diff --git a/wario/contact_features.ipynb b/wario/contact_features.ipynb index 0e6a95b9598f7b8b3d11b4cb1e0dc4ab5585fceb..f63ac11a8a3f6677bc7101bd59e1bfbd93a25d95 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,