From ddcab40a51ee49ce974162922502176d4c282189 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Javier=20Gonz=C3=A1lez-Delgado?= <jgonzalezd@laas.fr>
Date: Thu, 16 Nov 2023 09:23:57 +0000
Subject: [PATCH] Add multiframe .pdb conversion to .xtc + .pdb format.
---
wario/utils.ipynb | 23 ++++++++++++++++++++++-
1 file changed, 22 insertions(+), 1 deletion(-)
diff --git a/wario/utils.ipynb b/wario/utils.ipynb
index f165da0..25f5652 100644
--- a/wario/utils.ipynb
+++ b/wario/utils.ipynb
@@ -16,7 +16,28 @@
"import pandas as pd\n",
"import itertools\n",
"from tqdm import tqdm \n",
- "import ot"
+ "import ot\n",
+ "import MDAnalysis"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "1219123d-f44f-4e08-9e71-4dc45cd81ced",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def multiframe_pdb_to_xtc(pdb_file, save_path, prot_name):\n",
+ " \n",
+ " u = MDAnalysis.core.universe.Universe(pdb_file)\n",
+ " at = u.atoms\n",
+ " \n",
+ " os.chdir(save_path)\n",
+ " \n",
+ " # Write the trajectory in .xtc format\n",
+ " at.write(\".\".join([prot_name,'xtc']), frames='all')\n",
+ " # Write a frame of the trajectory in .pdb format for topology information\n",
+ " at.write(\".\".join([prot_name,'pdb']))"
]
},
{
--
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