def run_docking(vina_program, vina_conf, receptor, path_ligand_pdbqt, path_struct, path_log):
name_receptor = get_name_receptor(receptor)
all_ligands = get_files_pdbqt(path_ligand_pdbqt)
for ligand in all_ligands:
name_ligand = pdbqt.get_name_ligand(ligand)
f_out = os.path.join(path_struct, get_name_out(name_receptor, name_ligand))
f_log = os.path.join(path_log, get_name_log(name_receptor, name_ligand))
process = Popen(
[
vina_program,
"--config",
vina_conf,
"--receptor",
receptor,
"--ligand",
ligand,
"--out",
f_out,
"--log",
f_log,
],
stdout=PIPE,
stderr=PIPE,
)
stdout, stderr = process.communicate()
def build_database(database_path_file, pdbqt_path_file):
line = ""
f_database = open(database_path_file, 'w')
line = str(";Ligand\t") + str("Torsion\t") + str("Atoms\t") + str("\n")
f_database.write(line)
all_pdbqt = pdbqt.get_files_pdbqt_no_sort(pdbqt_path_file)
for f_pdbqt in all_pdbqt:
ligand_name = pdbqt.get_name_ligand(f_pdbqt)
torsion_angle = int(pdbqt.get_number_torsion_angle(f_pdbqt))
atom_number = int(pdbqt.get_number_atom(f_pdbqt))
line = ligand_name + str("\t")+ str(torsion_angle) + str("\t") + str(atom_number) + str("\n")
f_database.write(line)
f_database.close()
def run_docking(vina_program, vina_conf, receptor, path_ligand_pdbqt,
path_struct, path_log):
name_receptor = get_name_receptor(receptor)
all_ligands = get_files_pdbqt(path_ligand_pdbqt)
for ligand in all_ligands:
name_ligand = pdbqt.get_name_ligand(ligand)
f_out = os.path.join(path_struct,
get_name_out(name_receptor, name_ligand))
f_log = os.path.join(path_log, get_name_log(name_receptor,
name_ligand))
process = Popen([
vina_program, '--config', vina_conf, '--receptor', receptor,
'--ligand', ligand, '--out', f_out, '--log', f_log
],
stdout=PIPE,
stderr=PIPE)
stdout, stderr = process.communicate()