def ketone(length, pos, name="ketone", short="KET", is_h=True):
"""This function generates linear ketone molecules.
Parameters
----------
length : integer
Number of carbon atoms
pos : integer
Position of the oxygen atom
name : string, optional
Molecule name
short : string, optional
Molecule short name
is_h : bool
True if hydrogens are needed
Returns
-------
mol : Molecule
Molecule object
"""
# Check input
if length < 3:
print("Specified length is too small for ketones ...")
return
# Initialize Molecule
mol = Molecule(name, short)
# Define bond lengths and angles
b = {"cc": 0.153, "ch": 0.109, "co": 0.123}
a = {"ccc": 30.00, "cch": 109.47}
# Add carbons
mol.add("C", [0, 0, 0])
angle = a["ccc"]
for i in range(length-1):
angle *= -1
mol.add("C", mol.get_num()-1, r=b["cc"], theta=angle)
# Add oxygen
angle = -90 if pos % 2 == 0 else 90
mol.add("O", pos-1, r=b["co"], theta=angle)
# Add hydrogens
if is_h:
angle = -90
for i in range(length):
# Boundary
if i==0 or i==length-1:
for j in range(3):
mol.add("H", i, r=b["ch"], theta=angle-30, phi=120*j)
# Inner
elif not i == pos-1:
mol.add("H", i, r=b["ch"], theta=angle, phi=a["cch"])
mol.add("H", i, r=b["ch"], theta=angle, phi=-a["cch"])
# Switch orientation
angle *= -1
# Move to zero
mol.zero()
# Return molecule
return mol
def alcohol(length, name="alcohol", short="ALC", is_h=True):
"""This function generates linear alcohol molecules.
Parameters
----------
length : integer
Number of carbon atoms
name : string, optional
Molecule name
short : string, optional
Molecule short name
is_h : bool, optional
True if hydrogens are needed
Returns
-------
mol : Molecule
Molecule object
"""
# Initialize Molecule
mol = Molecule(name, short)
# Define bond lengths and angles
b = {"cc": 0.153, "ch": 0.109, "co": 0.143, "oh": 0.098}
a = {"ccc": 30.00, "cch": 109.47, "occ": 30.00, "coh": 109.47}
# Add carbons
mol.add("C", [0, 0, 0])
angle = a["ccc"]
for i in range(length-1):
angle *= -1
mol.add("C", mol.get_num()-1, r=b["cc"], theta=angle)
# Add hydroxy
mol.add("O", mol.get_num()-1, r=b["co"], theta=-angle)
mol.add("H", mol.get_num()-1, r=b["oh"], theta=angle)
# Add hydrogens
if is_h:
if length > 1:
angle = -90
for i in range(length):
# Boundary
if i==0:
for j in range(3):
mol.add("H", i, r=b["ch"], theta=angle-30, phi=120*j)
# Inner
else:
mol.add("H", i, r=b["ch"], theta=angle, phi=a["cch"])
mol.add("H", i, r=b["ch"], theta=angle, phi=-a["cch"])
# Switch orientation
angle *= -1
# Methanol
else:
for i in range(3):
mol.add("H", 0, r=b["ch"], theta=a["cch"], phi=i*120)
# Move to zero
mol.zero()
# Return molecule
return mol
def pattern(self):
"""Construct minimal block structure.
Returns
-------
block : Molecule
Minimal block structure
"""
# Initialize
mols = [self._hexagonal() for x in range(3)]
# Combine three hexagonal molecules
mols[0].add("O", 2, r=self._b)
mols[0].add("O", 6, r=self._b)
mols[0].add("O", 10, r=self._b)
mols[1].move(0, mols[0].pos(12))
mols[1].translate([0, 0, self._b])
mols[1].delete([1, 2, 3, 4, 5, 6, 7])
mols[2].move(0, mols[0].pos(14))
mols[2].translate([0, 0, self._b])
mols[2].delete([2, 3, 4, 5, 6, 7, 8, 9, 10, 11])
# Build block
block = []
for i in range(11):
block.append(Molecule(inp=copy.deepcopy(mols)))
block[1].rotate("x", 180)
block[1].move(18, block[0].pos(18))
block[1].translate([0, 0, self._b * 2])
block[1].add("O", block[0].pos(18), r=self._b)
block[2].rotate("x", 180)
block[2].move(0, block[0].pos(18))
block[3].move(4, block[0].pos(15))
block[4].rotate("x", 180)
block[4].move(16, block[0].pos(18))
block[4].delete([21, 19, 15, 20, 14, 12, 10, 2, 11, 1, 0])
block[5].move(6, block[1].pos(16))
block[5].delete([21, 19, 15, 20, 14, 12, 10, 2, 11, 1, 0])
# Delete overlapping molecules
block = Molecule(inp=block)
overlap = block.overlap()
block.delete(sum([overlap[x] for x in overlap], []))
# Check overlapping atoms due to repetition
for dim in range(3):
for pm in range(2):
# Define translate vector
translate = [0, 0, 0]
translate[dim] = self._repeat[dim]
translate[dim] *= -1 if pm == 1 else 1
# Remove atoms
block = Molecule(inp=[block])
mol_repeat = copy.deepcopy(block)
mol_repeat.translate(translate)
block.delete([
x for x in Molecule(inp=[block, mol_repeat]).overlap()
if x < block.get_num()
])
# Move to zero
block.zero()
return block