def test_write_stereo_cistrans(self):
"""Test writing cis-trans stereochemistry."""
# (Superfluous?) parity value is not set to same/opposite (1/2). unknown (255) is valid though.
# Cis
mols = list(
pybel.readfile("pcjson", os.path.join(filedir,
'CID_643833_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'], [{
'planar': {
'type': 1,
'ltop': 1,
'left': 3,
'right': 4,
'rbottom': 6,
'lbottom': 5,
'rtop': 2,
'parity': 255
}
}])
# Trans
mols = list(
pybel.readfile("pcjson", os.path.join(filedir,
'CID_638186_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'], [{
'planar': {
'type': 1,
'ltop': 2,
'left': 3,
'right': 4,
'rbottom': 1,
'lbottom': 5,
'rtop': 6,
'parity': 255
}
}])
# Any
mols = list(
pybel.readfile("pcjson", os.path.join(filedir,
'CID_10900_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(
output['PC_Compounds'][0]['stereo'][0]['planar']['left'], 3)
self.assertEqual(
output['PC_Compounds'][0]['stereo'][0]['planar']['right'], 4)
self.assertEqual(
output['PC_Compounds'][0]['stereo'][0]['planar']['left'], 3)
def test_write_cid(self):
"""Test writing a PubChem compound CID."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_2244_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(len(output['PC_Compounds']), 1)
self.assertTrue('id' in output['PC_Compounds'][0])
self.assertEqual(output['PC_Compounds'][0]['id']['id']['cid'], '2244')
def test_read_atoms(self):
"""Test reading atoms for a PubChem compound."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6857552_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(len(mols[0].atoms), 14)
self.assertEqual([a.atomicnum for a in mols[0].atoms], [8, 8, 8, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1])
self.assertEqual([a.formalcharge for a in mols[0].atoms], [0, -1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
def test_write_stereo_tetrahedral(self):
"""Test writing tetrahedral stereochemistry."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6137_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'], [
{'tetrahedral': {'above': 12, 'below': 5, 'bottom': 8, 'center': 6, 'parity': 1, 'top': 4, 'type': 1}}
])
def test_write_minified(self):
"""Test writing minified output."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
output = mols[0].write('cdjson', opt={'m': None})
self.assertTrue('\n' not in output)
output = mols[0].write('cdjson')
self.assertTrue('\n' in output)
def test_read_atoms(self):
"""Test reading atoms for a PubChem compound."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6857552_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(len(mols[0].atoms), 14)
self.assertEqual([a.atomicnum for a in mols[0].atoms], [8, 8, 8, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1])
self.assertEqual([a.formalcharge for a in mols[0].atoms], [0, -1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
def test_read_proton(self):
"""Test reading a file with a single hydrogen atom (and no bonds)."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'proton.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].OBMol.NumAtoms(), 1)
self.assertEqual(mols[0].OBMol.GetAtom(1).GetFormalCharge(), 1)
self.assertEqual(mols[0].OBMol.NumBonds(), 0)
def test_write_stereo_tetrahedral(self):
"""Test writing tetrahedral stereochemistry."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6137_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'], [
{'tetrahedral': {'above': 12, 'below': 5, 'bottom': 8, 'center': 6, 'parity': 1, 'top': 4, 'type': 1}}
])
def test_write_charge(self):
"""Test writing molecule charge."""
mols = list(
pybel.readfile("pcjson", os.path.join(filedir,
'CID_1038_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['charge'], 1)
def test_read_multiple(self):
"""Test reading a file with multiple molecules."""
mols = list(
pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
self.assertEqual(len(mols), 2)
self.assertEqual(mols[0].OBMol.NumAtoms(), 4)
self.assertEqual(mols[1].OBMol.NumAtoms(), 4)
def test_write_cid(self):
"""Test writing a PubChem compound CID."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_2244_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(len(output['PC_Compounds']), 1)
self.assertTrue('id' in output['PC_Compounds'][0])
self.assertEqual(output['PC_Compounds'][0]['id']['id']['cid'], '2244')
def test_write_atoms(self):
"""Test writing atoms for a PubChem compound."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6857552_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['atoms']['aids'], list(range(1, 15)))
self.assertEqual(output['PC_Compounds'][0]['atoms']['element'], [8, 8, 8, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1])
self.assertEqual(output['PC_Compounds'][0]['atoms']['charge'][0], {'aid': 2, 'value': -1})
self.assertEqual(output['PC_Compounds'][0]['atoms']['charge'][1], {'aid': 4, 'value': 1})
def test_write_atoms(self):
"""Test writing atoms."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
output = json.loads(mols[0].write('cdjson'))
self.assertEqual(len(output['m'][0]['a']), 4)
for a in output['m'][0]['a']:
self.assertTrue('x' in a)
self.assertTrue('y' in a)
def test_read_bonds(self):
"""Test reading bonds."""
mols = list(
pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
self.assertEqual(mols[0].OBMol.NumBonds(), 3)
self.assertEqual(
[mols[0].OBMol.GetBond(i).GetBondOrder() for i in range(0, 3)],
[1, 1, 1])
def test_read_cid(self):
"""Test reading a PubChem compound CID."""
mols = list(
pybel.readfile("pcjson", os.path.join(filedir,
'CID_2244_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].data['cid'], '2244')
self.assertEqual(mols[0].title, '2244')
def test_read_sid(self):
"""Test reading a PubChem substance SID."""
