630 lines
20 KiB
Python
630 lines
20 KiB
Python
#!/usr/bin/env python
|
|
"""
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/ Sandia National Laboratories
|
|
LAMMPS Development team: developers@lammps.org
|
|
|
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
certain rights in this software. This software is distributed under
|
|
the GNU General Public License.
|
|
|
|
See the README file in the top-level LAMMPS directory.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
|
|
------------------------------------------------------------------------- */
|
|
"""
|
|
|
|
|
|
"""
|
|
Import basic modules
|
|
"""
|
|
|
|
# for python2/3 compatibility
|
|
from __future__ import print_function
|
|
|
|
import sys, os, timeit
|
|
|
|
from timeit import default_timer as timer
|
|
start_time = timer()
|
|
"""
|
|
Try to import numpy; if failed, import a local version mynumpy
|
|
which needs to be provided
|
|
"""
|
|
try:
|
|
import numpy as np
|
|
except:
|
|
print("numpy not found. Exiting.", file=sys.stderr)
|
|
sys.exit(1)
|
|
|
|
"""
|
|
Check that the required arguments (box offset and size in simulation units
|
|
and the sequence file were provided
|
|
"""
|
|
try:
|
|
box_offset = float(sys.argv[1])
|
|
box_length = float(sys.argv[2])
|
|
infile = sys.argv[3]
|
|
except:
|
|
print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
|
|
"box offset", "box length", "file with sequences"), file=sys.stderr)
|
|
sys.exit(1)
|
|
box = np.array ([box_length, box_length, box_length])
|
|
|
|
"""
|
|
Try to open the file and fail gracefully if file cannot be opened
|
|
"""
|
|
try:
|
|
inp = open (infile, 'r')
|
|
inp.close()
|
|
except:
|
|
print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
|
|
sys.exit(2)
|
|
|
|
# return parts of a string
|
|
def partition(s, d):
|
|
if d in s:
|
|
sp = s.split(d, 1)
|
|
return sp[0], d, sp[1]
|
|
else:
|
|
return s, "", ""
|
|
|
|
"""
|
|
Define the model constants
|
|
"""
|
|
# set model constants
|
|
PI = np.pi
|
|
POS_BASE = 0.4
|
|
POS_BACK = -0.4
|
|
EXCL_RC1 = 0.711879214356
|
|
EXCL_RC2 = 0.335388426126
|
|
EXCL_RC3 = 0.52329943261
|
|
|
|
"""
|
|
Define auxiliary variables for the construction of a helix
|
|
"""
|
|
# center of the double strand
|
|
CM_CENTER_DS = POS_BASE + 0.2
|
|
|
|
# ideal distance between base sites of two nucleotides
|
|
# which are to be base paired in a duplex
|
|
BASE_BASE = 0.3897628551303122
|
|
|
|
# cutoff distance for overlap check
|
|
RC2 = 16
|
|
|
|
# squares of the excluded volume distances for overlap check
|
|
RC2_BACK = EXCL_RC1**2
|
|
RC2_BASE = EXCL_RC2**2
|
|
RC2_BACK_BASE = EXCL_RC3**2
|
|
|
|
# enumeration to translate from letters to numbers and vice versa
|
|
number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
|
|
base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
|
|
'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
|
|
|
|
# auxiliary arrays
|
|
positions = []
|
|
a1s = []
|
|
a3s = []
|
|
quaternions = []
|
|
|
|
newpositions = []
|
|
newa1s = []
|
|
newa3s = []
|
|
|
|
basetype = []
|
|
strandnum = []
|
|
|
|
bonds = []
|
|
|
|
"""
|
|
Convert local body frame to quaternion DOF
|
|
"""
|
|
def exyz_to_quat (mya1, mya3):
|
|
|
|
mya2 = np.cross(mya3, mya1)
|
|
myquat = [1,0,0,0]
|
|
|
|
q0sq = 0.25 * (mya1[0] + mya2[1] + mya3[2] + 1.0)
|
|
q1sq = q0sq - 0.5 * (mya2[1] + mya3[2])
|
|
q2sq = q0sq - 0.5 * (mya1[0] + mya3[2])
|
|
q3sq = q0sq - 0.5 * (mya1[0] + mya2[1])
|
|
|
|
# some component must be greater than 1/4 since they sum to 1
|
|
# compute other components from it
|
|
|
|
if q0sq >= 0.25:
