def test_add_dance_property_appends_to_empty_list(self):
mol, prop = oechem.OEMol(), danceprops.DanceProperties()
props = []
danceprops.add_dance_property(mol, prop, props)
assert len(props) == 1
assert mol.GetData(danceprops.DANCE_PROPS_KEY) == 0
assert props[-1] == prop
def test_add_dance_property_appends_to_small_list(
self, small_mols_and_props_list):
mols, props = small_mols_and_props_list
mol, prop = oechem.OEMol(), danceprops.DanceProperties()
mols.append(mol)
danceprops.add_dance_property(mol, prop, props)
assert len(props) == 5
assert mol.GetData(danceprops.DANCE_PROPS_KEY) == 4
assert props[-1] == prop
def _calc_properties(mol: oechem.OEMol) -> danceprops.DanceProperties:
"""
Calculates properties of the given molecule and returns a
DanceProperties object holding them.
Based on Victoria Lim's am1wib.py - see
https://github.com/vtlim/misc/blob/master/oechem/am1wib.py
"""
props = danceprops.DanceProperties()
for conf in mol.GetConfs():
charged_copy = oechem.OEMol(conf)
results = oequacpac.OEAM1Results()
if not AM1.CalcAM1(results, charged_copy):
logging.debug(
f"failed to assign partial charges to {mol.GetTitle()}")
return props
DanceGenerator._add_charge_props(mol, charged_copy, results)
# Sum bond orders, bond lengths, and bond angles
for atom in charged_copy.GetAtoms(oechem.OEIsInvertibleNitrogen()):
nbors = list(atom.GetAtoms()) # (neighbors)
ang1 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[0], atom, nbors[1]))
ang2 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[1], atom, nbors[2]))
ang3 = math.degrees(
oechem.OEGetAngle(charged_copy, nbors[2], atom, nbors[0]))
props.tri_n_bond_angle = ang1 + ang2 + ang3
for nbor in nbors:
bond_order = results.GetBondOrder(atom.GetIdx(),
nbor.GetIdx())
bond_length = oechem.OEGetDistance(charged_copy, atom,
nbor)
element = nbor.GetAtomicNum()
props.tri_n_bonds.append(
danceprops.DanceTriNBond(bond_order, bond_length,
element))
props.tri_n_bond_order += bond_order
props.tri_n_bond_length += bond_length
break # terminate after one trivalent nitrogen
break # terminate after one conformation
return props
def test_append_properties_list_appends_small_list(
self, small_mols_and_props_list):
old_mols, old_props = small_mols_and_props_list
mols, props = old_mols.copy(), old_props.copy()
mols2 = [oechem.OEMol() for i in range(2)]
oechem.OESmilesToMol(mols2[0], "CN=C=O")
oechem.OESmilesToMol(mols2[1], "[C-]#[O+]")
danceprops.set_dance_property(mols2[0], 1)
danceprops.set_dance_property(mols2[1], 0)
old_mols2 = [oechem.OEMol(m) for m in mols2]
props2 = [danceprops.DanceProperties() for i in range(2)]
danceprops.append_properties_list(mols, props, mols2, props2)
# The properties obtained from the molecules put in the new list should
# be the same as the properties in the old list.
assert danceprops.get_dance_property(
mols[4],
props) == danceprops.get_dance_property(old_mols2[0], props2)
assert danceprops.get_dance_property(
mols[5],
props) == danceprops.get_dance_property(old_mols2[1], props2)
def small_mols_and_props_list() -> ([oechem.OEMol],
[danceprops.DanceProperties]):
"""
Returns a list of 4 molecules, as well as another list with their 4
corresponding properties. Note that the properties are actually empty.
Molecules will be as follows - the index of their properties in the props
list is given in parens:
[ N (2), N#N (3), O=C=O (0), C#N (1) ]
"""
# yapf: enable
smiles = ["N", "N#N", "O=C=O", "C#N"]
mols = [oechem.OEMol() for _ in range(4)]
for i in range(4):
oechem.OESmilesToMol(mols[i], smiles[i])
mols[0].SetData(danceprops.DANCE_PROPS_KEY, 2)
mols[1].SetData(danceprops.DANCE_PROPS_KEY, 3)
mols[2].SetData(danceprops.DANCE_PROPS_KEY, 0)
mols[3].SetData(danceprops.DANCE_PROPS_KEY, 1)
props = [danceprops.DanceProperties() for _ in range(4)]
return (mols, props)