def __init__(self):
self._angle_dict = {}
f = open(context.get_share_filename("toyff_angles.txt"))
for line in f:
if line[0] != "#":
key = tuple(int(word) for word in line[0 : line.index(":")].split(","))
value = numpy.pi / 180.0 * float(line[line.index(":") + 1 : -1])
self._angle_dict[key] = value
def __init__(self):
self.angle_dict = {}
f = open(context.get_share_filename('toyff_angles.txt'))
for line in f:
if line[0] != '#':
key = tuple(int(word) for word in line[0:line.index(':')].split(","))
value = numpy.pi/180.0*float(line[line.index(':')+1:-1])
self.angle_dict[key] = value
pair = frozenset([n1, n2])
result = None
for bond_type in bond_types:
bond_length = self.lengths[bond_type].get(pair)
if (bond_length is not None) and \
(distance < bond_length * self.bond_tolerance):
if result is None:
result = bond_type
deviation = abs(bond_length - distance)
else:
new_deviation = abs(bond_length - distance)
if deviation > new_deviation:
result = bond_type
deviation = new_deviation
return result
def get_length(self, n1, n2, bond_type=BOND_SINGLE):
"""
Return the length of a bond between n1 and n2 of type bond_type.
This is a safe method for querying a bond_length. If no answer can be
found, this get_length returns None.
"""
dataset = self.lengths.get(bond_type)
if dataset == None:
return None
return dataset.get(frozenset([n1, n2]))
bonds = BondData(context.get_share_filename("bonds.csv"), periodic)
if word == "NA":
atom_info.add_attribute(name, None)
else:
atom_info.add_attribute(name, convertor(word))
self.add_atom_info(atom_info)
if self.max_radius < atom_info.radius:
self.max_radius = atom_info.radius
lines_read += 1
f.close()
def add_atom_info(self, atom_info):
self.atoms_by_number[atom_info.number] = atom_info
self.atoms_by_symbol[atom_info.symbol.lower()] = atom_info
def __len__(self):
return len(self.atoms_by_symbol)
def __getitem__(self, index):
result = self.atoms_by_number.get(index)
if (result is None) and isinstance(index, basestring):
return self.atoms_by_symbol.get(index.lower())
else:
return result
def yield_numbers(self):
for number in self.atoms_by_number:
yield number
periodic = PeriodicData(context.get_share_filename("periodic.csv"))
if (bond_length is not None) and \
(distance < bond_length * self.bond_tolerance):
if result is None:
result = bond_type
deviation = abs(bond_length - distance)
else:
new_deviation = abs(bond_length - distance)
if deviation > new_deviation:
result = bond_type
deviation = new_deviation
return result
def get_length(self, n1, n2, bond_type=BOND_SINGLE):
"""
Return the length of a bond between n1 and n2 of type bond_type.
This is a safe method for querying a bond_length. If no answer can be
found, this get_length returns None.
"""
dataset = self.lengths.get(bond_type)
if dataset == None:
return None
return dataset.get(frozenset([n1, n2]))
bonds = BondData(context.get_share_filename("bonds.csv"), periodic)
n_masses[Z+N] = mass
f = file(filename)
for i in xrange(39):
f.next()
for line in f:
N = int(line[ 5:10])
Z = int(line[10:15])
mass = float(line[96:114].replace(" ", "").replace("#", ""))*1e-6*amu
add_mass(N, Z, mass)
f.close()
ame2003 = Ame2003(context.get_share_filename("mass.mas03"))
class NubTab03(object):
"""An interface to a subset of the data that from NubTab03.
This object contains an attribute abundances. This is a dictionary whose
keys are the proton numbers (Z) and values are the corresponding values
are again dictionaries. The latter dictionaries have the mass number (A)
as keys and the corresponding isotope abundances as values. E.g.
self.masses[6][12] is the abundance of carbon 12.
If you use this interface, cite the following reference:
The NUBASE evaluation of nuclear and decay properties. G. Audi, O. Bersillon,
J. Blachot and A.H. Wapstra, Nuclear Physics A729, 3-128 (2003)
def _add_atom_info(self, atom_info):
"""Add an atom info object to the database"""
self.atoms_by_number[atom_info.number] = atom_info
self.atoms_by_symbol[atom_info.symbol.lower()] = atom_info
def __len__(self):
return len(self.atoms_by_symbol)
def __getitem__(self, index):
result = self.atoms_by_number.get(index)
if (result is None) and isinstance(index, basestring):
return self.atoms_by_symbol.get(index.lower())
else:
return result
def iter_numbers(self):
"""Iterate over all atom numbers in the periodic system
Usage::
>>> from molmod.periodic import periodic
>>> for number in periodic.iter_numbers():
... print number, periodic[number].mass
"""
for number in sorted(self.atoms_by_number):
yield number
periodic = PeriodicData(context.get_share_filename("periodic.csv"))
