def __init__(self, group=Group('all'), style='create', *args, **kwargs):
Item.__init__(self, group=group, style=style, args=args, **kwargs)
if self.seed is None:
self.seed = randint(10000, 99999)
if self.temperature is None:
self.temperature = 300.0
if args:
self.from_args = True
def __init__(self, n=1, region=Region(), *args, **kwargs):
Item.__init__(self, n=n, region=region, args=args, kwargs=kwargs)
def __init__(self, name='all', style='id', *args, **kwargs):
Item.__init__(self, name=name, style=style, args=args, **kwargs)
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
from pysimm import error_print
from pysimm import warning_print
from pysimm import verbose_print
from pysimm import debug_print
from pysimm.utils import Item, ItemContainer
element_names_by_mass = {1: 'H', 4: 'He', 7: 'Li', 9: 'Be', 11: 'B', 12: 'C',
14: 'N', 16: 'O', 19: 'F', 20: 'Ne', 23: 'Na',
24: 'Mg', 27: 'Al', 28: 'Si', 31: 'P', 32: 'S',
35: 'Cl', 39: 'K', 40: 'Ca', 80: 'Br', 127: 'I'}
gasteiger_parameters = ItemContainer()
gasteiger_parameters.add(Item(tag='H_', name='H_', a=7.17, b=6.24, c=-0.56))
gasteiger_parameters.add(Item(tag='C_3', name='C_3', a=7.98, b=9.18, c=1.88))
gasteiger_parameters.add(Item(tag='C_2', name='C_2', a=8.79, b=9.32, c=1.51))
gasteiger_parameters.add(Item(tag='C_R', name='C_R', a=8.79, b=9.32, c=1.51))
gasteiger_parameters.add(Item(tag='C_1', name='C_1', a=10.39, b=9.45, c=0.73))
gasteiger_parameters.add(Item(tag='N_3', name='N_3', a=11.54, b=10.82, c=1.36))
gasteiger_parameters.add(Item(tag='N_2', name='N_2', a=12.87, b=11.15, c=0.85))
gasteiger_parameters.add(Item(tag='N_R', name='N_R', a=12.87, b=11.15, c=0.85))
gasteiger_parameters.add(Item(tag='N_1', name='N_1', a=15.68, b=11.7, c=-0.27))
gasteiger_parameters.add(Item(tag='O_3', name='O_3', a=14.18, b=12.92, c=1.39))
gasteiger_parameters.add(Item(tag='O_2', name='O_2', a=17.07, b=13.79, c=0.47))
gasteiger_parameters.add(Item(tag='O_R', name='O_R', a=17.07, b=13.79, c=0.47))
gasteiger_parameters.add(Item(tag='F_', name='F_', a=14.66, b=13.85, c=2.31))
gasteiger_parameters.add(Item(tag='Cl_', name='Cl_', a=11.00, b=9.69, c=1.35))
gasteiger_parameters.add(Item(tag='Br_', name='Br_', a=10.08, b=8.47, c=1.16))
gasteiger_parameters.add(Item(tag='I_', name='I_', a=9.90, b=7.96, c=0.96))
