def lewis2xyz(lewis,f='SMILES',aromatic=False,dim=2,addH=True):
# Input
# lewis ... smiles format string
# aromatic ... is the system aromatic
# dim ... 2d == 2 and 3d == 3
# Output
# Bonding information
# Lewis pictures
# sdf and xyz files
if f == 'pdb':
m = Chem.MolFromPDBFile(lewis)
if f == 'xyz':
struct = read(lewis)
write('lewis.pdb',struct,'proteindatabank')
m = Chem.MolFromPDBFile(lewis)
if f == 'SMILES':
m = Chem.MolFromSmiles(lewis)
# Change armatic bonds to alternate single and double bonds
if aromatic == True:
if m.GetBondWithIdx(0).GetIsAromatic() == True:
Chem.Kekulize(m)
if addH == True:
m=Chem.AddHs(m)
if dim == 1 or dim == 2:
AllChem.Compute2DCoords(m)
if dim == 3:
AllChem.EmbedMolecule(m)
AllChem.UFFOptimizeMolecule(m)
fods = Atoms()
# core electrons
for atom in m.GetAtoms():
idx = atom.GetIdx()
# atomic number
N = m.GetAtomWithIdx(idx).GetAtomicNum()
# number of valence electrons
V = m.GetAtomWithIdx(idx).GetTotalValence()
# number of radicals
R = atom.GetNumRadicalElectrons()
# formal charge of the atom
F = atom.GetFormalCharge()
# number of core electrons
C = N-V-R-F
# lone pairs
#L = 0
#bonds = atom.GetBonds()
#for b in range(len(bonds)):
# bond_type = bonds[b].GetBondType()
# if str(bond_type) == 'SINGLE':
# L = L + 1
# if str(bond_type) == 'DOUBLE':
# L = L + 2
# if str(bond_type) == 'TRIPLE':
# L = L + 3
#print(V-L)
if C > 0:
pos = m.GetConformer().GetAtomPosition(idx)
offset = 0.002
if C == 1:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
if C == 2:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
if C == 3:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
fods.append(Atom('X',[pos[0]+offset,pos[1]+offset,pos[2]+4*offset]))
if C == 4:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
fods.append(Atom('X',[pos[0]+offset,pos[1]+offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]-40*offset]))
if C == 5:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
fods.append(Atom('X',[pos[0]+offset,pos[1]+offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]-40*offset]))
fods.append(Atom('X',[pos[0]+40*offset,pos[1]+40*offset,pos[2]+offset]))
if C == 6:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
fods.append(Atom('X',[pos[0]+40*offset,pos[1]+40*offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+offset,pos[1]-40*offset,pos[2]-40*offset]))
fods.append(Atom('X',[pos[0]-40*offset,pos[1]+40*offset,pos[2]-40*offset]))
fods.append(Atom('He',[pos[0]-40*offset,pos[1]-40*offset,pos[2]+40*offset]))
if C == 7:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
fods.append(Atom('X',[pos[0]+40*offset,pos[1]+40*offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+offset,pos[1]-40*offset,pos[2]-40*offset]))
fods.append(Atom('X',[pos[0]-40*offset,pos[1]+40*offset,pos[2]-40*offset]))
fods.append(Atom('He',[pos[0]-40*offset,pos[1]-40*offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+42*offset,pos[1]+42*offset,pos[2]+42*offset]))
if C == 8:
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
fods.append(Atom('He',[pos[0]+offset,pos[1]+offset,pos[2]+offset]))
fods.append(Atom('X',[pos[0]+40*offset,pos[1]+40*offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+40*offset,pos[1]-40*offset,pos[2]-40*offset]))
