def add_number(m, key, table, column, row):
try:
v = table.get_value(column, row)
if v in ('', '?', '.'):
return False
m[key] = CIF.makeNumber(v)
return True
except (IndexError, KeyError, ValueError):
return False
def add_number(m, key, table, column, row):
try:
v = table.get_value(column, row)
if v in ('', '?', '.'):
return False
m[key] = CIF.makeNumber(v)
return True
except (IndexError, KeyError, ValueError):
return False
def read_start(self, filobj):
## parse the CIF file
cif_file = CIF.CIFFile()
cif_file.load_file(filobj)
if len(cif_file.data_blocks) != 1:
warning("read_start: only single-structure CIF files supported")
self.halt = True
return
self.cif = cif_file.data_blocks[0]
self.get_cell_parameters()
self.atom_site_name_map = {}
def get_cell_parameters(self):
"""Read unit information form various tags and compute
the fractional-to-Cartesian conversion matrix.
"""
a = CIF.makeNumber(self.cif.tags["cell_length_a"])
b = CIF.makeNumber(self.cif.tags["cell_length_b"])
c = CIF.makeNumber(self.cif.tags["cell_length_c"])
alpha_degrees = CIF.makeNumber(self.cif.tags["cell_angle_alpha"])
beta_degrees = CIF.makeNumber(self.cif.tags["cell_angle_beta"])
gamma_degrees = CIF.makeNumber(self.cif.tags["cell_angle_gamma"])
z = self.cif.tags["cell_formula_units_z"]
space_group = self.cif.tags.get("symmetry_space_group_name_h-m", None)
unit_cell = {
"length_a": a,
"length_b": b,
"length_c": c,
"angle_alpha": alpha_degrees,
"angle_beta": beta_degrees,
"angle_gamma": gamma_degrees,
"z": z,
"space_group": space_group
}
self.load_unit_cell(unit_cell)
#
# Transformation matrix from
# http://www.ccl.net/cca/documents/molecular-modeling/node4.html
#
import math
alpha = math.radians(alpha_degrees)
cosa = math.cos(alpha)
sina = math.sin(alpha)
beta = math.radians(beta_degrees)
cosb = math.cos(beta)
sinb = math.sin(beta)
gamma = math.radians(gamma_degrees)
cosg = math.cos(gamma)
sing = math.sin(gamma)
V = a * b * c * math.sqrt(1 - cosa * cosa - cosb * cosb - cosg * cosg +
2 * cosa * cosb * cosg)
self.xform = [
[a, b * cosg, c * cosb],
[0, b * sing, c * (cosa - cosb * cosg) / sing],
[0, 0, V / (a * b * sing)],
]
def get_cell_parameters(self):
"""Read unit information form various tags and compute
the fractional-to-Cartesion conversion matrix.
"""
a = CIF.makeNumber(self.cif.tags["cell_length_a"])
b = CIF.makeNumber(self.cif.tags["cell_length_b"])
c = CIF.makeNumber(self.cif.tags["cell_length_c"])
alpha_degrees = CIF.makeNumber(self.cif.tags["cell_angle_alpha"])
beta_degrees = CIF.makeNumber(self.cif.tags["cell_angle_beta"])
gamma_degrees = CIF.makeNumber(self.cif.tags["cell_angle_gamma"])
z = self.cif.tags["cell_formula_units_z"]
space_group = self.cif.tags.get("symmetry_space_group_name_h-m", None)
unit_cell = {
"length_a": a,
"length_b": b,
"length_c": c,
"angle_alpha": alpha_degrees,
"angle_beta": beta_degrees,
"angle_gamma": gamma_degrees,
"z": z,
"space_group": space_group
}
self.load_unit_cell(unit_cell)
#
# Transformation matrix from
# http://www.ccl.net/cca/documents/molecular-modeling/node4.html
#
import math
alpha = math.radians(alpha_degrees)
cosa = math.cos(alpha)
sina = math.sin(alpha)
beta = math.radians(beta_degrees)
cosb = math.cos(beta)
sinb = math.sin(beta)
gamma = math.radians(gamma_degrees)
cosg = math.cos(gamma)
sing = math.sin(gamma)
V = a * b * c * math.sqrt(1 - cosa * cosa - cosb * cosb
- cosg * cosg + 2 * cosa * cosb * cosg)
self.xform = [
[ a, b * cosg, c * cosb ],
[ 0, b * sing, c * (cosa - cosb * cosg) / sing ],
[ 0, 0, V / (a * b * sing) ],
]
import CIF
circuit = CIF.Circuit("Transistor", "micro", 0.001)
poly1 = CIF.Polygon(6)
poly1.addPoint(130, 290)
poly1.addPoint(540, 290)
poly1.addPoint(540, 690)
poly1.addPoint(130, 690)
circuit.addPolygon(poly1)
poly2 = CIF.Polygon(17)
poly2.addPoint(305, 150)
poly2.addPoint(365, 150)
poly2.addPoint(365, 830)
poly2.addPoint(305, 830)
circuit.addPolygon(poly2)
circuit.writeToFile("./transistor.cif")
