def bring_in_dstrand(s1, s2, initial, radius):
R = utils.get_random_rotation_matrix()
s1.rotate(R)
s2.rotate(R, s1.cm_pos)
start_from = [s1, s2][np.random.random_integers(0, 1)]._nucleotides[np.random.random_integers(-1, 0)].cm_pos
new_pos = initial + utils.get_random_vector_in_sphere(radius)
disp = new_pos - start_from
s1.cm_pos = s1.cm_pos + disp
s2.cm_pos = s2.cm_pos + disp
def generate_rw(self, sequence, start_pos=np.array([0., 0., 0.])):
"""
Generate ssDNA as a random walk (high-energy configurations are possible):
generate(bp=45,double=False,circular=False,random_walk=True)
"""
# random walk generator
base.Logger.log(
"Generating strand as a random walk. Remember to equilibrate the configuration with MC",
base.Logger.WARNING)
d = np.array([0.7525, 0., 0.])
pos = start_pos
rw = []
rw.append(pos)
for i, _ in enumerate(sequence[1:]):
overlap = True
while overlap:
overlap = False
R = utils.get_random_rotation_matrix()
dd = np.dot(R, d)
trypos = pos + np.dot(R, d)
overlap = False
for r in rw:
dd = trypos - r
if np.dot(dd, dd) < 0.40 * 0.40:
overlap = True
pos = trypos
rw.append(pos)
# print >> sys.stderr, "# nucleotide", i + 1, "inserted"
# we get the a1 vectors in a smart way
a1s = []
d = rw[1] - rw[0]
a1s.append(d / np.sqrt(np.dot(d, d)))
for i in range(1, len(rw) - 1):
d = (rw[i + 1] + rw[i - 1]) * 0.5
d = rw[i] - d
a1s.append(d / np.sqrt(np.dot(d, d)))
d = rw[len(rw) - 1] - rw[len(rw) - 2]
a1s.append(d / np.sqrt(np.dot(d, d)))
s = base.Strand()
for i, r in enumerate(rw):
a1, _, a3 = utils.get_orthonormalized_base(
a1s[i], utils.get_random_vector(), utils.get_random_vector())
# print np.dot(a1, a1), np.dot(a2, a2), np.dot(a3, a3), np.dot(a1, a2), np.dot(a1, a3), np.dot(a2, a3)
# # POS_BACK is negative!
cm = r + a1s[i] * abs(base.POS_BACK)
s.add_nucleotide(base.Nucleotide(cm, a1, a3, sequence[i]))
return s
if np.dot (cdm, cdm) < 1.:
redo = False
final_box = np.array([box_side, box_side, box_side])
final = systems[0].copy()
final.print_lorenzo_output ("justone.dat", "justone.top")
njoined = 1
for S in systems[1:]:
base.Logger.log ("# Trying to join")
has_overlaps = True
while has_overlaps:
translated = S.copy()
nold = final.N_strands
translated.rotate(utils.get_random_rotation_matrix(), np.array([0.,0.,0.]))
translated.translate(np.random.rand(3) * final._box)
has_overlaps = False
for s1 in translated._strands:
if final.is_overlapping_better(s1):
has_overlaps = True
base.Logger.log (" # Overlap, retrying")
break
'''prova = final.join(translated, final_box)
for s1 in prova._strands[nold:]:
for s2 in prova._strands[:nold]:
if s1.overlaps_with(s2, final_box):
has_overlaps = True
base.Logger.log (" # Overlap, retrying")
if np.dot(cdm, cdm) < 1.:
redo = False
final_box = np.array([box_side, box_side, box_side])
final = systems[0].copy()
final.print_lorenzo_output("justone.dat", "justone.top")
njoined = 1
for S in systems[1:]:
base.Logger.log("# Trying to join")
has_overlaps = True
while has_overlaps:
translated = S.copy()
nold = final.N_strands
translated.rotate(utils.get_random_rotation_matrix(),
np.array([0., 0., 0.]))
translated.translate(np.random.rand(3) * final._box)
has_overlaps = False
for s1 in translated._strands:
if final.is_overlapping_better(s1):
has_overlaps = True
base.Logger.log(" # Overlap, retrying")
break
'''prova = final.join(translated, final_box)
for s1 in prova._strands[nold:]:
for s2 in prova._strands[:nold]:
if s1.overlaps_with(s2, final_box):
has_overlaps = True
base.Logger.log (" # Overlap, retrying")