fods.append(Atom('X',[pos[0]-40*offset,pos[1]+40*offset,pos[2]-40*offset]))
fods.append(Atom('He',[pos[0]-40*offset,pos[1]-40*offset,pos[2]+40*offset]))
fods.append(Atom('He',[pos[0]+42*offset,pos[1]+42*offset,pos[2]+42*offset]))
fods.append(Atom('X',[pos[0]+42*offset,pos[1]-42*offset,pos[2]-42*offset]))
# find radicals
for atom in m.GetAtoms():
rad = atom.GetNumRadicalElectrons()
#print(rad)
if rad == 1:
idx = atom.GetIdx()
pos = m.GetConformer().GetAtomPosition(idx)
bonds = atom.GetBonds()
vec_BA_x = 0
vec_BA_y = 0
vec_BA_z = 0
BA = []
for b in range(len(bonds)):
ai = bonds[b].GetBeginAtomIdx()
aj = bonds[b].GetEndAtomIdx()
bond_type = bonds[b].GetBondType()
# Positions
pos_ai = m.GetConformer().GetAtomPosition(ai)
pos_aj = m.GetConformer().GetAtomPosition(aj)
# adding bonding vectors for 3d
vec_BA_x = vec_BA_x + (pos_aj[0]-pos_ai[0])
vec_BA_y = vec_BA_y + (pos_aj[1]-pos_ai[1])
vec_BA_z = vec_BA_z + (pos_aj[2]-pos_ai[2])
# save bonding vectors for 2d
BA.append(np.array([(pos_aj[0]-pos_ai[0]),(pos_aj[1]-pos_ai[1]),(pos_aj[2]-pos_ai[2])]))
if dim == 1:
fods.append(Atom('X',[-1*BA[0][0],-1*BA[0][1],-1*BA[0][2]]))
if dim == 2:
vec = np.cross(BA[0],BA[1])
norm = np.sqrt(vec[0]**2 + vec[1]**2 + vec[2]**2)
pos = vec/norm
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
if dim == 3:
norm = np.sqrt(vec_BA_x**2 + vec_BA_y**2 + vec_BA_z**2)
pos = np.array([-1*vec_BA_x,-1*vec_BA_y,-1*vec_BA_z])/norm
fods.append(Atom('X',[pos[0],pos[1],pos[2]]))
bonds = m.GetBonds()
for b in range(len(bonds)):
ai = bonds[b].GetBeginAtomIdx()
aj = bonds[b].GetEndAtomIdx()
bond_type = bonds[b].GetBondType()
# Positions
pos_ai = m.GetConformer().GetAtomPosition(ai)
pos_aj = m.GetConformer().GetAtomPosition(aj)
# Bondlength
#print('%0.5f' % np.linalg.norm([pos_ai[0]-pos_aj[0],pos_ai[1]-pos_aj[1],pos_ai[2]-pos_aj[2]]))
# Middle of the vector
MP = [(pos_ai[0]+pos_aj[0])/2.,(pos_ai[1]+pos_aj[1])/2.,(pos_ai[2]+pos_aj[2])/2.]
#print('%0.5f %0.5f %0.5f' %(MP[0],MP[1],MP[2]))
# Print positions
#print('%0.5f %0.5f %0.5f' %(pos_ai[0],pos_ai[1],pos_ai[2]))
#print('%0.5f %0.5f %0.5f' %(pos_aj[0],pos_aj[1],pos_aj[2]))
for spin in ['He','X']:
if spin == 'He':
offset = 0.000
if spin == 'X':
#offset = 0.002
offset = 0.02
if str(bond_type) == 'SINGLE':
#print('%s %0.5f %0.5f %0.5f' %(spin,MP[0]+offset,MP[1]+offset,MP[2]+offset))
fods.append(Atom(spin,[MP[0]+offset,MP[1]+offset,MP[2]+offset]))
if str(bond_type) == 'DOUBLE':
#print('%s %0.5f %0.5f %0.5f' %(spin,MP[0]+offset,MP[1]+offset,MP[2]+0.5+offset))
#print('%s %0.5f %0.5f %0.5f' %(spin,MP[0]+offset,MP[1]+offset,MP[2]-0.5+offset))
fods.append(Atom(spin,[MP[0]+offset,MP[1]+offset,MP[2]+0.5+offset]))
fods.append(Atom(spin,[MP[0]+offset,MP[1]+offset,MP[2]-0.5+offset]))
if str(bond_type) == 'TRIPLE':
#print('%s %0.5f %0.5f %0.5f' %(spin,MP[0]+offset,MP[1]+offset,MP[2]+0.5+offset))
#print('%s %0.5f %0.5f %0.5f' %(spin,MP[0]+offset,MP[1]+offset,MP[2]-0.5+offset))
#print('%s %0.5f %0.5f %0.5f' %(spin,MP[0]-0.5+offset,MP[1]+offset,MP[2]+offset))
fods.append(Atom(spin,[MP[0]+offset,MP[1]+offset,MP[2]+0.5+offset]))
fods.append(Atom(spin,[MP[0]+offset,MP[1]+offset,MP[2]-0.5+offset]))
fods.append(Atom(spin,[MP[0]-0.5+offset,MP[1]+offset,MP[2]+offset]))
