def test_get_bond_order(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0, 1.08])
self.assertAlmostEqual(CovalentBond(site1, site2).get_bond_order(), 1)
bond = CovalentBond(Site("C", [0, 0, 0]), Site("Br", [0, 0, 2]))
self.assertAlmostEqual(bond.get_bond_order(0.5, 1.9),
0.894736842105263)
def test_get_bond_order(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0, 1.08])
self.assertAlmostEqual(
CovalentBond(site1, site2).get_bond_order(), 1)
bond = CovalentBond(Site("C", [0, 0, 0]), Site("Br", [0, 0, 2]))
self.assertAlmostEqual(
bond.get_bond_order(0.5, 1.9), 0.894736842105263)
def test_is_bonded(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0, 1])
self.assertTrue(CovalentBond.is_bonded(site1, site2))
site2 = Site("H", [0, 0, 1.5])
self.assertFalse(CovalentBond.is_bonded(site1, site2))
site1 = Site("U", [0, 0, 0])
self.assertRaises(ValueError, CovalentBond.is_bonded, site1, site2)
self.assertTrue(CovalentBond.is_bonded(site1, site2, default_bl=2))
def test_is_bonded(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0, 1])
self.assertTrue(CovalentBond.is_bonded(site1, site2))
site2 = Site("H", [0, 0, 1.5])
self.assertFalse(CovalentBond.is_bonded(site1, site2))
site1 = Site("U", [0, 0, 0])
self.assertRaises(ValueError, CovalentBond.is_bonded, site1, site2)
self.assertTrue(CovalentBond.is_bonded(site1, site2, default_bl=2))
def make_graph(mol, tol=0.2):
"""
make graph object for the input molecule
"""
G = nx.Graph()
names = {}
for i, site in enumerate(mol._sites):
names[i] = site.specie.value
for i in range(len(mol) - 1):
site1 = mol.sites[i]
for j in range(i + 1, len(mol)):
site2 = mol.sites[j]
#remove short X-H distances
if names[i] == "H" and names[j] == "H":
factor = -0.5
elif [names[i], names[j]] in [["S", "S"], ["S", "O"], ["O", "S"],
["F", "O"], ["O", "F"]]:
factor = 0.05
elif "H" in [names[i], names[j]]:
factor = 0.5
else:
factor = 1.0
try:
if CovalentBond.is_bonded(site1, site2, factor * tol):
G.add_edge(i, j)
#print(names[i], names[j], mol.get_distance(i, j))
except ValueError:
pass
nx.set_node_attributes(G, names, 'name')
return G
def make_bonds(scene, structure, line_width=0.08, tol=0.2, color=[.1, .1, .1]):
bonds = []
for site0, site1 in itertools.combinations(structure, 2):
if CovalentBond.is_bonded(site0, site1, default_bl=0.5):
dist = site0.distance(site1)
if np.isclose(np.linalg.norm(site0.coords - site1.coords),
dist,
rtol=5e-3):
bonds.append([site0.coords.tolist(), site1.coords.tolist()])
# elif draw_pbc:
# for p in itertools.product([1, 0, -1], repeat=3):
# vec = site1.coords + np.dot(p, structure.lattice.matrix)
# if np.isclose(np.linalg.norm(site0.coords - vec),
# dist, rtol=5e-3):
# bonds.append([site0.coords.tolist(), vec.tolist()])
# break
# for p in itertools.product([1, 0, -1], repeat=3):
# vec = site0.coords + np.dot(p, structure.lattice.matrix)
# if np.isclose(np.linalg.norm(vec - site1.coords),
# dist, rtol=5e-3):
# bonds.append([vec.tolist(), site1.coords.tolist()])
# break
bonds_geom = fresnel.geometry.Cylinder(scene, N=len(bonds))
bonds_geom.points[:] = bonds
bonds_geom.radius[:] = line_width * np.ones(len(bonds))
bonds_geom.material = fresnel.material.Material(
color=fresnel.color.linear(color))
return bonds_geom
def from_molecule(molecule, tol=0.1):
"""
Return Topology object from molecule.
