def GetBondGraph(mol):
"""Build graph of which atoms are covalently bonded and bond lengths.
Search all atom pairs to find those within a threshold of the sum of the
interatomic covalent radii. Append those found to the bond graph dictionary of
each Atom object within the Molecule object.
First atomic index is the array index. Second atomic index is a dictionary
key. The value is the bond length [Angstrom] of the bond.
Args:
mol (mmlib.molecule.Molecule): Molecule object with Atom objects with
geometry and mm parameter data.
"""
mol.bond_graph = [{} for i in range(mol.n_atoms)]
bond_thresh = const.BONDTHRESHOLD
for i in range(mol.n_atoms):
at1 = mol.atoms[i]
for j in range(i + 1, mol.n_atoms):
at2 = mol.atoms[j]
thresh = bond_thresh * (at1.covrad + at2.covrad)
r2_12 = geomcalc.GetR2ij(at1.coords, at2.coords)
if r2_12 < thresh**2:
r_12 = math.sqrt(r2_12)
mol.bond_graph[i][j] = r_12
mol.bond_graph[j][i] = r_12
def GetBondGraph(atoms):
"""Build graph of which atoms are covalently bonded and bond lengths.
Search all atom pairs to find those within a threshold of the sum of the
interatomic covalent radii. Append those found to the bond graph dictionary of
each Atom object within the Molecule object.
First atomic index is the array index. Second atomic index is a dictionary
key. The value is the bond length [Angstrom] of the bond.
Args:
atoms (mmlib.molecule.Atom*): Array of Atom objects with coordinate and MM
parameter data.
Returns:
bond_graph (int:(int:float)): Dictionary of bond connectivity.
"""
bond_graph = {i: {} for i in range(len(atoms))}
for i, j in itertools.combinations(range(len(atoms)), 2):
at1, at2 = atoms[i], atoms[j]
threshold = const.BONDTHRESHOLD * (at1.covrad + at2.covrad)
r2_12 = geomcalc.GetR2ij(at1.coords, at2.coords)
if r2_12 < threshold**2:
r_12 = math.sqrt(r2_12)
bond_graph[i][j] = bond_graph[j][i] = r_12
return bond_graph
def testUnitLength(self):
"""Asserts unit value for points one distance unit apart."""
params = ORIGIN, NEGATIVE_UNIT_X
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 1.0)
def testSamePoint(self):
"""Asserts zero distance between identical points."""
params = ARBITRARY_XYZ1, ARBITRARY_XYZ1
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 0.0)
def testReflexive(self):
"""Asserts same value for inverted order of inputs."""
params = ARBITRARY_XYZ2, ARBITRARY_XYZ1
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 148.0921993)
def testArbitrary(self):
"""Asserts correct value for arbitrary points in 3d space."""
params = ARBITRARY_XYZ1, ARBITRARY_XYZ2
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 148.0921993)
def testOnAxisZ(self):
"""Asserts correct value for points separated along z-axis."""
params = POSITIVE_ARBITRARY_Z, NEGATIVE_ARBITRARY_Z
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 159.3847166)
def testOnAxisY(self):
"""Asserts correct value for points separated along y-axis."""
params = NEGATIVE_ARBITRARY_Y, POSITIVE_ARBITRARY_Y
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 149.8505274)
def testOnAxisX(self):
"""Asserts correct value for points separated along x-axis."""
params = POSITIVE_ARBITRARY_X, NEGATIVE_ARBITRARY_X
self.assertAlmostEqual(geomcalc.GetR2ij(*params), 151.5346474)
