def testBadInput(self):
"""Asserts raise of ValueError for missing element input."""
with self.assertRaises(ValueError) as e:
param.GetCovRad('AA')
self.assertEqual(str(e.exception),
'No covalent radius found for element: AA')
def testEmptyInput(self):
"""Asserts raise of ValueError for empty string input."""
with self.assertRaises(ValueError) as e:
param.GetCovRad('')
self.assertEqual(str(e.exception),
'No covalent radius found for element: ')
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, eps, mass):
self.type_ = type_
self.element = fileio.GetElement(type_)
self.SetCoords(coords)
self.SetCharge(charge)
self.SetRo(ro)
self.SetEps(eps)
self.SetMass(mass)
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 __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 _GetAtom(mol, record):
"""Parse atom record into an atom object and append to molecule.
Appends mmlib.molecule.Atom object to mmlib.molecule.Molecule object. Contents
of atom object include (float*) xyz cartesian coordinates [Angstrom], (float)
partial charge [e], (float) van der Waals radius [Angstrom], (float) van der
Waals epsilon [kcal/mol], (str) atom type, (str) atomic element, (float)
covalent radius, [Angstrom], and (float) mass [amu].
Args:
mol (mmlib.molecule.Molecule): Molecule to append atom.
record (str*): Array of strings from line of prm file.
"""
at_type = record[2]
at_coords = numpy.array(list(map(float, record[3:3+const.NUMDIM])))
at_charge, at_ro, at_eps = list(map(float, record[6:9]))
at_element = GetElement(at_type)
at_mass = param.GetAtMass(at_element)
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 testHeaviestAtom(self):
"""Asserts correct radius for heaviest present atom."""
self.assertEqual(param.GetCovRad('Kr'), 1.03)
def testHydrogen(self):
"""Asserts correct radius for hydrogen atom."""
self.assertEqual(param.GetCovRad('H'), 0.37)
def testDummyInput(self):
"""Asserts zero radius for dummy atom input."""
self.assertEqual(param.GetCovRad('X'), 0.0)
