class TestDBWriter:
ses = create_session()
def test_write_new_mol_and_new_0_conf(self):
rism_toluene = RISM_3D_calculation('test/toluene')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene)
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_can = str(db_mol.SMILES)
db_conf = db_mol.find_0rmsd_conformation()
pymol = pybel.readstring('mol', str(db_conf.Mol))
assert can == db_can
# assert xyz == db_xyz
self.ses.rollback()
def test_write_new_mol_and_new_conf_and_conf_props(self):
rism_toluene = RISM_3D_calculation('test/toluene')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene, {'Source': 'David'})
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
assert str(db_conf.Source) == 'David'
self.ses.rollback()
def test_update_existing_conf(self):
rism_toluene = RISM_3D_calculation('test/toluene')
rism_toluene_copy = RISM_3D_calculation('test/toluene_copy')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene)
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
assert str(db_conf.Source) == 'None'
wr.write_rism(rism_toluene_copy, {'Source': 'David'})
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
assert str(db_conf.Source) == 'David'
self.ses.rollback()
def test_write_rism_calculation(self):
rism_toluene = RISM_3D_calculation('test/toluene')
can = 'Cc1ccccc1'
wr = Writer(self.ses)
wr.write_rism(rism_toluene, {'Source': 'David'})
dbi = DBInterface(self.ses)
db_mol = dbi.get_molecule(can)
db_conf = db_mol.find_0rmsd_conformation()
db_calc = db_conf.get_rism_calculations()[0]
assert db_calc.SolvE == 1.34305025E+001
assert db_calc.Temperature == '298'
self.ses.rollback()
def parse_rism_folders(base_folder):
ses = create_session()
dbi = DBInterface(ses)
dirs = os.walk(base_folder)
for p, _, filenames in dirs:
dbfs = get_dbf(filenames)
for dbf in dbfs:
try:
add_meta_f_to_db(dbf, p, dbi)
except NoResultFound:
print 'No results found for {}'.format(dbf)
ses.commit()
ses.close()
def parse_smd_folders(folders):
"""Accepts list (or tuple) of folders and writes
smd_calculation data to db.
"""
ses = create_session()
wr = Writer(ses)
for folder in folders:
try:
smd = SMD_calculation(folder)
wr.write_smd(smd, conf_attributes)
ses.commit()
print folder + ' written'
except OSError, e:
warnings.warn(str(e), UserWarning)
except TypeError, e:
warnings.warn(str(e), UserWarning)
def main():
"""Should only be used to handle arguments from command line.
Accepts list of folders and calls parse_rism_folders to handle the rest
"""
args = docopt(__doc__, version=0.01)
# print args
parse_args(args)
if args['create_db']:
check_connection()
if args['add']:
if args['rism']:
parse_rism_folders(args['<folder>'])
if args['smd']:
parse_smd_folders(args['<folder>'])
if args['smvle']:
parse_smvle_folders(args['<folder>'])
if args['exp_data']:
ses = create_session()
read_csv(args['<csv_file>'], ses)
ses.close()
"""
Created on Tue Aug 19 13:17:48 2014
@author: max
"""
import numpy as np
import statsmodels.api as sm
import solvation_database as sd
from db_interface import create_session
from sqlalchemy import and_
import matplotlib.pyplot as plt
ses = create_session()
avgd_points = open('averaged_points.txt', 'a')
interp_points = open('interpoltd_points.txt', 'a')
class PointBrowser:
"""
Delete stuff
Press d to delete point
Press x to delete molecule (deprecated)
Close figure to continue
"""
def __init__(self, fig, ax, int_t, int_v, avg_t, avg_v,
line, title, true_t, true_v):
self.fig = fig
self.line = line
class TestDBInterface:
ses = create_session()
def test_check_molecule_non_existing(self):
SMILES='CCCCC'
dbi = DBInterface(self.ses)
with pytest.raises(NoResultFound) as e:
dbi.get_molecule(SMILES)
def test_add_molecule(self):
smiles = 'CCCCCCC'
mol = Molecule(SMILES=smiles, IUPACName='Heptane')
dbi = DBInterface(self.ses)
dbi.add_molecule(mol)
data_mol = dbi.get_molecule(smiles)
assert str(data_mol.SMILES) == str(mol.SMILES)
def test_find_most_similair_conformation(self):
molref = """
OpenBabel12071321472D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END"""
mol = """
OpenBabel12071321472D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
"""
can = mol_2_can(mol)
dbi = DBInterface(self.ses)
db_ethane = Molecule(SMILES='CC')
dbi.add_molecule(db_ethane)
db_mol = dbi.get_molecule(can)
db_mol.add_conformation(Conformation(Mol=molref))
self.ses.add(db_mol)
db_conf = db_mol.find_most_similair_conf(mol)[0]
assert str(db_conf.Mol) == molref
def test_add_0_rmsd_conf_existing_mol(self):
coord = """
OpenBabel12071320143D
5 4 0 0 0 0 0 0 0 0999 V2000
1.0663 0.0688 -0.0295 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1585 0.0688 -0.0295 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7023 0.7365 0.7544 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7023 -0.9440 0.1568 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7023 0.4138 -0.9997 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
"""
conf = Conformation(Mol=coord, Molecule_SMILES='C')
can = mol_2_can(coord)
dbi = DBInterface(self.ses)
db_methane = Molecule(SMILES='C')
dbi.add_molecule(db_methane)
db_mol = dbi.get_molecule(can)
db_mol.add_conformation(conf)
self.ses.add(db_mol)
db_conf = db_mol.get_conformation(coord, 0.0000001)
assert db_conf == conf
def main(csv_path):
ses = create_session()
read_csv(csv_path, ses)
ses.close()