def rpoly_to_oxDNA(opts):
# Read File
# 'data' stores helix coordinates + rotaion in quaternion
data = []
rev_helix_connections = [] # staple connection information,
fwd_helix_connections = [] # scaffold connections
count = 0
polyFile = open(opts.file_name_in, 'r')
try:
for line in polyFile:
if line.startswith('hb'):
data.insert(count, line.split(' '))
count += 1
elif line.startswith('c'):
if 'f3' not in line:
rev_helix_connections.append([
int(re.search('c helix_(.+?) ', line).group(1)),
int(re.search('\' helix_(.+?) ', line).group(1))
]) # Extract connection information
else:
fwd_helix_connections.append([
int(re.search('c helix_(.+?) ', line).group(1)),
int(re.search('\' helix_(.+?) ', line).group(1))
])
except Exception:
print('Failed to read the file')
generator = cu.StrandGenerator()
staple_fragments = base.System(
[100, 100, 100]
) # temporary system to store staple fragments before later connecting them
scaffold_fragments = base.System([100, 100, 100])
# Reads orientation from the "data" and produces rotations from the Quaternian coordinates
largest_size = 0.0
for n, i in enumerate(data):
position = [
float(i[3]) / 0.84,
float(i[4]) / 0.84,
float(i[5]) / 0.84
] # 0.84 scaling is ad hoc solution to get good looking models
n_bp = int(i[2])
q = Quaternion(w=float(i[9]),
x=float(i[6]),
y=float(i[7]),
z=float(i[8])) # find the helix roation Info from file
vec = q.rotate(np.array([0.0, 0.0,
1.0])) # use it to figure out direction
vec2 = q.rotate(
[0.65, -0.76,
0.0]) # ad hoc onversion between rpoly rotation and cadnano utils
new_position = move_along_vector(
position, vec, n_bp
) # rpoly helix coordinates are defined in center of helix, cadnano utils have positions in the base of helix.
for j in new_position: # go through every coordinate to find the largest coordinate to figure out box size
if j > largest_size:
largest_size = j
else:
pass
# strand 0 is the scaffold and strand 1 is the staple
new_strands = generator.generate_or_sq(bp=n_bp,
start_pos=new_position,
direction=vec,
perp=vec2)
fragment1, fragment2 = new_strands[1].cut_in_two(
) # cut strand 1 into two equal lengh staple fragments for later connections
# store the fragments in this system for later connections
staple_fragments.add_strand(fragment1)
staple_fragments.add_strand(fragment2)
scaffold_fragments.add_strand(new_strands[0])
output_system = base.System(
[largest_size * 3.0, largest_size * 3.0, largest_size * 3.0])
for n in rev_helix_connections: # iterate through staple strand connections and connect the previously generated fragments
connect_from = n[0] * 2 - 1
connect_to = n[1] * 2 - 2
staple_strand = staple_fragments._strands[connect_from].copy()
staple_strand = staple_strand.append(
staple_fragments._strands[connect_to].copy())
output_system.add_strand(staple_strand)
scaffold_strand = scaffold_fragments._strands[0].copy()
for n in fwd_helix_connections[:-1]:
next_segment_adress = n[1] - 1
next_segment = scaffold_fragments._strands[next_segment_adress].copy()
scaffold_strand = scaffold_strand.append(next_segment)
scaffold_strand.make_circular()
output_system.add_strand(scaffold_strand)
basename = os.path.basename(opts.file_name_in)
top_file = basename + ".top"
conf_file = basename + ".oxdna"
output_system.print_lorenzo_output(conf_file, top_file)
vhelix_counter = 0
if not side:
side = cadsys.bbox()
base.Logger.log(
"Using default box size, a factor %s larger than size of cadnano system"
% str(BOX_FACTOR), base.Logger.INFO)
vhelix_direction_initial = np.array([0., 0., 1.])
vhelix_perp_initial = np.array([1., 0., 0.])
if origami_sq:
vhelix_perp_initial = vhelix_rotation_origami_sq(
vhelix_direction_initial, vhelix_perp_initial)
elif origami_he:
vhelix_perp_initial = vhelix_rotation_origami_he(
vhelix_direction_initial, vhelix_perp_initial)
slice_sys = base.System([side, side, side])
final_sys = base.System([side, side, side])
strand_number = -1
partner_list_scaf = []
partner_list_stap = []
found_partner = False
join_list_scaf = []
join_list_stap = []
begin_helix = -1
end_helix = -1
for h in cadsys.vhelices:
h.cad_index = vhelix_counter
if origami_sq:
strands, helix_angles, pos, rot, vhelix_direction, vhelix_perp = generate_vhelices_origami_sq(
vhelix_direction_initial, vhelix_perp_initial, h,
sequence_file, single_strand_system, vhelix_counter)
box_low = np.array([1e6, 1e6, 1e6], dtype=np.float64)
box_high = np.array([-1e6, -1e6, -1e6], dtype=np.float64)
for nucl in itertools.chain(*pdb_strands):
com = nucl.get_com()
for i in range(3):
if com[i] < box_low[i]:
box_low[i] = com[i]
elif com[i] > box_high[i]:
box_high[i] = com[i]
L = 2 * np.max(box_high - box_low) * FROM_ANGSTROM_TO_OXDNA
box = np.array([L, L, L])
print >> sys.stderr, "Using a box of size %g in oxDNA units (twice as big as the PDB bounding box size)" % (L)
system = base.System(box)
strand = base.Strand()
for pdb_strand in pdb_strands:
strand = base.Strand()
for nucl in pdb_strand:
nucl.compute_as()
com = nucl.get_com() * FROM_ANGSTROM_TO_OXDNA
new_oxDNA_nucl = base.Nucleotide(com, nucl.a1, nucl.a3, nucl.base[0])
strand.add_nucleotide(new_oxDNA_nucl)
system.add_strand(strand, check_overlap=False)
basename = os.path.basename(pdb_file)
