Skip to content

Update cookbooks for openfe 1.0 #122

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
IAlibay merged 2 commits into from
Apr 4, 2024
Merged

Update cookbooks for openfe 1.0 #122

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ea738ba
Update cookbooks for openfe 1.0
IAlibay Apr 3, 2024
bee9d44
Address review comments
IAlibay Apr 4, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
228 changes: 112 additions & 116 deletions cookbook/choose_protocol.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

10 changes: 2 additions & 8 deletions cookbook/create_alchemical_network.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@
"cell_type": "markdown",
"id": "471531a1-a351-413b-b147-794f9af4e0f8",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand Down Expand Up @@ -109,7 +108,6 @@
"execution_count": 4,
"id": "d3054cfc-5040-4882-b3a3-92aba7ab5d1d",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand Down Expand Up @@ -225,7 +223,7 @@
" transformation = openfe.Transformation(\n",
" stateA=system_a,\n",
" stateB=system_b,\n",
" mapping={'ligand': mapping},\n",
" mapping=mapping,\n",
" protocol=protocol,\n",
" # Using the same name as to_rbfe_alchemical_network()\n",
" name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n",
Expand Down Expand Up @@ -265,7 +263,6 @@
"execution_count": 8,
"id": "c9baa54c-513a-486a-a06a-fd8fd5d19fa5",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -284,7 +281,6 @@
"cell_type": "markdown",
"id": "b17669f6-a205-420d-96c3-1a9c92d0e13b",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -298,7 +294,6 @@
"cell_type": "markdown",
"id": "682b45eb-4c79-4a68-b0a8-534544c0f0a7",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -315,7 +310,6 @@
"execution_count": 9,
"id": "2da4dafb-20d6-4ce7-ab83-4690528097d6",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand Down Expand Up @@ -350,7 +344,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.11.6"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down
12 changes: 2 additions & 10 deletions cookbook/generate_ligand_network.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

39 changes: 2 additions & 37 deletions cookbook/generate_lomap_network.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

14 changes: 7 additions & 7 deletions cookbook/hand_write_ligand_network.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

128 changes: 62 additions & 66 deletions cookbook/ligandnetwork_vis.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

28 changes: 1 addition & 27 deletions cookbook/loading_molecules.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
"cell_type": "raw",
"id": "4d9beae7-b6bd-4743-9614-42450df0697d",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -22,7 +21,6 @@
"cell_type": "markdown",
"id": "088a1bc4-e5f3-47ac-8ebf-1a904fa82f80",
"metadata": {
"editable": true,
"nbsphinx": "hidden",
"slideshow": {
"slide_type": ""
Expand All @@ -37,7 +35,6 @@
"cell_type": "raw",
"id": "acb1ed05-1874-4dd3-a41d-e18623bece44",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -53,7 +50,6 @@
"cell_type": "markdown",
"id": "00d9ca69-1b38-4cf8-9c93-1fc4c08dae15",
"metadata": {
"editable": true,
"nbsphinx": "hidden",
"slideshow": {
"slide_type": ""
Expand All @@ -68,7 +64,6 @@
"cell_type": "markdown",
"id": "8bc61b88-0c8d-4b89-b704-8ac4ade19c6c",
"metadata": {
"editable": true,
"raw_mimetype": "",
"slideshow": {
"slide_type": ""
Expand All @@ -94,7 +89,6 @@
"cell_type": "raw",
"id": "d7277536-be61-4d45-b09f-1a7b355bee82",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -112,7 +106,6 @@
"cell_type": "markdown",
"id": "d2658885-8ad9-4142-b163-17c8aa576b00",
"metadata": {
"editable": true,
"nbsphinx": "hidden",
"slideshow": {
"slide_type": ""
Expand All @@ -127,7 +120,6 @@
"cell_type": "markdown",
"id": "15115699-8bdb-4261-9afd-18ebd55bd06a",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -142,7 +134,6 @@
"execution_count": 1,
"id": "1436cd71-2a65-4cef-9f9f-73013c791a17",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -163,7 +154,6 @@
"cell_type": "markdown",
"id": "8c78efe2-5a0d-4aac-afd1-3e6c5b7a1efc",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -179,7 +169,6 @@
"cell_type": "markdown",
"id": "b092b780-a2cb-4ece-9d77-c09f2e035b8f",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -195,7 +184,6 @@
"execution_count": 2,
"id": "7f7e56c9-2bee-46a1-9ccf-7003b4886249",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -213,7 +201,6 @@
"cell_type": "markdown",
"id": "2dbd57c0-87ee-426a-b0ac-1861480a0d34",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -233,7 +220,6 @@
"execution_count": 3,
"id": "85704a16-86b6-4c25-9a4d-050fd215a2ef",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -257,7 +243,6 @@
"cell_type": "raw",
"id": "b1c7eea8-7aaa-4a72-8d48-dfb7c32a60eb",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -275,7 +260,6 @@
"cell_type": "markdown",
"id": "852c038e-d4dc-4fac-975c-d5e6baee719e",
"metadata": {
"editable": true,
"nbsphinx": "hidden",
"slideshow": {
"slide_type": ""
Expand All @@ -290,7 +274,6 @@
"cell_type": "markdown",
"id": "13839df1-fa2c-4e0a-8322-56ce466aea37",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -307,7 +290,6 @@
"execution_count": 4,
"id": "669ea0d6-3f49-4e91-b992-95f1bd5e7174",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -325,7 +307,6 @@
"cell_type": "raw",
"id": "f0e245cc-8763-48da-8908-1ab28e6b84d9",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -343,7 +324,6 @@
"cell_type": "markdown",
"id": "21ebdadc-1bf6-4ad2-827e-b6b7dc19572a",
"metadata": {
"editable": true,
"nbsphinx": "hidden",
"slideshow": {
"slide_type": ""
Expand All @@ -358,7 +338,6 @@
"cell_type": "markdown",
"id": "40e3a23f-cc13-402e-8197-9552fbb387e7",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -375,7 +354,6 @@
"execution_count": 5,
"id": "e6c35e81-d0c9-4680-bb35-e7ae2b3fd2da",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -394,7 +372,6 @@
"cell_type": "raw",
"id": "02e4137f-f823-4dd7-beaa-a8382735bc64",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand All @@ -412,7 +389,6 @@
"cell_type": "markdown",
"id": "1e388bd2-f1b3-4a90-970e-72b652f6227b",
"metadata": {
"editable": true,
"nbsphinx": "hidden",
"raw_mimetype": "",
"slideshow": {
Expand All @@ -428,7 +404,6 @@
"cell_type": "markdown",
"id": "10655021-f3f0-4b21-9d8b-fc5a885555e4",
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
Expand All @@ -447,7 +422,6 @@
"execution_count": 6,
"id": "bf52b73e-5705-48e7-b69a-fb63748588d8",
"metadata": {
"editable": true,
"raw_mimetype": "text/restructuredtext",
"slideshow": {
"slide_type": ""
Expand Down Expand Up @@ -491,7 +465,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
"version": "3.11.6"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down
4 changes: 2 additions & 2 deletions cookbook/network_from_orion_fepp.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

Loading