w = Chem.SDWriter('%s.sdf' % 'pylewis')
w.write(m)
w.flush()
# sdf2xyz
struct = read('%s.sdf' % 'pylewis')
struct_fods = Atoms()
struct_fods.extend(struct)
struct_fods.extend(fods)
#print(struct.get_chemical_symbols())
write('%s.xyz' % 'pylewis',struct,'xyz')
write('%s_fods.xyz' % 'pylewis',struct_fods,'xyz')
class SelectorTests(unittest.TestCase):
def _set_atoms_pos(self, atoms, pos):
p = atoms.get_positions()
p = p + np.array(pos)
atoms.set_positions(p)
def _set_molecule_pos(self, atoms, molecule, pos):
p = atoms.get_positions()
dx = pos[0] - p[molecule[0]][0]
dy = pos[1] - p[molecule[0]][1]
dz = pos[2] - p[molecule[0]][2]
for i in molecule:
p[i][0] += dx
p[i][1] += dy
p[i][2] += dz
atoms.set_positions(p)
def setUp(self):
self._atoms = Atoms()
self._mcount = 5
self._edge = 100.0
x = np.linspace(-self._edge/2.0, self._edge/2.0, self._mcount)
c = 0
for i in x:
for j in x:
for k in x:
ch4 = molecule("CH4")
self._set_atoms_pos(ch4, (i,j,k))
self._atoms.extend(ch4)
c += 1
Mixer.set_atom_ids(self._atoms)
def test_calcbox_all(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
dim=(self._edge + 5, self._edge + 5, self._edge + 5))
sa, srmap, sw = cb.select_atoms(self._atoms)
ra = self._atoms
self.assertEqual(ra, sa)
def test_calcbox_subset(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
cutoff=0.0,
dim=(50.0, 50.0, 50.0))
sa, srmap, sw = cb.select_atoms(self._atoms)
correct_ids = set([307, 215, 405, 280, 281, 410, 155, 156, 285, 286,
415, 160, 289, 290, 419, 165, 294, 455, 430, 432, 305, 306, 435,
180, 414, 310, 439, 312, 185, 186, 315, 188, 190, 181, 193, 343,
161, 457, 330, 311, 332, 205, 462, 335, 337, 210, 340, 213, 313,
218, 314, 465, 444, 338, 437, 440, 318, 319, 460])
self.assertEqual(set(Mixer.get_atom_ids(sa)), correct_ids)
def test_calcbox_moving_ch4(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
cutoff=2.0,
dim=(55.0, 55.0, 55.0),
debug=0)
ch4 = [0, 1, 2, 3] # these are atoms indexes and ids
z = np.linspace(-self._edge/2.0 - 25, self._edge/2.0 + 25, 100)
x = np.zeros_like(z)
y = np.zeros_like(z)
pos = np.column_stack((x, y, z))
for i in range(len(pos)):
self._set_molecule_pos(self._atoms,
ch4,
pos[i])
sa, srmap, sw = cb.select_atoms(self._atoms)
s_ids = set(Mixer.get_atom_ids(sa))
all_ids = set(Mixer.get_atom_ids(self._atoms))
inside_ids = s_ids.intersection(set(ch4))
if not (len(inside_ids) == 0 or len(inside_ids) == 4):
print("CH4 pos: %s" % pos[i])
print("CH4 in selection: %s" % inside_ids)
def test_weights(self):
cb = CalcBox(name="testbox", pos=(0., 0., 0.),
cutoff=2.0,
dim=(100.0, 100.0, 100.0),
inner_dim=(50.0, 50.0, 50.0))
# test all three axis
test_positions = np.column_stack((np.linspace(-55.0, 55.0, 100),
np.zeros(100),
np.zeros(100)))
test_positions = np.append(test_positions, np.column_stack(
(np.zeros(100),
np.linspace(-55.0, 55.0, 100),
np.zeros(100))), axis=0)
test_positions = np.append(test_positions, np.column_stack(
(np.zeros(100),
np.zeros(100),
np.linspace(-55.0, 55.0, 100))),
axis=0)
# and all 8 corners too
a = 37.5
test_positions = np.append(test_positions, np.array((
(-a, -a, -a),
(-a, -a, a),
(-a, a, -a),
(-a, a, -a),
(a, -a, -a),
(a, -a, a),
(a, a, -a),
(a, a, a))),
axis=0)
