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def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
v1 = cpv.sub(p1, p2)
v2 = cpv.sub(p3, p2)
normal = cpv.cross_product(v1, v2)
if 'translate' in settings:
vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
p1_t = cpv.sub(p1, vtran)
p2_t = cpv.sub(p2, vtran)
p3_t = cpv.sub(p3, vtran)
print("New coordinates are:")
print_info("New", p1_t, p2_t, p3_t)
print("New coordinates are for normalized plane:")
v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
p1_t2 = cpv.add(v1_t, p2_t)
p3_t2 = cpv.add(v2_t, p2_t)
print_info("Newnormal", p1_t2, p2_t, p3_t2)
if vm1!=None:
v1 = cpv.scale(cpv.normalize(v1), vm1)
if vm2!=None:
v2 = cpv.scale(cpv.normalize(v2), vm2)
centrum = p2
if center:
corner1 = cpv.add(cpv.add(centrum, v1), v2)
corner2 = cpv.sub(cpv.add(centrum, v1), v2)
corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
corner4 = cpv.add(cpv.sub(centrum, v1), v2)
def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
v1 = cpv.sub(p1, p2)
v2 = cpv.sub(p3, p2)
normal = cpv.cross_product(v1, v2)
if 'translate' in settings:
vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
p1_t = cpv.sub(p1, vtran)
p2_t = cpv.sub(p2, vtran)
p3_t = cpv.sub(p3, vtran)
print("New coordinates are:")
print_info("New", p1_t, p2_t, p3_t)
print("New coordinates are for normalized plane:")
v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
p1_t2 = cpv.add(v1_t, p2_t)
p3_t2 = cpv.add(v2_t, p2_t)
print_info("Newnormal", p1_t2, p2_t, p3_t2)
if vm1!=None:
v1 = cpv.scale(cpv.normalize(v1), vm1)
if vm2!=None:
v2 = cpv.scale(cpv.normalize(v2), vm2)
centrum = p2
if center:
corner1 = cpv.add(cpv.add(centrum, v1), v2)
corner2 = cpv.sub(cpv.add(centrum, v1), v2)
corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
corner4 = cpv.add(cpv.sub(centrum, v1), v2)
v1 = cpv.sub(p1, p2)
v2 = cpv.sub(p3, p2)
normal = cpv.cross_product(v1, v2)
if 'translate' in settings:
vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
p1_t = cpv.sub(p1, vtran)
p2_t = cpv.sub(p2, vtran)
p3_t = cpv.sub(p3, vtran)
print("New coordinates are:")
print_info("New", p1_t, p2_t, p3_t)
print("New coordinates are for normalized plane:")
v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
p1_t2 = cpv.add(v1_t, p2_t)
p3_t2 = cpv.add(v2_t, p2_t)
print_info("Newnormal", p1_t2, p2_t, p3_t2)
if vm1!=None:
v1 = cpv.scale(cpv.normalize(v1), vm1)
if vm2!=None:
v2 = cpv.scale(cpv.normalize(v2), vm2)
centrum = p2
if center:
corner1 = cpv.add(cpv.add(centrum, v1), v2)
corner2 = cpv.sub(cpv.add(centrum, v1), v2)
corner3 = cpv.sub(cpv.sub(centrum, v1), v2)
corner4 = cpv.add(cpv.sub(centrum, v1), v2)
else:
def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
v1 = cpv.sub(p1, p2)
v2 = cpv.sub(p3, p2)
normal = cpv.cross_product(v1, v2)
if 'translate' in settings:
vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
p1_t = cpv.sub(p1, vtran)
p2_t = cpv.sub(p2, vtran)
p3_t = cpv.sub(p3, vtran)
print("New coordinates are:")
print_info("New", p1_t, p2_t, p3_t)
print("New coordinates are for normalized plane:")
v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
p1_t2 = cpv.add(v1_t, p2_t)
p3_t2 = cpv.add(v2_t, p2_t)
print_info("Newnormal", p1_t2, p2_t, p3_t2)
def planeFromPoints(p1, p2, p3, vm1=None, vm2=None, center=True, settings={}):
v1 = cpv.sub(p1, p2)
v2 = cpv.sub(p3, p2)
normal = cpv.cross_product(v1, v2)
if 'translate' in settings:
vtran = cpv.scale(cpv.normalize(normal), settings['translate'])
p1_t = cpv.sub(p1, vtran)
p2_t = cpv.sub(p2, vtran)
p3_t = cpv.sub(p3, vtran)
print("New coordinates are:")
print_info("New", p1_t, p2_t, p3_t)
print("New coordinates are for normalized plane:")
v1_t = cpv.normalize(cpv.sub(p1_t, p2_t))
v2_t = cpv.normalize(cpv.sub(p3_t, p2_t))
normal_t = cpv.normalize(cpv.cross_product(v1_t, v2_t))
v2_t = cpv.normalize(cpv.cross_product(normal_t, v1_t))
p1_t2 = cpv.add(v1_t, p2_t)
p3_t2 = cpv.add(v2_t, p2_t)
print_info("Newnormal", p1_t2, p2_t, p3_t2)
# populate the position array
pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
# if the data are incomplete for any residues, ignore
if None in pos:
if not quiet:
print(' bbPlane: peptide bond %s -> %s incomplete' % (curIdx, nextIdx))
continue
if cpv.distance(pos[0], pos[3]) > 4.0:
if not quiet:
print(' bbPlane: %s and %s not adjacent' % (curIdx, nextIdx))
continue
normal = cpv.normalize(cpv.cross_product(
cpv.sub(pos[1], pos[0]),
cpv.sub(pos[2], pos[0])))
obj.append(cgo.NORMAL)
obj.extend(normal)
# need to order vertices to generate correct triangles for plane
if cpv.dot_product(cpv.sub(pos[0], pos[1]), cpv.sub(pos[2], pos[3])) < 0:
vorder = [0, 1, 2, 2, 3, 0]
else:
vorder = [0, 1, 2, 3, 2, 1]
# fill in the vertex data for the triangles;
for i in vorder:
obj.append(VERTEX)
obj.extend(pos[i])