def testTwoAtoms(self):
"""Asserts correct atoms returned from two atom input."""
param = [['2'], [], ['N*', '1.0', '0.1', '-.2', '+0.553'],
['H4', '0.523', '-100.12', '5.5', '-0.27']]
test_output = fileio.GetAtomsFromXyzq(param)
ref_output = [
molecule.Atom('N*', [1.0, 0.1, -0.2], 0.553),
molecule.Atom('H4', [0.523, -100.12, 5.5], -0.27)
]
test.assertObjectArrayEqual(self, test_output, ref_output)
def testOneAtom(self):
"""Asserts correct atom returned from one atom input."""
param = [['1'], ['ignored', 'comment'],
['H', '0.0', '0.0', '0.0', '0.0']]
test_output = fileio.GetAtomsFromXyzq(param)
ref_output = [molecule.Atom('H', [0.0, 0.0, 0.0], 0.0)]
test.assertObjectArrayEqual(self, test_output, ref_output)
def GetAtomFromXyzq(row):
"""Parses and validates a row of input from xyzq file into an Atom object.
Args:
row (str*): Array of strings from row of xyzq file.
Returns:
atom (mmlib.molecule.Atom): Atom object.
Raises:
IndexError: If insufficient number of fields.
ValueError: If incorrect data type of any field.
"""
if len(row) < 2+const.NUMDIM:
raise IndexError('Insufficient columns to parse xyzq file row into Atom '
'object: %s' % ' '.join(row))
type_ = row[0]
coords = row[1:1+const.NUMDIM]
charge = row[1+const.NUMDIM]
if not type_ or not type_[0].isalpha():
raise ValueError('Atom type must begin with letter: %s' % type_)
if not _AreAllType(float, coords):
raise ValueError(
'Atomic coordinates must be numeric values: %s' % ' '.join(coords))
if not _IsType(float, charge):
raise ValueError('Atomic charge must be numeric value: %s' % charge)
return molecule.Atom(type_, numpy.fromiter(coords, float), float(charge))
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 get_atom(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.zeros(3)
for j in range(3):
at_coords[j] = float(record[j+3])
at_charge, at_ro, at_eps = (float(record[6]), float(record[7]),
float(record[8]))
at_element = (at_type[0:2].capitalize() if at_type[-1].islower()
else at_type[0])
at_mass = param.get_at_mass(at_element)
atom = molecule.Atom(at_type, at_coords, at_charge, at_ro, at_eps, at_mass)
atom.set_covrad(param.get_cov_rad(at_element))
mol.atoms.append(atom)
mol.mass += at_mass
def get_geom(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 = get_file_string_array(mol.infile)
mol.n_atoms = int(infile_array[0][0])
mol.bond_lenths = [{} for i in range(mol.n_atoms)]
for i in range(mol.n_atoms):
at_type = infile_array[i+2][0]
at_coords = numpy.zeros(3)
for j in range(3):
at_coords[j] = float(infile_array[i+2][j+1])
at_charge = float(infile_array[i+2][4])
at_element = (at_type[0:2].capitalize() if at_type[-1].islower()
else at_type[0])
at_mass = param.get_at_mass(at_element)
at_ro, at_eps = param.get_vdw_param(at_type)
new_atom = molecule.Atom(at_type, at_coords, at_charge, at_ro, at_eps,
at_mass)
new_atom.set_covrad(param.get_cov_rad(at_element))
mol.atoms.append(new_atom)
mol.mass += at_mass
def GetAtomFromPrm(record):
"""Parses atom record into an Atom object.
Args:
record (str*): Array of strings from line of prm file.
Returns:
atom (mmlib.molecule.Atom): Atom object with attributes from record.
"""
type_ = record[2]
coords = numpy.array(tuple(map(float, record[3:3 + const.NUMDIM])))
charge, ro, eps = tuple(
map(float, record[3 + const.NUMDIM:6 + const.NUMDIM]))
return molecule.Atom(type_, coords, charge, ro, eps)
def GetAtoms(records):
"""Parses atom records into an array of Atom objects.