correct_weights = np.loadtxt("weight_test.csv", delimiter=",")
for i in range(len(test_positions)):
w = cb.get_weight(test_positions[i])
self.assertEqual(correct_weights[i], w)
class SelectorTests(unittest.TestCase):
def _set_atoms_pos(self, atoms, pos):
p = atoms.get_positions()
p = p + np.array(pos)
atoms.set_positions(p)
def _set_molecule_pos(self, atoms, molecule, pos):
p = atoms.get_positions()
dx = pos[0] - p[molecule[0]][0]
dy = pos[1] - p[molecule[0]][1]
dz = pos[2] - p[molecule[0]][2]
for i in molecule:
p[i][0] += dx
p[i][1] += dy
p[i][2] += dz
atoms.set_positions(p)
def setUp(self):
self._atoms = Atoms()
self._mcount = 5
self._edge = 100.0
x = np.linspace(-self._edge / 2.0, self._edge / 2.0, self._mcount)
c = 0
for i in x:
for j in x:
for k in x:
ch4 = molecule("CH4")
self._set_atoms_pos(ch4, (i, j, k))
self._atoms.extend(ch4)
c += 1
Mixer.set_atom_ids(self._atoms)
def test_calcbox_all(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
dim=(self._edge + 5, self._edge + 5, self._edge + 5))
sa, srmap, sw = cb.select_atoms(self._atoms)
ra = self._atoms
self.assertEqual(ra, sa)
def test_calcbox_subset(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
cutoff=0.0,
dim=(50.0, 50.0, 50.0))
sa, srmap, sw = cb.select_atoms(self._atoms)
correct_ids = set([
307, 215, 405, 280, 281, 410, 155, 156, 285, 286, 415, 160, 289,
290, 419, 165, 294, 455, 430, 432, 305, 306, 435, 180, 414, 310,
439, 312, 185, 186, 315, 188, 190, 181, 193, 343, 161, 457, 330,
311, 332, 205, 462, 335, 337, 210, 340, 213, 313, 218, 314, 465,
444, 338, 437, 440, 318, 319, 460
])
self.assertEqual(set(Mixer.get_atom_ids(sa)), correct_ids)
def test_calcbox_moving_ch4(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
cutoff=2.0,
dim=(55.0, 55.0, 55.0),
debug=0)
ch4 = [0, 1, 2, 3] # these are atoms indexes and ids
z = np.linspace(-self._edge / 2.0 - 25, self._edge / 2.0 + 25, 100)
x = np.zeros_like(z)
y = np.zeros_like(z)
pos = np.column_stack((x, y, z))
for i in range(len(pos)):
self._set_molecule_pos(self._atoms, ch4, pos[i])
sa, srmap, sw = cb.select_atoms(self._atoms)
s_ids = set(Mixer.get_atom_ids(sa))
all_ids = set(Mixer.get_atom_ids(self._atoms))
inside_ids = s_ids.intersection(set(ch4))
if not (len(inside_ids) == 0 or len(inside_ids) == 4):
print("CH4 pos: %s" % pos[i])
print("CH4 in selection: %s" % inside_ids)
def test_weights(self):
cb = CalcBox(name="testbox",
pos=(0., 0., 0.),
cutoff=2.0,
dim=(100.0, 100.0, 100.0),
inner_dim=(50.0, 50.0, 50.0))
# test all three axis
test_positions = np.column_stack(
(np.linspace(-55.0, 55.0, 100), np.zeros(100), np.zeros(100)))
test_positions = np.append(test_positions,
np.column_stack(
(np.zeros(100),
np.linspace(-55.0, 55.0,
100), np.zeros(100))),
axis=0)
test_positions = np.append(test_positions,
np.column_stack(
(np.zeros(100), np.zeros(100),
np.linspace(-55.0, 55.0, 100))),
axis=0)
# and all 8 corners too
a = 37.5
test_positions = np.append(test_positions,
np.array(
((-a, -a, -a), (-a, -a, a), (-a, a, -a),
(-a, a, -a), (a, -a, -a), (a, -a, a),
(a, a, -a), (a, a, a))),
axis=0)
correct_weights = np.loadtxt("weight_test.csv", delimiter=",")
for i in range(len(test_positions)):
w = cb.get_weight(test_positions[i])
self.assertEqual(correct_weights[i], w)
