def testBadInput(self):
"""Asserts raise of ValueError for missing atom type input."""
with self.assertRaises(ValueError) as e:
param.GetVdwParam('AA')
self.assertEqual(str(e.exception),
'No vdw param found for atom type: AA')
def testEmptyInput(self):
"""Asserts raise of ValueError for empty string input."""
with self.assertRaises(ValueError) as e:
param.GetVdwParam('')
self.assertEqual(str(e.exception),
'No vdw param found for atom type: ')
def GetGeom(mol):
"""Read in molecular geometry data from molecule xyzq file.
Parse 2-d array of strings from xyzq file into atomic data. First line
contains (int) number of atoms. Second line is ignored comment. Each line
after (3 to [n+2]) contains atom type, (float) 3 xyz cartesian coordinates
[Angstrom], and (float) charge [e].
Args:
mol (mmlib.molecule.Molecule): molecule with an associated xyzq input file.
"""
infile_array = _GetFileStringArray(mol.infile)
mol.n_atoms = int(infile_array[0][0])
for i in range(mol.n_atoms):
at_type = infile_array[i+2][0]
at_coords = numpy.array(
list(map(float, infile_array[i+2][1:1+const.NUMDIM])))
at_charge = float(infile_array[i+2][4])
at_element = GetElement(at_type)
at_mass = param.GetAtMass(at_element)
at_ro, at_eps = param.GetVdwParam(at_type)
atom = molecule.Atom(at_type, at_coords, at_charge, at_ro, at_eps, at_mass)
atom.SetCovRad(param.GetCovRad(at_element))
mol.atoms.append(atom)
mol.mass += at_mass
def __init__(self, type_, coords, charge, ro=None, eps=None):
self.SetType(type_)
self.SetCoords(coords)
self.SetCharge(charge)
if ro == None or eps == None:
ro, eps = param.GetVdwParam(self.type_)
self.SetRo(ro)
self.SetEps(eps)
self.SetElement(param.GetElement(type_))
self.SetMass(param.GetMass(self.element))
self.SetCovRad(param.GetCovRad(self.element))
self.SetVels(numpy.zeros(const.NUMDIM))
self.SetAccs(numpy.zeros(const.NUMDIM))
self.SetPVels(numpy.zeros(const.NUMDIM))
self.SetPAccs(numpy.zeros(const.NUMDIM))
def testAromaticCarbon(self):
"""Asserts correct parameters for carbon atom type."""
self.assertEqual(param.GetVdwParam('CA'), (1.9080, 0.0860))
def testDummyInput(self):
"""Asserts zero parameters for dummy atom type."""
self.assertEqual(param.GetVdwParam('X'), (0.0000, 0.00000))
def testWaterOxygen(self):
"""Asserts correct parameters for water oxygen atom type."""
self.assertEqual(param.GetVdwParam('OW'), (1.7683, 0.1520))