Args:
molecule (Molecule)
tol (float): Relative tolerance to test in determining the bonds
in the molecule. Basically, the code checks if the distance
between the sites is less than (1 + tol) * typical bond
distances. Defaults to 0.1, i.e., 10% longer.
Returns:
Topology object
"""
bonds = molecule.get_covalent_bonds(tol=tol)
angles = []
dihedrals = []
for bond1, bond2 in itertools.combinations(bonds, 2):
bond1_sites = [bond1.site1, bond1.site2]
bond2_sites = [bond2.site1, bond2.site2]
s_bond1 = set(bond1_sites)
s_bond2 = set(bond2_sites)
common_site = s_bond1.intersection(s_bond2)
if common_site:
site1 = (s_bond1 - s_bond2).pop()
site2 = common_site.pop()
site3 = (s_bond2 - s_bond1).pop()
angle = [molecule.index(site1), molecule.index(site2),
molecule.index(site3),
(str(site1.specie), str(site2.specie),
str(site3.specie))]
angles.append(angle)
else:
for site1, site2 in itertools.product(bond1_sites,
bond2_sites):
if CovalentBond.is_bonded(site1, site2, tol=tol):
bond1_sites.remove(site1)
bond2_sites.remove(site2)
dihedral = bond1_sites + [site1,
site2] + bond2_sites
dihedral = [molecule.index(dihedral[0]),
molecule.index(dihedral[1]),
molecule.index(dihedral[2]),
molecule.index(dihedral[3]),
(str(dihedral[0].specie),
str(dihedral[1].specie),
str(dihedral[2].specie),
str(dihedral[3].specie))]
dihedrals.append(dihedral)
break
atoms = [[str(site.specie), str(site.specie)] for site in molecule]
bonds = [[molecule.index(b.site1), molecule.index(b.site2),
(str(b.site1.specie), str(b.site2.specie))] for b in bonds]
charges = None
if hasattr(molecule[0], "charge"):
charges = [site.charge for site in molecule]
return Topology(atoms, bonds, angles, charges=charges, dihedrals=dihedrals)
def from_molecule(molecule, tol=0.1):
"""
Return Topology object from molecule.
Args:
molecule (Molecule)
tol (float): Relative tolerance to test in determining the bonds
in the molecule. Basically, the code checks if the distance
between the sites is less than (1 + tol) * typical bond
distances. Defaults to 0.1, i.e., 10% longer.
Returns:
Topology object
"""
bonds = molecule.get_covalent_bonds(tol=tol)
angles = []
dihedrals = []
for bond1, bond2 in itertools.combinations(bonds, 2):
bond1_sites = [bond1.site1, bond1.site2]
bond2_sites = [bond2.site1, bond2.site2]
s_bond1 = set(bond1_sites)
s_bond2 = set(bond2_sites)
common_site = s_bond1.intersection(s_bond2)
if common_site:
site1 = (s_bond1 - s_bond2).pop()
site2 = common_site.pop()
site3 = (s_bond2 - s_bond1).pop()
angle = [
molecule.index(site1),
molecule.index(site2),
molecule.index(site3),
(str(site1.specie), str(site2.specie), str(site3.specie))
]
angles.append(angle)
else:
for site1, site2 in itertools.product(bond1_sites,
bond2_sites):
if CovalentBond.is_bonded(site1, site2):
bond1_sites.remove(site1)
bond2_sites.remove(site2)
dihedral = bond1_sites + [site1, site2] + bond2_sites
dihedral = [
molecule.index(dihedral[0]),
molecule.index(dihedral[1]),
molecule.index(dihedral[2]),
molecule.index(dihedral[3]),
(str(dihedral[0].specie), str(dihedral[1].specie),
str(dihedral[2].specie), str(dihedral[3].specie))
]
dihedrals.append(dihedral)
break
atoms = [[str(site.specie), str(site.specie)] for site in molecule]
bonds = [[
molecule.index(b.site1),
molecule.index(b.site2), (str(b.site1.specie), str(b.site2.specie))
] for b in bonds]
return Topology(atoms, bonds, angles, dihedrals=dihedrals)
def find_covalent_bonds(molecule):
import itertools
from pymatgen.core.bonds import CovalentBond
number_of_sites = len(molecule.sites)
bonds=[]
for a,b in itertools.combinations(range(number_of_sites),2):
if CovalentBond.is_bonded(molecule.sites[a], molecule.sites[b], default_bl=2.0):
bonds.append([a,b])
return np.array(bonds)
def check_one_site(struc, site0, visited):
neigh_sites = struc.get_neighbors(site0, 3.0)
ids = [m.index for m in visited]
sites_add = []
ids_add = []
for site1 in neigh_sites:
if (site1.index not in ids + ids_add):
if CovalentBond.is_bonded(site0, site1, tol):
sites_add.append(site1)
ids_add.append(site1.index)
if len(sites_add) > 0:
visited.extend(sites_add)
return sites_add, visited
def get_covalent_bonds(self, tol=0.2):
"""
Determines the covalent bonds in a molecule.
