From 5365b706237bbbdea34da11a38cc05c164a84d8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Javier=20Gonz=C3=A1lez-Delgado?= <jgonzalezd@laas.fr>
Date: Wed, 8 Nov 2023 14:09:09 +0000
Subject: [PATCH] Add option to only analyze an arbitrary sequence subset
---
wario/contact_features.ipynb | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/wario/contact_features.ipynb b/wario/contact_features.ipynb
index 0e6a95b..f63ac11 100644
--- a/wario/contact_features.ipynb
+++ b/wario/contact_features.ipynb
@@ -37,11 +37,11 @@
"metadata": {},
"outputs": [],
"source": [
- "def contact_features(ensemble_path, ensemble_name, thresholds, interactive = True, N_cores = 1, start = None, end = None, sel_chain = None, umap_dim = 10):\n",
+ "def contact_features(ensemble_path, ensemble_name, thresholds, interactive = True, N_cores = 1, start = None, end = None, subsequence = None, sel_chain = None, umap_dim = 10):\n",
" \n",
" # Initial parameters\n",
" var_dict = {'multiframe' : 'n', 'check_folder' : True, 'do_xtc' : False, 'do_pdb' : False,\n",
- " 'N' : 1, 'start' : start, 'end' : end,\n",
+ " 'N' : 1, 'start' : start, 'end' : end, 'subsequence' : subsequence,\n",
" 'ensemble_name' : ensemble_name, 'ensemble_path' : ensemble_path}\n",
" \n",
" var_dict['xtc_files'] = [file for file in os.listdir(ensemble_path) if file.endswith(\".xtc\")] \n",
@@ -179,7 +179,7 @@
" \n",
" wcontact_matrix(thresholds, xtc_file = \"/\".join([var_dict[\"xtc_root_path\"],var_dict[\"xtc_files\"][0]]), top_file = \"/\".join([var_dict[\"xtc_root_path\"],var_dict[\"pdb_files\"][0]]),\n",
" pdb_folder = None, num_cores = n_cores, prot_name = ensemble_name, save_to = results_path,\n",
- " start = var_dict[\"start\"], end = var_dict[\"end\"], \n",
+ " start = var_dict[\"start\"], end = var_dict[\"end\"], subsequence = var_dict[\"subsequence\"],\n",
" select_chain = sel_chain,\n",
" name_variable = 'ipynb.fs.full.wcontact_matrix')\n",
" \n",
@@ -187,7 +187,7 @@
" \n",
" wcontact_matrix(thresholds, xtc_file = None, top_file = None, pdb_folder = \"/\".join([var_dict[\"ensemble_path\"],var_dict[\"folders\"][0]]), num_cores = n_cores,\n",
" prot_name = ensemble_name, save_to = results_path,\n",
- " start = var_dict[\"start\"], end = var_dict[\"end\"],\n",
+ " start = var_dict[\"start\"], end = var_dict[\"end\"], subsequence = var_dict[\"subsequence\"],\n",
" select_chain = sel_chain,\n",
" name_variable = 'ipynb.fs.full.wcontact_matrix')\n",
" \n",
@@ -237,7 +237,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.16"
+ "version": "3.10.9"
}
},
"nbformat": 4,
--
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