Args:
records (str**): 2d array of strings from lines of prm file.
Returns:
atoms (mmlib.molecule.Atom*): Array of Atom object with parameters from
records.
"""
atoms = []
for record in records:
if not record[0].upper() == 'ATOM':
continue
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]))
atoms.append(
molecule.Atom(at_type, at_coords, at_charge, at_ro, at_eps))
return atoms
def GetAtomsFromXyzq(input_rows):
"""Reads in molecular geometry data from molecule xyzq file.
First line contains (int) number of atoms. Second line is ignored comment.
Each line afterward (3 to [n+2]) contains atom type, (float) 3 xyz Cartesian
coordinates [Angstrom], and (float) charge [e].
Args:
input_file (str**): 2d array of string from xyzq input file.
Returns:
atoms (mmlib.molecule.Atom*): Array of molecule's Atom objects.
"""
atoms = []
n_atoms = int(input_rows[0][0])
for row in input_rows[2:n_atoms + 2]:
at_type = row[0]
at_coords = numpy.array(list(map(float, row[1:1 + const.NUMDIM])))
at_charge = float(row[1 + const.NUMDIM])
atoms.append(molecule.Atom(at_type, at_coords, at_charge))
return atoms
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 GetAtomFromPrm(row):
"""Parses atom row into an Atom object.
Args:
row (str*): Array of strings from line of prm file.
Returns:
atom (mmlib.molecule.Atom): Atom object with attributes from row.
Raises:
IndexError: If insufficient number of fields.
ValueError: If incorrect data type of any field.
"""
if len(row) < 6+const.NUMDIM:
raise IndexError('Insufficient columns to parse prm file row into Atom '
'object: %s' % ' '.join(row))
type_ = row[2]
coords = row[3:3+const.NUMDIM]
charge, ro, eps = row[3+const.NUMDIM:6+const.NUMDIM]
if not type_ or not type_[0].isalpha():
raise ValueError('Atom type must begin with letter: %s' % type_)
if not _AreAllType(float, coords):
raise ValueError(
'Atomic coordinates must be numeric values: %s' % ' '.join(coords))
if not _IsType(float, charge):
raise ValueError('Atomic charge must be numeric value: %s' % charge)
if not _IsType(float, ro) or not float(ro) > 0.0:
raise ValueError(
'Atomic vdw radius must be positive numeric value: %s' % ro)
if not _IsType(float, eps) or not float(eps) >= 0.0:
raise ValueError(
'Atomic epsilon must be non-negative numeric value: %s' % eps)
return molecule.Atom(type_, numpy.fromiter(coords, float), float(charge),
float(ro), float(eps))
def testArbitrary(self):
"""Asserts correct output for arbitrary Atom inputs."""
param = ['N*', '999.9', '-0.0001', '2.0', '-0.52']
output = molecule.Atom('N*', [999.9, -0.0001, 2.0], -0.52)
test.assertObjectEqual(self, fileio.GetAtomFromXyzq(param), output)
def testZeroValues(self):
"""Asserts correct output for zero value numeric inputs."""
param = ['OW', '0.0', '0.0', '0.0', '0.0']
output = molecule.Atom('OW', [0.0, 0.0, 0.0], 0.0)
test.assertObjectEqual(self, fileio.GetAtomFromXyzq(param), output)
def testArbitrary(self):
"""Asserts correct Atom object for arbitrary input parameters."""
param = ['ATOM', '7', 'NA', '1.1', '2.2', '3.3', '4.4', '5.5', '6.6']
test.assertObjectEqual(
self, fileio.GetAtomFromPrm(param),
molecule.Atom('NA', [1.1, 2.2, 3.3], 4.4, 5.5, 6.6))
def testZeroValues(self):
"""Asserts correct Atom object for zero value numeric inputs."""
param = ['ATOM', '6', 'X', '0.', '0.', '0.', '0.', '0.1', '0.']
test.assertObjectEqual(self, fileio.GetAtomFromPrm(param),
molecule.Atom('X', [0., 0., 0.], 0., 0.1, 0.))