Args:
tol:
The tol to determine bonds in a structure. See
CovalentBond.is_bonded.
Returns:
List of bonds
"""
bonds = []
for site1, site2 in itertools.combinations(self._sites, 2):
if CovalentBond.is_bonded(site1, site2, tol):
bonds.append(CovalentBond(site1, site2))
return bonds
def check_one_site(struc, site0, visited, rmax=2.9):
neigh_sites = struc.get_neighbors(site0, rmax)
ids = [m.index for m in visited]
sites_add = []
ids_add = []
for site1 in neigh_sites:
if (site1.index not in ids+ids_add):
if CovalentBond.is_bonded(site0, site1, tol):
(d, image) = site0.distance_and_image(site1)
site1.frac_coords += image
#print(d, image, site1)
sites_add.append(site1)
ids_add.append(site1.index)
if len(sites_add) > 0:
visited.extend(sites_add)
return sites_add, visited
def belongs_to_cluster(site, cluster):
for test_site in cluster:
if CovalentBond.is_bonded(site, test_site, tol=tol):
return True
return False
def test_str(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0.7, 0.6])
self.assertIsNotNone(CovalentBond(site1, site2))
def from_molecule(molecule, tol=0.1, ff_map="ff_map"):
"""
Return Topology object from molecule. Charges are also set if the
molecule has 'charge' site property.
Args:
molecule (Molecule)
tol (float): Relative tolerance to test in determining the bonds
in the molecule. Basically, the code checks if the distance
between the sites is less than (1 + tol) * typical bond
distances. Defaults to 0.1, i.e., 10% longer.
ff_map (string): Ensure this site property is set for each site if
atoms need to be mapped to its forcefield name.
eg: Carbon atom, 'C', on different sites can be mapped to
either 'Ce' or 'Cm' depending on how the forcefield parameters
are set.
Returns:
Topology object
"""
type_attrib = ff_map if hasattr(molecule[0], ff_map) else "specie"
bonds = molecule.get_covalent_bonds(tol=tol)
angles = []
dihedrals = []
for bond1, bond2 in itertools.combinations(bonds, 2):
bond1_sites = [bond1.site1, bond1.site2]
bond2_sites = [bond2.site1, bond2.site2]
s_bond1 = set(bond1_sites)
s_bond2 = set(bond2_sites)
common_site = s_bond1.intersection(s_bond2)
if common_site:
site1 = (s_bond1 - s_bond2).pop()
site2 = common_site.pop()
site3 = (s_bond2 - s_bond1).pop()
angle = [
molecule.index(site1),
molecule.index(site2),
molecule.index(site3),
(str(getattr(site1, type_attrib)),
str(getattr(site2, type_attrib)),
str(getattr(site3, type_attrib)))
]
angles.append(angle)
else:
for site1, site2 in itertools.product(bond1_sites,
bond2_sites):
if CovalentBond.is_bonded(site1, site2, tol=tol):
bond1_sites.remove(site1)
bond2_sites.remove(site2)
dihedral = bond1_sites + [site1, site2] + bond2_sites
dihedral = [
molecule.index(dihedral[0]),
molecule.index(dihedral[1]),
molecule.index(dihedral[2]),
molecule.index(dihedral[3]),
(str(getattr(dihedral[0], type_attrib)),
str(getattr(dihedral[1], type_attrib)),
str(getattr(dihedral[2], type_attrib)),
str(getattr(dihedral[3], type_attrib)))
]
dihedrals.append(dihedral)
break
atoms = [[str(site.specie),
str(getattr(site, type_attrib))] for site in molecule]
bonds = [[
molecule.index(b.site1),
molecule.index(b.site2),
(str(getattr(b.site1,
