def test_c5h6o(self):
inchi = "InChI=1S/C5H6O/c6-5-3-1-2-4-5/h1-3,5H,4H2"
mol = Molecule().from_inchi(inchi)
start = mol.atoms[1]
path = find_allyl_end_with_charge(start)[0]
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [2, 1, 3]
self.assertEquals(idx_path, expected_idx_path)
def test_c3h4o4(self):
inchi = "InChI=1S/C3H4O4/c4-3(5)1-2-7-6/h1-3,6H"
mol = Molecule().from_inchi(inchi)
start = mol.atoms[6]
path = find_allyl_end_with_charge(start)[0]
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [7, 2, 1]
self.assertEquals(idx_path, expected_idx_path)
def test_c3h4(self):
inchi = "InChI=1S/C3H4/c1-3-2/h1,3H,2H2"
mol = Molecule().from_inchi(inchi)
start = mol.atoms[0]
path = find_allyl_end_with_charge(start)[0]
idx_path = [mol.atoms.index(atom) + 1 for atom in path[0::2]]
expected_idx_path = [1, 3, 2]
self.assertEquals(idx_path, expected_idx_path)
def fix_oxygen_unsaturated_bond(mol, u_indices):
"""
Searches for a radical or a charged oxygen atom connected to
a closed-shell carbon via an unsatured bond.
Decrements the unsatured bond,
transfers the unpaired electron from O to C or
converts the charge from O to an unpaired electron on C,
increases the lone pair count of O to 2.
Only do this once per molecule.
"""
for at in mol.atoms:
if at.isOxygen() and at.radicalElectrons == 1 and at.lonePairs == 1:
bonds = mol.getBonds(at)
oxygen = at
for atom2, bond in bonds.iteritems():
if bond.isTriple():
bond.decrementOrder()
oxygen.radicalElectrons -= 1
atom2.radicalElectrons += 1
oxygen.lonePairs += 1
return
elif at.isOxygen() and at.charge == 1 and at.lonePairs == 1:
bonds = mol.getBonds(at)
oxygen = at
start = oxygen
# search for 3-atom-2-bond [X=X-X] paths
paths = pathfinder.find_allyl_end_with_charge(start)
for path in paths:
end = path[-1]
start.charge += 1 if start.charge < 0 else -1
end.charge += 1 if end.charge < 0 else -1
start.lonePairs += 1
# filter bonds from path and convert bond orders:
bonds = path[1::2]#odd elements
for bond in bonds[::2]:# even bonds
assert isinstance(bond, Bond)
bond.decrementOrder()
for bond in bonds[1::2]:# odd bonds
assert isinstance(bond, Bond)
bond.incrementOrder()
return
else:
for atom2, bond in bonds.iteritems():
if not bond.isSingle() and atom2.charge == 0:
oxygen.charge -= 1
if (mol.atoms.index(atom2) + 1) in u_indices:
bond.decrementOrder()
atom2.radicalElectrons += 1
u_indices.remove(mol.atoms.index(atom2) + 1)
oxygen.lonePairs += 1
return
def fix_oxygen_unsaturated_bond(mol, u_indices):
"""
Searches for a radical or a charged oxygen atom connected to
a closed-shell carbon via an unsatured bond.
Decrements the unsatured bond,
transfers the unpaired electron from O to C or
converts the charge from O to an unpaired electron on C,
increases the lone pair count of O to 2.
Only do this once per molecule.
"""
for at in mol.atoms:
if at.isOxygen() and at.radicalElectrons == 1 and at.lonePairs == 1:
bonds = mol.getBonds(at)
oxygen = at
for atom2, bond in bonds.iteritems():
if bond.isTriple():
bond.decrementOrder()
oxygen.radicalElectrons -= 1
atom2.radicalElectrons += 1
oxygen.lonePairs += 1
return
elif at.isOxygen() and at.charge == 1 and at.lonePairs == 1:
bonds = mol.getBonds(at)
oxygen = at
start = oxygen
# search for 3-atom-2-bond [X=X-X] paths
paths = pathfinder.find_allyl_end_with_charge(start)
for path in paths:
end = path[-1]
start.charge += 1 if start.charge < 0 else -1
end.charge += 1 if end.charge < 0 else -1
start.lonePairs += 1
# filter bonds from path and convert bond orders:
bonds = path[1::2]#odd elements
for bond in bonds[::2]:# even bonds
assert isinstance(bond, Bond)
bond.decrementOrder()
for bond in bonds[1::2]:# odd bonds
assert isinstance(bond, Bond)
bond.incrementOrder()
return
else:
for atom2, bond in bonds.iteritems():
if not bond.isSingle() and atom2.charge == 0:
oxygen.charge -= 1
if (mol.atoms.index(atom2) + 1) in u_indices:
bond.decrementOrder()
atom2.radicalElectrons += 1
u_indices.remove(mol.atoms.index(atom2) + 1)
oxygen.lonePairs += 1
return
def test_c2h2o3(self):
adjlist = """
1 C u0 p0 c0 {5,D} {6,S} {7,S}
2 C u0 p0 c0 {3,D} {4,S} {5,S}
3 O u0 p2 c0 {2,D}
4 O u0 p3 c-1 {2,S}
5 O u0 p1 c+1 {1,D} {2,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
start = mol.atoms[2]
paths = find_allyl_end_with_charge(start)
idx_path = sorted([[mol.atoms.index(atom) + 1 for atom in path[0::2]] for path in paths])
expected_idx_path = [[3, 2, 4], [3, 2, 5]]
self.assertEquals(idx_path, expected_idx_path)
def test_c3h2o3(self):
adjlist = """
1 C u0 p0 c0 {2,D} {7,S} {8,S}
2 C u0 p0 c0 {1,D} {3,D}
3 C u0 p0 c0 {2,D} {4,S} {6,S}
4 O u0 p3 c-1 {3,S}
5 O u0 p2 c0 {6,D}
6 O u0 p1 c+1 {3,S} {5,D}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {1,S}
"""
mol = Molecule().from_adjacency_list(adjlist)
start = mol.atoms[1]
paths = find_allyl_end_with_charge(start)
idx_paths = sorted([[mol.atoms.index(atom) + 1 for atom in path[0::2]] for path in paths])
idx_paths = sorted(idx_paths)
expected_idx_paths = [[2, 3, 4], [2, 3, 6]]
self.assertEquals(idx_paths, expected_idx_paths)
def _convert_3_atom_2_bond_path(start, mol):
"""
Searches for 3-atom-2-bond [X=X-X+] paths paths starting from the parameter atom.
