diff --git a/README.md b/README.md index 51f7d45..f79bcd8 100644 --- a/README.md +++ b/README.md @@ -124,7 +124,11 @@ a4 av bm cd d4 dv em fd g4 gv hm id j4 jv km ld m4 mv nm od p4 pr a5 aw bn ce d5 dw en fe g5 gw hn ie j5 jw kn le m5 mw nn oe p5 ps qj ra s1 ss tj ua v1 vs wj xa y1 ys zj ``` -Then preprocess the raw data as follow to prepare data for rigid body docking: +###Note: +The raw data `DIPS/data/DIPS/interim/pairs-pruned/` can also be downloaded from https://www.dropbox.com/s/sqknqofy58nlosh/DIPS.zip?dl=0 + +Finally, preprocess the raw data as follow to prepare data for rigid body docking: + ``` # prepare data for rigid body docking python preprocess_raw_data.py -n_jobs 60 -data dips -graph_nodes residues -graph_cutoff 30 -graph_max_neighbor 10 -graph_residue_loc_is_alphaC -pocket_cutoff 8 -data_fraction 1.0 diff --git a/src/inference_rigid.py b/src/inference_rigid.py index db66b71..0357299 100644 --- a/src/inference_rigid.py +++ b/src/inference_rigid.py @@ -16,7 +16,7 @@ dataset = 'dips' method_name = 'equidock' -remove_clashes = True # Set to true if you want to remove (most of the) steric clashes. Will increase run time. +remove_clashes = False # Set to true if you want to remove (most of the) steric clashes. Will increase run time. if remove_clashes: method_name = method_name + '_no_clashes' print('Inference with postprocessing to remove clashes') @@ -120,9 +120,12 @@ def main(args): input_dir = './test_sets_pdb/' + dataset + '_test_random_transformed/random_transformed/' ground_truth_dir = './test_sets_pdb/' + dataset + '_test_random_transformed/complexes/' - output_dir = './test_sets_pdb/' + dataset + '_' + method_name + '_results/' - create_dir(output_dir) + + input_dir = './test_sets_pdb/jean/' + ground_truth_dir = './test_sets_pdb/jean/' + output_dir = './test_sets_pdb/jean_out/' + # create_dir(output_dir) pdb_files = [f for f in os.listdir(input_dir) if os.path.isfile(os.path.join(input_dir, f)) and f.endswith('.pdb')] for file in pdb_files: