id = id.strip('\n')
molecule.add(id)
molecule.commit()
# download ligand structures
def save(id, s, format, dir):
filename = '{}/{}.{}'.format(dir, id, format)
with open(filename, 'w') as file:
file.write(s)
print(id)
structure_dir = project_dir + '/data/structure/ligand'
molecule.foreachStructure(
lambda id, s, format: save(id, s, format, structure_dir))
print('convert to pdb')
def convert(id, dir, fromformat, toformat):
org = '{}/{}.{}'.format(dir, id, fromformat)
dst = '{}/{}.{}'.format(dir, id, toformat)
os.system('obabel -i{} {} -o{} > {}'.format(fromformat, org, toformat,
dst))
os.system('rm ' + org)
print(id)
molecule.foreach(lambda data: convert(data[1][1], structure_dir, 'sdf', 'pdb'))
def instage(id, pt):
return pt.filename('{}.pdb'.format(id), pt.stage, '*.pdb') != None
def copy(id, dir, pt, pids):
try:
stagefile = pt.filename('{}.pdb'.format(id), pt.stage, '*.pdb')
os.system('cp {} {}/{}.pdb'.format(stagefile, dir, id.upper()))
print('!', 'stage: ', id, sep='\t')
except:
print('?', 'stage: ', id, sep='\t')
pids.append(id)
def save(id, s, format, dir):
filename = '{}/{}.{}'.format(dir, id, format)
with open(filename, 'w') as file:
file.write(s)
print(id)
structure_dir = project_dir + '/data/structure/ligand'
pids = []
molecule.foreachStructure(
lambda id, s, format: save(id, s, format, structure_dir),
lambda id: not instage(id, pt),
lambda id: copy(str(id), structure_dir, pt, pids))
molecule.close()