type_attrib)), str(getattr(b.site2, type_attrib)))
] for b in bonds]
charges = None
if hasattr(molecule[0], "charge"):
charges = [site.charge for site in molecule]
return Topology(atoms,
bonds,
angles,
charges=charges,
dihedrals=dihedrals)
def test_length(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0.7, 0.6])
self.assertAlmostEqual(
CovalentBond(site1, site2).length, 0.92195444572928864)
def test_is_bonded(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0, 1])
self.assertTrue(CovalentBond.is_bonded(site1, site2))
site2 = Site("H", [0, 0, 1.5])
self.assertFalse(CovalentBond.is_bonded(site1, site2))
def test_is_bonded(self):
site1 = Site("C", [0, 0, 0])
site2 = Site("H", [0, 0, 1])
self.assertTrue(CovalentBond.is_bonded(site1, site2))
site2 = Site("H", [0, 0, 1.5])
self.assertFalse(CovalentBond.is_bonded(site1, site2))
def from_molecule(molecule, tol=0.1, ff_map="ff_map"):
"""
Return Topology object from molecule. Charges are also set if the
molecule has 'charge' site property.
Args:
molecule (Molecule)
tol (float): Relative tolerance to test in determining the bonds
in the molecule. Basically, the code checks if the distance
between the sites is less than (1 + tol) * typical bond
distances. Defaults to 0.1, i.e., 10% longer.
ff_map (string): Ensure this site property is set for each site if
atoms need to be mapped to its forcefield name.
eg: Carbon atom, 'C', on different sites can be mapped to
either 'Ce' or 'Cm' depending on how the forcefield parameters
are set.
Returns:
Topology object
"""
type_attrib = ff_map if hasattr(molecule[0], ff_map) else "specie"
bonds = molecule.get_covalent_bonds(tol=tol)
angles = []
dihedrals = []
for bond1, bond2 in itertools.combinations(bonds, 2):
bond1_sites = [bond1.site1, bond1.site2]
bond2_sites = [bond2.site1, bond2.site2]
s_bond1 = set(bond1_sites)
s_bond2 = set(bond2_sites)
common_site = s_bond1.intersection(s_bond2)
if common_site:
site1 = (s_bond1 - s_bond2).pop()
site2 = common_site.pop()
site3 = (s_bond2 - s_bond1).pop()
angle = [molecule.index(site1), molecule.index(site2),
molecule.index(site3),
(str(getattr(site1, type_attrib)),
str(getattr(site2, type_attrib)),
str(getattr(site3, type_attrib)))]
angles.append(angle)
else:
for site1, site2 in itertools.product(bond1_sites,
bond2_sites):
if CovalentBond.is_bonded(site1, site2, tol=tol):
bond1_sites.remove(site1)
bond2_sites.remove(site2)
dihedral = bond1_sites + [site1,
site2] + bond2_sites
dihedral = [molecule.index(dihedral[0]),
molecule.index(dihedral[1]),
molecule.index(dihedral[2]),
molecule.index(dihedral[3]),
(str(getattr(dihedral[0], type_attrib)),
str(getattr(dihedral[1], type_attrib)),
str(getattr(dihedral[2], type_attrib)),
str(getattr(dihedral[3], type_attrib)))]
dihedrals.append(dihedral)
break
atoms = [[str(site.specie), str(getattr(site, type_attrib))]
for site in molecule]
bonds = [[molecule.index(b.site1), molecule.index(b.site2),
(str(getattr(b.site1, type_attrib)),
str(getattr(b.site2, type_attrib)))] for b in bonds]
charges = None
if hasattr(molecule[0], "charge"):
charges = [site.charge for site in molecule]
return Topology(atoms, bonds, angles,
charges=charges, dihedrals=dihedrals)
