if len(final_sys._strands) > 1:
base.Logger.log(
"more than one strand detected - sequence file will not be read",
base.Logger.WARNING)
final_sys._strands[0].set_sequence(
np.random.randint(0, 4, len(final_sys._strands[0]._nucleotides)
)) # this line does not work
# # Fix to reverse the direction of every strand so that the 3' to 5' direction is the same
# # as in Cadnano. In cadnano the strands point in the 5' to 3' direction, whereas in oxDNA
# # they point in the 3' to 5' direction. Ben 29/11/13
rev_sys = base.System(final_sys._box)
for strand in final_sys._strands:
reverse_nucs = [nuc for nuc in strand._nucleotides]
reverse_nucs.reverse()
rev_strand = base.Strand()
for nuc in reverse_nucs:
rev_strand.add_nucleotide(
base.Nucleotide(nuc.cm_pos, nuc._a1, -nuc._a3, nuc._base,
nuc._btype))
if strand._circular:
rev_strand.make_circular(check_join_len=True)
rev_sys.add_strand(rev_strand, check_overlap=False)
# # also reverse the vhelix_vbase_to_nucleotide order so it corresponds to the reversed system
vh_vb2nuc_rev = cu.vhelix_vbase_to_nucleotide()
# count the number of nucleotides up to but not including the nucleotides in strand ii
nnucs_to_here = range(rev_sys._N_strands)
nuc_total = 0
for strandii, strand in enumerate(rev_sys._strands):
nnucs_to_here[strandii] = nuc_total
nuc_total += len(strand._nucleotides)
print >> sys.stderr, "USAGE: %s lammps_data_file [lammps_trajectory_file]" % sys.argv[
0]
sys.exit(1)
conf = reader_lammps_init.Lammps_parser(sys.argv[1])
N = conf.natoms
box = np.array([0, 0., 0.])
box[0] = conf.Lx
box[1] = conf.Ly
box[2] = conf.Lz
system = base.System(box)
strands = []
for i in range(conf.nstrands):
strands.append(base.Strand())
for i in range(N):
cm = conf.xyz[i, :]
quaternions = conf.ellipsoids[i, :]
a1, a3 = quat_to_exyz(quaternions)
b = number_oxdna_to_lammps[(conf.bases[i] + 3) % 4]
v = np.array(conf.v[i, :]) * np.sqrt(mass_in_lammps)
Lv = np.array(conf.Lv[i, :]) / np.sqrt(inertia_in_lammps)
strands[conf.strand[i] - 1].add_nucleotide(
base.Nucleotide(cm, a1, a3, b, b, v, Lv))
# close strand
next_bond = conf.bonds[i][1]
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)
topology_file = basename + ".top"
print >> sys.stderr, "The sequence file '%s' is unreadable" % opts.sequence_file
exit(1)
contents = seq_file.read()
# remove all whitespace from the file's contents
sequence = ''.join(contents.split())
if len(sequence) != nbases:
print >> sys.stderr, "The length of the given sequence (%d) should be equal to the number of coordinates in the centerline file (%d)" % (
len(sequence), nbases)
exit(1)
ssdna1_base = map(lambda x: base.base_to_number[x], sequence)
seq_file.close()
strand1 = base.Strand()
for c in range(nbases):
b = ssdna1_base[c]
strand1.add_nucleotide(
base.Nucleotide(ssdna1[c], v_perp_ssdna1[c], dist_norm[c], b, b))
if opts.closed:
strand1.make_circular()
system.add_strand(strand1)
if opts.double:
strand2 = base.Strand()
for c in range(nbases):
reverse_idx = nbases - 1 - c
b = 3 - ssdna1_base[reverse_idx]
strand2.add_nucleotide(
base.Nucleotide(ssdna2[reverse_idx],
