Skip to content

Commit 853eee3

Browse files
hannahbaumannhannahbaumann
committed
Small update
1 parent 5255932 commit 853eee3

1 file changed

Lines changed: 7 additions & 132 deletions

File tree

‎cookbook/repairing_broken_networks.ipynb‎

Lines changed: 7 additions & 132 deletions
Original file line numberDiff line numberDiff line change
@@ -500,7 +500,7 @@
500500
},
501501
{
502502
"cell_type": "code",
503-
"execution_count": 14,
503+
"execution_count": 16,
504504
"id": "fbdc9724",
505505
"metadata": {},
506506
"outputs": [],
@@ -565,143 +565,26 @@
565565
" return AlchemicalNetwork(transformations)\n",
566566
"\n",
567567
"\n",
568-
"def dump_transformations(network, out_dir):\n",
568+
"def save_transformations(network, out_dir):\n",
569569
" out_dir = pathlib.Path(out_dir)\n",
570570
" (out_dir / \"transformations\").mkdir(parents=True, exist_ok=True)\n",
571571
" with open(out_dir / \"alchemical_network.json\", \"w\") as f:\n",
572572
" json.dump(network.to_dict(), f, cls=JSON_HANDLER.encoder)\n",
573573
" for transform in network.edges:\n",
574-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")"
574+
" transform.to_json(out_dir / \"transformations\" / f\"{transform.name}.json\")"
575575
]
576576
},
577577
{
578578
"cell_type": "code",
579-
"execution_count": null,
579+
"execution_count": 18,
580580
"id": "42ac44ab",
581581
"metadata": {},
582582
"outputs": [
583583
{
584-
"name": "stderr",
584+
"name": "stdout",
585585
"output_type": "stream",
586586
"text": [
587-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
588-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
589-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
590-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
591-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
592-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
593-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
594-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
595-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
596-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
597-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
598-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
599-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
600-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
601-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
602-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
603-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
604-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
605-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
606-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
607-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
608-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
609-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
610-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
611-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
612-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
613-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
614-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
615-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
616-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
617-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
618-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
619-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
620-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
621-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
622-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
623-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
624-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
625-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
626-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
627-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
628-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
629-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
630-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
631-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
632-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
633-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
634-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
635-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
636-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
637-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
638-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
639-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
640-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
641-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
642-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
643-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
644-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
645-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
646-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
647-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
648-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
649-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
650-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
651-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
652-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
653-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
654-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
655-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
656-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
657-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
658-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
659-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
660-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
661-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
662-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
663-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
664-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
665-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
666-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
667-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
668-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
669-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
670-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
671-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
672-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
673-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
674-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
675-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
676-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
677-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
678-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
679-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
680-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
681-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
682-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
683-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
684-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
685-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
686-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
687-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
688-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
689-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
690-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
691-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
692-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
693-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
694-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
695-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
696-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
697-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
698-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
699-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
700-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
701-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
702-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n",
703-
"/var/folders/56/3yvgkyg96rvchgjgzfbf16gc0000gn/T/ipykernel_13875/1175382448.py:67: DeprecationWarning: `.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead.\n",
704-
" transform.dump(out_dir / \"transformations\" / f\"{transform.name}.json\")\n"
587+
"wrote 90 transformations\n"
705588
]
706589
}
707590
],
@@ -712,17 +595,9 @@
712595
"alchemical_network = build_alchemical_network(\n",
713596
" repair_network, reference_complex_system, reference_protocol\n",
714597
")\n",
715-
"dump_transformations(alchemical_network, \"repair_transformations\")\n",
598+
"save_transformations(alchemical_network, \"repair_transformations\")\n",
716599
"print(\"wrote\", len(alchemical_network.edges), \"transformations\")"
717600
]
718-
},
719-
{
720-
"cell_type": "code",
721-
"execution_count": null,
722-
"id": "478b5cf2-e8f1-4694-9908-43f35389b80e",
723-
"metadata": {},
724-
"outputs": [],
725-
"source": []
726601
}
727602
],
728603
"metadata": {

0 commit comments

Comments
 (0)