mols = list(
pybel.readfile("pcjson",
os.path.join(filedir, 'SID_348356775_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].data['sid'], '348356775')
self.assertEqual(mols[0].title, '348356775')
def test_write_atoms(self):
"""Test writing atoms for a PubChem compound."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6857552_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['atoms']['aids'], list(range(1, 15)))
self.assertEqual(output['PC_Compounds'][0]['atoms']['element'], [8, 8, 8, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1])
self.assertEqual(output['PC_Compounds'][0]['atoms']['charge'][0], {'aid': 2, 'value': -1})
self.assertEqual(output['PC_Compounds'][0]['atoms']['charge'][1], {'aid': 4, 'value': 1})
def test_write_complex_bonds(self):
"""Test writing complex bonds."""
mols = list(
pybel.readfile("pcjson",
os.path.join(filedir, 'CID_368849_2D.json'),
opt={'s': None}))
output = json.loads(mols[0].write('pcjson', opt={'w': None}))
self.assertEqual(output['PC_Compounds'][0]['bonds']['order'][:4],
[6, 6, 6, 6])
def test_read_bonds(self):
"""Test reading bonds for a PubChem compound."""
mols = list(
pybel.readfile("pcjson",
os.path.join(filedir, 'CID_6857552_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].OBMol.NumBonds(), 13)
self.assertEqual(
[mols[0].OBMol.GetBond(i).GetBO() for i in range(0, 13)],
[1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1])
def test_write_stereo_cistrans(self):
"""Test writing cis-trans stereochemistry."""
# (Superfluous?) parity value is not set to same/opposite (1/2). unknown (255) is valid though.
# Cis
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_643833_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'], [
{'planar': {'type': 1, 'ltop': 1, 'left': 3, 'right': 4, 'rbottom': 6, 'lbottom': 5, 'rtop': 2, 'parity': 255}}
])
# Trans
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_638186_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'], [
{'planar': {'type': 1, 'ltop': 2, 'left': 3, 'right': 4, 'rbottom': 1, 'lbottom': 5, 'rtop': 6, 'parity': 255}}
])
# Any
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_10900_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['stereo'][0]['planar']['left'], 3)
self.assertEqual(output['PC_Compounds'][0]['stereo'][0]['planar']['right'], 4)
self.assertEqual(output['PC_Compounds'][0]['stereo'][0]['planar']['left'], 3)
def test_write_bonds(self):
"""Test writing bonds."""
mols = list(
pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
output = json.loads(mols[0].write('cdjson'))
self.assertEqual(output['m'][0]['b'], [{
'b': 0,
'e': 1
}, {
'b': 0,
'e': 2
}, {
'b': 0,
'e': 3
}])
def test_read_atoms(self):
"""Test reading atoms."""
mols = list(
pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
self.assertEqual([a.atomicnum for a in mols[0].atoms], [6, 6, 6, 6])
self.assertEqual([a.formalcharge for a in mols[0].atoms], [0, 0, 0, 0])
def test_write_complex_bonds(self):
"""Test writing complex bonds."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_368849_2D.json'), opt={'s': None}))
output = json.loads(mols[0].write('pcjson', opt={'w': None}))
self.assertEqual(output['PC_Compounds'][0]['bonds']['order'][:4], [6, 6, 6, 6])
def test_read_empty(self):
"""Test reading a file with an empty molecules array."""
mols = list(
pybel.readfile("cdjson", os.path.join(filedir, 'empty.json')))
self.assertEqual(mols, [])
def test_write_charge(self):
"""Test writing molecule charge."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_1038_2D.json')))
output = json.loads(mols[0].write('pcjson'))
self.assertEqual(output['PC_Compounds'][0]['charge'], 1)
def test_write_bonds(self):
"""Test writing bonds."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
output = json.loads(mols[0].write('cdjson'))
self.assertEqual(output['m'][0]['b'], [{'b': 0, 'e': 1}, {'b': 0, 'e': 2}, {'b': 0, 'e': 3}])
def test_read_atoms(self):
"""Test reading atoms."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
self.assertEqual([a.atomicnum for a in mols[0].atoms], [6, 6, 6, 6])
self.assertEqual([a.formalcharge for a in mols[0].atoms], [0, 0, 0, 0])
def test_read_bonds(self):
"""Test reading bonds."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
self.assertEqual(mols[0].OBMol.NumBonds(), 3)
self.assertEqual([mols[0].OBMol.GetBond(i).GetBO() for i in range(0, 3)], [1, 1, 1])
def test_read_multiple(self):
"""Test reading a file with multiple molecules."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'butane.json')))
self.assertEqual(len(mols), 2)
self.assertEqual(mols[0].OBMol.NumAtoms(), 4)
self.assertEqual(mols[1].OBMol.NumAtoms(), 4)
def test_read_sid(self):
"""Test reading a PubChem substance SID."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'SID_348356775_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].data['sid'], '348356775')
self.assertEqual(mols[0].title, '348356775')
def test_read_empty(self):
"""Test reading a file with an empty molecules array."""
mols = list(pybel.readfile("cdjson", os.path.join(filedir, 'empty.json')))
self.assertEqual(mols, [])
def test_read_cid(self):
"""Test reading a PubChem compound CID."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_2244_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].data['cid'], '2244')
self.assertEqual(mols[0].title, '2244')
def test_read_bonds(self):
"""Test reading bonds for a PubChem compound."""
mols = list(pybel.readfile("pcjson", os.path.join(filedir, 'CID_6857552_2D.json')))
self.assertEqual(len(mols), 1)
self.assertEqual(mols[0].OBMol.NumBonds(), 13)
self.assertEqual([mols[0].OBMol.GetBond(i).GetBO() for i in range(0, 13)], [1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1])
