Hello!
I am trying to run your notebooks, but keep getting assertion error
AssertionError Traceback (most recent call last)
Cell In[3], line 13
10 scfv = ['4gqp', '3etb', '3gkz', '3uze', '3uzq', '3gm0', '4f9l', '6ejg', '6ejm', '1h8s', '5dfw', '6cbp', '4f9p', '5kov', '1dzb', '5j74', '5aaw', '3uzv', '5aam', '3ux9', '5a2j', '5a2k', '5a2i', '3fku', '5yy4', '3uyp', '5jyl', '1y0l', '1p4b', '3kdm', '4lar', '4ffy', '2ybr', '1mfa', '5xj3', '5xj4', '4kv5', '5vyf']
11 pathological += scfv
---> 13 preprocessed_data = Preprocessing(data_path = '/home/georgii/PycharmProjects/CSM-AB2/ANTIPASTI/data/', dccm_map_path=dccm_map_path, modes=modes, pathological=pathological, renew_maps=renew_maps, renew_residues=renew_residues, ag_agnostic=ag_agnostic, cmaps=contact_maps, cmaps_thr=cmaps_thr)
File ~/PycharmProjects/CSM-AB2/ANTIPASTI/antipasti/preprocessing/preprocessing.py:131, in Preprocessing.init(self, data_path, scripts_path, structures_path, df, modes, chain_lengths_path, dccm_map_path, residues_path, file_type_input, selection, pathological, renew_maps, renew_residues, cmaps, cmaps_thr, ag_agnostic, affinity_entries_only, stage, test_data_path, test_dccm_map_path, test_residues_path, test_structure_path, test_pdb_id, alphafold, h_offset, l_offset, ag_residues)
129 self.df_path = data_path + df
130 self.entries, self.affinity, self.df = self.clean_df()
--> 131 self.heavy, self.light, self.selected_entries = self.initialisation(renew_maps, renew_residues)
132 self.max_res_list_h, self.max_res_list_l, self.min_res_list_h, self.min_res_list_l = self.get_max_min_chains()
133 self.train_x, self.train_y, self.labels, self.raw_imgs = self.load_training_images()
File ~/PycharmProjects/CSM-AB2/ANTIPASTI/antipasti/preprocessing/preprocessing.py:453, in Preprocessing.initialisation(self, renew_maps, renew_residues)
450 heavy = np.load(self.chain_lengths_path+'heavy_lengths.npy').astype(int)
451 light = np.load(self.chain_lengths_path+'light_lengths.npy').astype(int)
--> 453 assert list(np.load(self.chain_lengths_path+'selected_entries.npy')) == selected_entries
455 for entry in selected_entries:
456 assert len(np.load(self.residues_path+entry+'.npy'))-2 == heavy[selected_entries.index(entry)] + light[selected_entries.index(entry)]
AssertionError:
P.S.
Also I had issues with data_path -- user needs to give it manually