If a correct path is found, the starting atom receives an unpaired electron while
the bonds in the delocalization path are "inverted". A unit of charge on the
end atom is neutralized and a lone pair is added.
If it turns out the path was invalid, the actions are reverted, and another path
is tried instead.
To facilitate reverting the changes, we use a reaction recipe and populate it
with a number of actions that reflect the changes in bond orders and unpaired
electrons that the molecule should undergo.
"""
from rmgpy.data.kinetics.family import ReactionRecipe
def is_valid(mol):
"""Check if total bond order of oxygen atoms is smaller than 4."""
for at in mol.atoms:
if at.number == 8:
order = at.get_total_bond_order()
not_correct = order >= 4
if not_correct:
return False
return True
paths = pathfinder.find_allyl_end_with_charge(start)
for path in paths:
# label atoms so that we can use the labels in the actions of the recipe
for i, at in enumerate(path[::2]):
at.label = str(i)
# we have found the atom we are looking for
recipe = ReactionRecipe()
recipe.add_action(['GAIN_RADICAL', start.label, 1])
end = path[-1]
end_original_charge = end.charge
# filter bonds from path and convert bond orders:
bonds = path[1::2] # odd elements
for bond in bonds[::2]: # even
recipe.add_action(
['CHANGE_BOND', bond.atom1.label, -1, bond.atom2.label])
for bond in bonds[1::2]: # odd
recipe.add_action(
['CHANGE_BOND', bond.atom1.label, 1, bond.atom2.label])
end.charge += 1 if end.charge < 0 else -1
recipe.apply_forward(mol)
if is_valid(mol):
# unlabel atoms so that they never cause trouble downstream
for i, at in enumerate(path[::2]):
at.label = ''
return True
else:
recipe.apply_reverse(mol)
end.charge = end_original_charge
# unlabel atoms so that they never cause trouble downstream
for i, at in enumerate(path[::2]):
assert isinstance(at, Atom)
at.label = ''
return False
def convert_3_atom_2_bond_path(start, mol):
"""
Searches for 3-atom-2-bond [X=X-X+] paths paths starting from the parameter atom.
If a correct path is found, the starting atom receives an unpaired electron while
the bonds in the delocalization path are "inverted". A unit of charge on the
end atom is neutralized and a lone pair is added.
If it turns out the path was invalid, the actions are reverted, and another path
is tried instead.
To facilitate reverting the changes, we use a reaction recipe and populate it
with a number of actions that reflect the changes in bond orders and unpaired
electrons that the molecule should undergo.
"""
from rmgpy.data.kinetics.family import ReactionRecipe
def is_valid(mol):
"""Check if total bond order of oxygen atoms is smaller than 4."""
for at in mol.atoms:
if at.number == 8:
order = sum([bond_orders[b.order] for _, b in at.bonds.iteritems()])
not_correct = order >= 4
if not_correct:
return False
return True
index = mol.atoms.index(start) + 1
paths = pathfinder.find_allyl_end_with_charge(start)
for path in paths:
# label atoms so that we can use the labels in the actions of the recipe
for i, at in enumerate(path[::2]):
at.label = str(i)
# we have found the atom we are looking for
recipe = ReactionRecipe()
recipe.addAction(['GAIN_RADICAL', start.label, 1])
end = path[-1]
end_original_charge = end.charge
# filter bonds from path and convert bond orders:
bonds = path[1::2]#odd elements
for bond in bonds[::2]:# even
recipe.addAction(['CHANGE_BOND', bond.atom1.label, -1, bond.atom2.label])
for bond in bonds[1::2]:# odd
recipe.addAction(['CHANGE_BOND', bond.atom1.label, 1, bond.atom2.label])
end.charge += 1 if end.charge < 0 else -1
recipe.applyForward(mol)
if is_valid(mol):
# unlabel atoms so that they never cause trouble downstream
for i, at in enumerate(path[::2]):
at.label = ''
return True
else:
recipe.applyReverse(mol)
end.charge = end_original_charge
# unlabel atoms so that they never cause trouble downstream
for i, at in enumerate(path[::2]):
assert isinstance(at, Atom)
at.label = ''
return False
