Commit 08a3ecf2 authored by Carlos GO's avatar Carlos GO
Browse files

mg checker

parent d4fcc33e
......@@ -40,16 +40,16 @@ amino_acids = [
def ligand_center(residue):
return np.mean(np.array([atom.coord for atom in residue.get_atoms()]), axis=0)
def is_valid_ligand(ligand_residue):
def _is_valid_ligand(ligand_residue):
#no ions
invalids = ['HOH', 'NCO', 'SO4', 'EPE', 'OHX', 'MPD']
if ligand_residue.resname in invalids or len(ligand_residue.resname) != 3:
return False
return True
def _is_valid_ligand(ligand_residue):
def is_valid_ligand(ligand_residue):
#no ions
return ligand_residue == 'MG'
return ligand_residue.resname.strip() == 'MG'
def pocket_res_count(struct, ligand_residue, radius=12):
"""
......@@ -147,7 +147,6 @@ def full_struc_analyse(strucpath):
for res in model[ligand.chain].get_residues():
if res.id[1] == ligand.position:
ligand_res = res
print(ligand_res)
if is_valid_ligand(ligand_res):
valid_ligands.append((ligand_res, f"#{'0' if num_models == 1 else '0.1'}", pocket_res_count(model, ligand_res)))
else:
......@@ -202,11 +201,10 @@ def process_all(pdb_path, dump_path, restart=None, parallel=False):
lig_ids = []
for l, model_id, radii in ligs:
info = f"{model_id}:{l.get_parent().id}:{l.resname}:{l.id[1]}"
print(info, radii)
lig_ids.append((info, radii))
lig_dict[os.path.basename(p)] = lig_ids
pickle.dump(lig_dict, open(dump_path, 'wb'))
pass
if __name__ == "__main__":
pdb_path = os.path.join("..", '..', 'carlos_docking', "data", "all_rna_with_lig_2019")
process_all(pdb_path, "../data/jacques.p")
pdb_path = os.path.join("..", '..', 'carlos_dock', "data", "all_rna_with_lig_2019")
process_all(pdb_path, "../data/jacques_mg_res.p")
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