def main():
#t = [1,2,3,[4,5],[],[6]]
#print(flatten(t))
#Simple test case, without nesting
s1 = 'CH3NH2SH'
t1 = set_bonds(parsing.number_list(parsing.make_list(
parsing.remove_h(s1))))
#Complicated example, with nesting and electron pairs
s2 = 'CH3N(CH2NHOH)SH'
t2 = set_bonds(parsing.number_list(parsing.make_list(
parsing.remove_h(s2))))
#print fill_hydrogens(flatten(t2))
#Another simple example, this time with no electron pairs
s3 = 'CH3CH2CH3'
t3 = set_bonds(parsing.number_list(parsing.make_list(
parsing.remove_h(s3))))
#An extremely simple test case...
s4 = 'CH4'
t4 = set_bonds(parsing.number_list(parsing.make_list(
parsing.remove_h(s4))))
print fill_hydrogens(flatten(t4))
def main():
t = [1,2,3,[4,5],[],[6]]
print flatten(t)
s1 = 'CH3CH2CH3'
print 's1:',
print parsing.remove_h(s1)
print parsing.make_list(parsing.remove_h(s1))
print parsing.number_list(parsing.make_list(parsing.remove_h(s1)))
print set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s1))))
def main():
t = [1, 2, 3, [4, 5], [], [6]]
print flatten(t)
s1 = 'CH3CH2CH3'
print 's1:',
print parsing.remove_h(s1)
print parsing.make_list(parsing.remove_h(s1))
print parsing.number_list(parsing.make_list(parsing.remove_h(s1)))
print set_bonds(
parsing.number_list(parsing.make_list(parsing.remove_h(s1))))
def main():
t = [1,2,3,[4,5],[],[6]]
print(flatten(t))
#set_bonds() works for chains...
s1 = 'CH3NH2SH'
t1 = parsing.number_list(parsing.make_list(parsing.remove_h(s1)))
print('s1: ')
print(t1)
print(set_bonds(t1))
#...but not for nested chains. It only evaluates the first atom in the chain, then ignores the rest! We should fix this.
s2 = 'CH3NH(CHNHOH)SH'
t2 = parsing.number_list(parsing.make_list(parsing.remove_h(s1)))
print('s2: ')
print(t2)
print(set_bonds(t2))
def main():
t = [1, 2, 3, [4, 5], [], [6]]
print(flatten(t))
#set_bonds() works for chains...
s1 = 'CH3NH2SH'
t1 = parsing.number_list(parsing.make_list(parsing.remove_h(s1)))
print('s1: ')
print(t1)
print(set_bonds(t1))
#...but not for nested chains. It only evaluates the first atom in the chain, then ignores the rest! We should fix this.
s2 = 'CH3NH(CHNHOH)SH'
t2 = parsing.number_list(parsing.make_list(parsing.remove_h(s1)))
print('s2: ')
print(t2)
print(set_bonds(t2))
def main():
#t = [1,2,3,[4,5],[],[6]]
#print(flatten(t))
#Simple test case, without nesting
#s1 = 'CH3NH2SH'
#t1 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s1))))
# Complicated example, with nesting and electron pairs
s2 = 'CH3N(CH2NHOH)SH'
t2 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s2))))
print(fill_hydrogens(flatten(t2)))
def main():
#t = [1,2,3,[4,5],[],[6]]
#print(flatten(t))
#Simple test case, without nesting
s1 = 'CH3NH2SH'
t1 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s1))))
#Complicated example, with nesting and electron pairs
s2 = 'CH3N(CH2NHOH)SH'
t2 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s2))))
#print fill_hydrogens(flatten(t2))
#Another simple example, this time with no electron pairs
s3 = 'CH3CH2CH3'
t3 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s3))))
#An extremely simple test case...
