Loading deepchem/molnet/load_function/pdbbind_datasets.py +29 −8 Original line number Diff line number Diff line Loading @@ -139,7 +139,11 @@ def load_pdbbind_grid(split="random", return tasks, (train, valid, test), transformers def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): def load_pdbbind(featurizer="grid", load_binding_pocket=False, split="random", subset="core", reload=True): """Load and featurize raw PDBBind dataset. Parameters Loading Loading @@ -191,9 +195,16 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): pdb = line[0] if len(pdb) == 4: pdbs.append(pdb) if load_binding_pocket: protein_files = [ os.path.join(data_folder, pdb, "%s_pocket.pdb" % pdb) for pdb in pdbs ] else: protein_files = [ os.path.join(data_folder, pdb, "%s_protein.pdb" % pdb) for pdb in pdbs ] ligand_files = [ os.path.join(data_folder, pdb, "%s_ligand.sdf" % pdb) for pdb in pdbs ] Loading Loading @@ -224,7 +235,13 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): elif featurizer == "atomic": # Pulled from PDB files. For larger datasets with more PDBs, would use # max num atoms instead of exact. frag1_num_atoms = 70 # for ligand atoms if load_binding_pocket: frag2_num_atoms = 1000 complex_num_atoms = 1070 else: frag2_num_atoms = 24000 # for protein atoms complex_num_atoms = 24070 # in total max_num_neighbors = 4 Loading @@ -236,6 +253,10 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): elif featurizer == "atomic_conv": frag1_num_atoms = 70 # for ligand atoms if load_binding_pocket: frag2_num_atoms = 1000 # for protein atoms complex_num_atoms = 1070 # in total else: frag2_num_atoms = 24000 # for protein atoms complex_num_atoms = 24070 # in total max_num_neighbors = 4 Loading Loading
deepchem/molnet/load_function/pdbbind_datasets.py +29 −8 Original line number Diff line number Diff line Loading @@ -139,7 +139,11 @@ def load_pdbbind_grid(split="random", return tasks, (train, valid, test), transformers def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): def load_pdbbind(featurizer="grid", load_binding_pocket=False, split="random", subset="core", reload=True): """Load and featurize raw PDBBind dataset. Parameters Loading Loading @@ -191,9 +195,16 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): pdb = line[0] if len(pdb) == 4: pdbs.append(pdb) if load_binding_pocket: protein_files = [ os.path.join(data_folder, pdb, "%s_pocket.pdb" % pdb) for pdb in pdbs ] else: protein_files = [ os.path.join(data_folder, pdb, "%s_protein.pdb" % pdb) for pdb in pdbs ] ligand_files = [ os.path.join(data_folder, pdb, "%s_ligand.sdf" % pdb) for pdb in pdbs ] Loading Loading @@ -224,7 +235,13 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): elif featurizer == "atomic": # Pulled from PDB files. For larger datasets with more PDBs, would use # max num atoms instead of exact. frag1_num_atoms = 70 # for ligand atoms if load_binding_pocket: frag2_num_atoms = 1000 complex_num_atoms = 1070 else: frag2_num_atoms = 24000 # for protein atoms complex_num_atoms = 24070 # in total max_num_neighbors = 4 Loading @@ -236,6 +253,10 @@ def load_pdbbind(featurizer="grid", split="random", subset="core", reload=True): elif featurizer == "atomic_conv": frag1_num_atoms = 70 # for ligand atoms if load_binding_pocket: frag2_num_atoms = 1000 # for protein atoms complex_num_atoms = 1070 # in total else: frag2_num_atoms = 24000 # for protein atoms complex_num_atoms = 24070 # in total max_num_neighbors = 4 Loading