|
|
myquat[0] = np.sqrt(q0sq)
|
|
myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
|
|
myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
|
|
myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
|
|
elif q1sq >= 0.25:
|
|
myquat[1] = np.sqrt(q1sq)
|
|
myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
|
|
myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
|
|
myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
|
|
elif q2sq >= 0.25:
|
|
myquat[2] = np.sqrt(q2sq)
|
|
myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
|
|
myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
|
|
myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
|
|
elif q3sq >= 0.25:
|
|
myquat[3] = np.sqrt(q3sq)
|
|
myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
|
|
myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
|
|
myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
|
|
|
|
norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
|
|
myquat[2]*myquat[2] + myquat[3]*myquat[3])
|
|
myquat[0] *= norm
|
|
myquat[1] *= norm
|
|
myquat[2] *= norm
|
|
myquat[3] *= norm
|
|
|
|
return np.array([myquat[0],myquat[1],myquat[2],myquat[3]])
|
|
|
|
"""
|
|
Adds a strand to the system by appending it to the array of previous strands
|
|
"""
|
|
def add_strands (mynewpositions, mynewa1s, mynewa3s):
|
|
overlap = False
|
|
|
|
# This is a simple check for each of the particles where for previously
|
|
# placed particles i we check whether it overlaps with any of the
|
|
# newly created particles j
|
|
|
|
print( "## Checking for overlaps", file=sys.stdout)
|
|
|
|
for i in range(len(positions)):
|
|
|
|
p = positions[i]
|
|
pa1 = a1s[i]
|
|
|
|
for j in range (len(mynewpositions)):
|
|
|
|
q = mynewpositions[j]
|
|
qa1 = mynewa1s[j]
|
|
|
|
# skip particles that are anyway too far away
|
|
dr = p - q
|
|
dr -= box * np.rint(dr / box)
|
|
if np.dot(dr, dr) > RC2:
|
|
continue
|
|
|
|
# base site and backbone site of the two particles
|
|
p_pos_back = p + pa1 * POS_BACK
|
|
p_pos_base = p + pa1 * POS_BASE
|
|
q_pos_back = q + qa1 * POS_BACK
|
|
q_pos_base = q + qa1 * POS_BASE
|
|
|
|
# check for no overlap between the two backbone sites
|
|
dr = p_pos_back - q_pos_back
|
|
dr -= box * np.rint(dr / box)
|
|
if np.dot(dr, dr) < RC2_BACK:
|
|
overlap = True
|
|
|
|
# check for no overlap between the two base sites
|
|
dr = p_pos_base - q_pos_base
|
|
dr -= box * np.rint(dr / box)
|
|
if np.dot(dr, dr) < RC2_BASE:
|
|
overlap = True
|
|
|
|
# check for no overlap between backbone site of particle p
|
|
# with base site of particle q
|
|
dr = p_pos_back - q_pos_base
|
|
dr -= box * np.rint (dr / box)
|
|
if np.dot(dr, dr) < RC2_BACK_BASE:
|
|
overlap = True
|
|
|
|
# check for no overlap between base site of particle p and
|
|
# backbone site of particle q
|
|
dr = p_pos_base - q_pos_back
|
|
dr -= box * np.rint (dr / box)
|
|
if np.dot(dr, dr) < RC2_BACK_BASE:
|
|
overlap = True
|
|
|
|
# exit if there is an overlap
|
|
if overlap:
|
|
return False
|
|
|
|
# append to the existing list if no overlap is found
|
|
if not overlap:
|
|
|
|
for p in mynewpositions:
|
|
positions.append(p)
|
|
for p in mynewa1s:
|
|
a1s.append (p)
|
|
for p in mynewa3s:
|
|
a3s.append (p)
|
|
# calculate quaternion from local body frame and append
|
|
for ia in range(len(mynewpositions)):
|
|
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
|
|
quaternions.append(mynewquaternions)
|
|
|
|
return True
|
|
|
|
|
|
"""
|
|
Returns the rotation matrix defined by an axis and angle
|
|
"""
|
|
def get_rotation_matrix(axis, anglest):