s4 = 'CH4'
t4 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s4))))
print fill_hydrogens(flatten(t4))
def main():
#t = [1,2,3,[4,5],[],[6]]
#print(flatten(t))
#Simple test case, without nesting
#s1 = 'CH3NH2SH'
#t1 = set_bonds(parsing.number_list(parsing.make_list(parsing.remove_h(s1))))
# Complicated example, with nesting and electron pairs
s2 = 'CH3N(CH2NHOH)SH'
t2 = set_bonds(parsing.number_list(parsing.make_list(
parsing.remove_h(s2))))
print(fill_hydrogens(flatten(t2)))
if len(bonds) == 3:
phi = theta + (2 * math.pi / 3)
phi2 = phi + (2 * math.pi / 3)
if isinstance(bonds[1], Atom):
atom.bonds[1].pos = [
atom.pos[0] - b * math.cos(phi),
atom.pos[1] - b * math.sin(phi), atom.pos[2]
]
if isinstance(bonds[2], Atom):
atom.bonds[2].pos = [
atom.pos[0] - b * math.cos(phi2),
atom.pos[1] - b * math.sin(phi2), atom.pos[2]
]
if len(bonds) == 4:
print("fix this")
if __name__ == "__main__":
s1 = 'CH3CH2CH(CH2CH3)CH2CH3'
t = set_bonds(number_list(make_list(remove_h(s1))))
t[1].pos = [2, 3, 0]
set_pos(t)
t2 = flatten(t)
for atom in t2:
print atom
print atom.pos
if len(bonds) == 3:
phi = theta + (2*math.pi/3)
phi2 = phi + (2*math.pi/3)
if isinstance(bonds[1],Atom):
atom.bonds[1].pos = [atom.pos[0] - b*math.cos(phi),atom.pos[1] - b*math.sin(phi),atom.pos[2]]
if isinstance(bonds[2],Atom):
atom.bonds[2].pos = [atom.pos[0] - b*math.cos(phi2),atom.pos[1]-b*math.sin(phi2), atom.pos[2]]
if len(bonds) ==4:
print ("fix this")
if __name__ == "__main__":
s1 = 'CH3CH2CH(CH2CH3)CH2CH3'
t = set_bonds(number_list(make_list(remove_h(s1))))
t[1].pos = [2,3,0]
set_pos(t)
t2 = flatten(t)
for atom in t2:
print atom
print atom.pos
def makeMolecule(formula):
#Creates list of atoms with appropriate bonds
t = fill_hydrogens(set_bonds(number_list(make_list(remove_h(formula)))))
#Base bond length
b = 3
if isinstance(t[0], Carbon):
t[1].pos = ((0,b*sqrt(t[0].radius)*sqrt(t[1].radius),0))
set_pos(t,b)
t2 = flatten(t)
bpy.ops.scene.delete()
bpy.ops.scene.new(type = 'NEW')
colors = {}
#Draws atom with appropriate color and size
for atom in t2:
elem = (atom.name[0:1])
#maps element to an appropriate material
colors[elem] = colors.get(elem, makeMaterial(elem,tuple(atom.color), (1,1,1),1))
#Draws atom and sets its material
bpy.ops.mesh.primitive_uv_sphere_add(location = atom.pos, size = atom.radius*1)
setMaterial(bpy.context.object, colors[(atom.name[0:1])])
bonds = atom.bonds
#Draws cylinders between atoms
for i in range(0, len(bonds)):
if isinstance(bonds[i], Atom):
hyd = (bonds[i].name[0:1])
list = [atom, bonds[i]]
bpy.ops.mesh.primitive_uv_sphere_add(location = bonds[i].pos, size = bonds[i].radius*1)
colors[hyd] = colors.get(hyd, makeMaterial(hyd,tuple(bonds[i].color), (1,1,1),1))
setMaterial(bpy.context.object, colors[hyd])
# Create curve
draw_curve = bpy.data.curves.new('draw_curve','CURVE')
draw_curve.dimensions = '3D'
spline = draw_curve.splines.new('BEZIER')
spline.bezier_points.add(len(list)-1)
curve = bpy.data.objects.new('curve',draw_curve)
bpy.context.scene.objects.link(curve)
# Curve settings for new curve
draw_curve.resolution_u = 64
draw_curve.fill_mode = 'FULL'
draw_curve.bevel_depth = 0.3
draw_curve.bevel_resolution = 5
# Assign bezier points to selection object locations
for i in range(len(list)):
p = spline.bezier_points[i]
p.co = list[i].pos
p.handle_right_type="VECTOR"
p.handle_left_type="VECTOR"
bpy.context.scene.objects.active = curve
bpy.ops.object.mode_set(mode='OBJECT')