670
],
669671
"source": [
670672
"df_raw"
671673
]
672-
},
673-
{
674-
"cell_type": "code",
675-
"execution_count": null,
676-
"id": "ae092ba5-3263-4e39-bc7d-82e8f1e1f58c",
677-
"metadata": {},
678-
"outputs": [],
679-
"source": []
680674
}
681675
],
682676
"metadata": {
@@ -695,7 +689,14 @@
695689
"name": "python",
696690
"nbconvert_exporter": "python",
697691
"pygments_lexer": "ipython3",
698-
"version": "3.12.10"
692+
"version": "3.12.11"
693+
},
694+
"widgets": {
695+
"application/vnd.jupyter.widget-state+json": {
696+
"state": {},
697+
"version_major": 2,
698+
"version_minor": 0
699+
}
699700
}
700701
},
701702
"nbformat": 4,

‎abfe_tutorial/abfe_json/toluene.json‎

Lines changed: 0 additions & 1 deletion
This file was deleted.

0 commit comments

Comments
 (0)