From 92a795c318a6cea9bf6a64588a396769982b45f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Javier=20Gonz=C3=A1lez-Delgado?= <jgonzalezd@laas.fr>
Date: Wed, 8 Nov 2023 14:09:42 +0000
Subject: [PATCH] Add option to only analyze an arbitrary sequence subset
---
wario/wcontact_matrix.ipynb | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/wario/wcontact_matrix.ipynb b/wario/wcontact_matrix.ipynb
index 53b5051..08bbe3f 100644
--- a/wario/wcontact_matrix.ipynb
+++ b/wario/wcontact_matrix.ipynb
@@ -27,12 +27,12 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 1,
"id": "32f62d90",
"metadata": {},
"outputs": [],
"source": [
- "def wcontact_matrix(thresholds, num_cores = 1, prot_name = None, save_to = None, pdb_folder = None, xtc_file = None, top_file = None, start = None, end = None, select_chain = None, name_variable = '__main__'):\n",
+ "def wcontact_matrix(thresholds, num_cores = 1, prot_name = None, save_to = None, pdb_folder = None, xtc_file = None, top_file = None, start = None, end = None, subsequence = None, select_chain = None, name_variable = '__main__'):\n",
" \n",
" if save_to is None and prot_name is None:\n",
" \n",
@@ -57,13 +57,13 @@
" quit('Please set pdb_folder != None and xtc_file = top_file = None, or pdb_folder = None and xtc_file != None, top_file != None.')\n",
" \n",
" \n",
- " def comp_function(conf_comp, thresholds_comp, pdb_data_comp, traj_data_comp, start_comp, end_comp, sel_chain):\n",
+ " def comp_function(conf_comp, thresholds_comp, pdb_data_comp, traj_data_comp, start_comp, end_comp, subset_comp, sel_chain):\n",
" \n",
- " coordinates = get_coordinates(conf_name = conf_comp, pdb = pdb_data_comp, traj = traj_data_comp, res_start = start_comp, res_end = end_comp, which_chain = sel_chain)\n",
+ " coordinates = get_coordinates(conf_name = conf_comp, pdb = pdb_data_comp, traj = traj_data_comp, res_start = start_comp, res_end = end_comp, seq_subset = subset_comp, which_chain = sel_chain)\n",
" contacts = get_contacts(coordinates, thresholds_comp)\n",
" return contacts\n",
" \n",
- " it_function = partial(comp_function, thresholds_comp = thresholds, pdb_data_comp = pdb_folder, traj_data_comp = traj_file, start_comp = start, end_comp = end, sel_chain = select_chain) \n",
+ " it_function = partial(comp_function, thresholds_comp = thresholds, pdb_data_comp = pdb_folder, traj_data_comp = traj_file, start_comp = start, end_comp = end, subset_comp = subsequence, sel_chain = select_chain) \n",
" N_pairs = len(it_function(conf_list[0])) \n",
" \n",
" def it_function_error(conf):\n",
@@ -118,7 +118,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.16"
+ "version": "3.10.9"
}
},
"nbformat": 4,
--
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