def process(infile):
df = pd.read_csv(infile, sep='\n', header=None)
df.dropna(inplace=True)
if not exists('input'):
os.mkdir('input')
for row in df.values:
mol = row[0]
if 'InChI' in mol:
key = inchi2key(mol)
ext = '.inchi'
else:
key = smi2key(mol)
ext = '.smi'
if key is not None:
write_string(mol, join('input', key + ext))
else:
print('Failed to hash %s.' % mol)
pass
else:
pka = read_pka(args.pkafile)
# generate adduct
if '+' in args.adduct:
mol = create_adduct(mol, args.adduct, pka['b1'],
forcefield=args.forcefield,
steps=args.steps)
elif '-' in args.adduct:
mol = create_adduct(mol, args.adduct, pka['a1'],
forcefield=args.forcefield,
steps=args.steps)
mol.write('mol2', args.mol2, overwrite=True)
mol.write('xyz', args.xyz, overwrite=True)
mol.write('pdb', args.pdb, overwrite=True)
# reassign charge
if args.adduct in ['+H', '+Na']:
# tmp = splitext(args.mol2)[0] + '.tmp.mol2'
# subprocess.call('obabel %s -O %s --partialcharge eem' % (args.mol2, tmp), shell=True)
# subprocess.call('mv %s %s' % (tmp, args.mol2), shell=True)
write_string('1.0', args.charge)
elif args.adduct == '-H':
write_string('-1.0', args.charge)
elif args.adduct == 'neutral':
write_string('0.0', args.charge)
parser.add_argument('infile', help='path to impact .out files')
parser.add_argument('mass', help='path to mass files.')
parser.add_argument('out_He', help='path to helium ccs output file')
parser.add_argument('out_N2', help='path to nitrogen ccs output file')
parser.add_argument('-a',
'--alpha',
type=float,
default=27.9,
help='alpha calibration')
parser.add_argument('-b',
'--beta',
type=float,
default=0.14,
help='beta calibration')
parser.add_argument('-v',
'--version',
action='version',
version=__version__,
help='print version and exit')
args = parser.parse_args()
# read inputs
ccs_He = read_impact(args.infile)
m = read_mass(args.mass)
ccs_N2 = ccs_He + args.alpha * m**args.beta
write_string(str(ccs_He), args.out_He)
write_string(str(ccs_N2), args.out_N2)
help='neutralize mode')
mode.add_argument('--tautomerize',
action='store_true',
help='tautomerize mode')
mode.add_argument('--formula', action='store_true', help='formula mode')
mode.add_argument('--canonicalize',
action='store_true',
help='canonicalization mode')
args = parser.parse_args()
s = read_string(args.infile)
if args.inchi is True:
smiles = inchi2smi(s)
elif args.desalt is True:
smiles = desalt(s)
elif args.neutralize is True:
smiles = neutralize(s)
elif args.tautomerize is True:
smiles = tautomerize(s)
elif args.formula is True:
smiles = smiles2formula(s)
elif args.canonicalize is True:
smiles = canonicalize(s)
if smiles is not None:
write_string(smiles, args.outfile)
else:
sys.exit(1)