def _approximate_unkown_bond_lengths(self):
"""Completes the bond length database with approximations based on VDW radii"""
dataset = self.lengths[BOND_SINGLE]
for n1 in periodic.iter_numbers():
for n2 in periodic.iter_numbers():
if n1 <= n2:
pair = frozenset([n1, n2])
atom1 = periodic[n1]
atom2 = periodic[n2]
#if (pair not in dataset) and hasattr(atom1, "covalent_radius") and hasattr(atom2, "covalent_radius"):
if (pair not in dataset) and (atom1.covalent_radius is not None) and (atom2.covalent_radius is not None):
dataset[pair] = (atom1.covalent_radius + atom2.covalent_radius)
dump_atom_fields, dump_overlap_matrices
from hipart.lebedev_laikov import get_grid as get_lebedev_grid
from hipart.log import log
from hipart.spline import CubicSpline
from molmod import Rotation, angstrom
from molmod.periodic import periodic
import os, numpy
__all__ = ["ParseError", "scheme_classes"]
noble_numbers = numpy.array([0,2,10,18,36,54,86,118])
core_sizes = dict((number, noble_numbers[noble_numbers<=number].max()) for number in periodic.iter_numbers())
class ParseError(Exception):
pass
class OnlyOnce(object):
def __init__(self, description):
self.description = description
def __call__(self, fn):
def wrapper(instance):
if fn.func_name in instance._done:
return
log.begin(self.description)