def R6a(coords, atmidx, dismat):
'''resolve a fragment of protein:
N1-C2-C3(=O)-N4-C5-C6(=O)-N7-C8-C9(=O)
known the coords of p1, p2, p8, p9, and all the bond length and
bond length and bond angles, to calculate the coords from p3 to p7
'''
r6sub = R6sub(coords, atmidx, dismat)
i1, i2, i3, i4, i5, i6, i7, i8, i9 = atmidx
steps = config.config.get('Mezei_R6_steps', 36)
stepsize = 2 * math.pi / steps
results = [r6sub(i*stepsize) for i in range(steps)]
results[0] = tuple(results[0])
results.append(results[0])
d46ref = dismat[i4, i6]
d46mat = [[getd46rela(ps[1], ps[3], d46ref) for ps in result]
for result in results]
results = []
for i in range(steps):
for j in range(16):
if d46mat[i][j] is not None \
and d46mat[i+1][j] is not None \
and d46mat[i][j] * d46mat[i+1][j] <= 0:
try:
angle = rtbis.rtbis(d46_Resolver(r6sub, j, d46ref),
i * stepsize,
(i+1) * stepsize,
math.radians(1.0))
result = tuple(r6sub(angle))[j]
yield {i3: result[0],
i4: result[1],
i5: result[2],
i6: result[3],
i7: result[4]}
except rtbis.Error:
pass
def __call__(self):
result = [[] for i in range(16)]
stepsize = math.pi * 2 / self.steps
ref = self._dismatrix(5, 7)
for i in range(self.steps):
p2 = self.p2o \
+ self.p2x * math.cos(stepsize * i) \
+ self.p2y * math.sin(stepsize * i)
tmps = list(self.get_p34567(p2))
assert len(tmps) == 16
for idx, tmp in enumerate(tmps):
if tmp[0] is None:
result[idx].append(None)
else:
result[idx].append(tools.length(tmp[2] - tmp[4]) - ref)
for i in range(16):
result[i].append(result[i][0])
for i in range(16):
def _Func(x):
try:
return tuple(self.get_r57_from_theta(x))[i] - ref
except TypeError:
return None
func = _Func
for j in range(self.steps):
if result[i][j] is None: continue
if result[i][j+1] is None: continue
if result[i][j] * result[i][j+1] > 0: continue
try:
tmp = rtbis.rtbis(func, j*stepsize, (j+1)*stepsize, self.acc)
p2 = self._theta_to_p2(tmp)
tmp2 = self.get_p34567(p2)
for _k in range(i+1):
tmp3 = tmp2.next()
yield tuple([p2,] + list(tmp3))
except rtbis.Error:
pass
def r6_base(self, points, len1, len2, error=0.1):
"""r6_base(points, len1, len2) -> iterator
len(points) == 4
len(len1) == 4
len(len2) == 5
return all results fulfill following conditions in a iterator,
len(result) will be 3.
distance(points[1], result[0]) = len1[0];
distance(result[0], result[1]) = len1[1];
distance(result[1], result[2]) = len1[2];
distance(result[2], points[2]) = len1[3];
distance(points[0], result[0]) = len2[0];
distance(points[1], result[1]) = len2[1];
distance(result[0], result[2]) = len2[2];
distance(result[1], points[2]) = len2[3];
distance(result[2], points[3]) = len2[4];
"""
assert(len(points) == 4 and
len(len1) == 4 and
len(len2) == 5)
p0, p1, p5, p6 = tuple(points)
d12, d23, d34, d45 = tuple(len1)
d02, d13, d24, d35, d46 = tuple(len2)
p3_result = self._calc_p3((p0, p1, p5), d13, d35)
if p3_result is None:
return
p3o, p3x, p3y = p3_result
steps = config.get('Mezei_R6_steps', 36)
step = 2 * pi / steps
d24s = numpy.zeros((4, steps+1), float)
for i in range(steps):
angle = i * step
p24_result = self._calc_p2_p4(points, len1, len2, p3_result, angle)
if p24_result:
p2s, p4s = p24_result
d24s[0][i] = tools.length(p2s[0] - p4s[0])
d24s[1][i] = tools.length(p2s[0] - p4s[1])
d24s[2][i] = tools.length(p2s[1] - p4s[0])
d24s[3][i] = tools.length(p2s[1] - p4s[1])
d24s[0][steps] = d24s[0][0]
d24s[1][steps] = d24s[1][0]
d24s[2][steps] = d24s[2][0]
d24s[3][steps] = d24s[3][0]
p24_res = self.p24_Resolver(points, len1, len2, p3_result)
for i in range(4):
p24_res.switch(i)
for j in range(steps):
if d24s[i][j] and d24s[i][j+1] and \
(d24s[i][j] - d24)*(d24s[i][j+1] - d24) <= 0:
try:
angle = rtbis.rtbis(p24_res, j*step, (j+1)*step, error)
yield (i, angle, p24_res.p2, p24_res.p3, p24_res.p4)
except rtbis.Error:
pass