|
|
# The argument anglest can be either an angle in radiants
|
|
# (accepted types are float, int or np.float64 or np.float64)
|
|
# or a tuple [angle, units] where angle is a number and
|
|
# units is a string. It tells the routine whether to use degrees,
|
|
# radiants (the default) or base pairs turns.
|
|
if not isinstance (anglest, (np.float64, np.float32, float, int)):
|
|
if len(anglest) > 1:
|
|
if anglest[1] in ["degrees", "deg", "o"]:
|
|
#angle = np.deg2rad (anglest[0])
|
|
angle = (np.pi / 180.) * (anglest[0])
|
|
elif anglest[1] in ["bp"]:
|
|
angle = int(anglest[0]) * (np.pi / 180.) * (35.9)
|
|
else:
|
|
angle = float(anglest[0])
|
|
else:
|
|
angle = float(anglest[0])
|
|
else:
|
|
angle = float(anglest) # in degrees (?)
|
|
|
|
axis = np.array(axis)
|
|
axis /= np.sqrt(np.dot(axis, axis))
|
|
|
|
ct = np.cos(angle)
|
|
st = np.sin(angle)
|
|
olc = 1. - ct
|
|
x, y, z = axis
|
|
|
|
return np.array([[olc*x*x+ct, olc*x*y-st*z, olc*x*z+st*y],
|
|
[olc*x*y+st*z, olc*y*y+ct, olc*y*z-st*x],
|
|
[olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
|
|
|
|
"""
|
|
Generates the position and orientation vectors of a
|
|
(single or double) strand from a sequence string
|
|
"""
|
|
def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
|
|
dir=np.array([0, 0, 1]), perp=False, double=True, rot=0.):
|
|
# generate empty arrays
|
|
mynewpositions, mynewa1s, mynewa3s = [], [], []
|
|
|
|
# cast the provided start_pos array into a numpy array
|
|
start_pos = np.array(start_pos, dtype=float)
|
|
|
|
# overall direction of the helix
|
|
dir = np.array(dir, dtype=float)
|
|
if sequence == None:
|
|
sequence = np.random.randint(1, 5, bp)
|
|
|
|
# the elseif here is most likely redundant
|
|
elif len(sequence) != bp:
|
|
n = bp - len(sequence)
|
|
sequence += np.random.randint(1, 5, n)
|
|
print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
|
|
|
|
# normalize direction
|
|
dir_norm = np.sqrt(np.dot(dir,dir))
|
|
if dir_norm < 1e-10:
|
|
print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
|
|
dir = np.array([0, 0, 1])
|
|
else: dir /= dir_norm
|
|
|
|
# find a vector orthogonal to dir to act as helix direction,
|
|
# if not provided switch off random orientation
|
|
if perp is None or perp is False:
|
|
v1 = np.random.random_sample(3)
|
|
v1 -= dir * (np.dot(dir, v1))
|
|
v1 /= np.sqrt(sum(v1*v1))
|
|
else:
|
|
v1 = perp;
|
|
|
|
# generate rotational matrix representing the overall rotation of the helix
|
|
R0 = get_rotation_matrix(dir, rot)
|
|
|
|
# rotation matrix corresponding to one step along the helix
|
|
R = get_rotation_matrix(dir, [1, "bp"])
|
|
|
|
# set the vector a1 (backbone to base) to v1
|
|
a1 = v1
|
|
|
|
# apply the global rotation to a1
|
|
a1 = np.dot(R0, a1)
|
|
|
|
# set the position of the fist backbone site to start_pos
|
|
rb = np.array(start_pos)
|
|
|
|
# set a3 to the direction of the helix
|
|
a3 = dir
|
|
for i in range(bp):
|
|
# work out the position of the centre of mass of the nucleotide
|
|
rcdm = rb - CM_CENTER_DS * a1
|
|
|
|
# append to newpositions
|
|
mynewpositions.append(rcdm)
|
|
mynewa1s.append(a1)
|
|
mynewa3s.append(a3)
|
|
|
|
# if we are not at the end of the helix, we work out a1 and rb for the
|
|
# next nucleotide along the helix
|
|
if i != bp - 1:
|
|
a1 = np.dot(R, a1)
|
|
rb += a3 * BASE_BASE
|
|
|
|
# if we are working on a double strand, we do a cycle similar
|
|
# to the previous one but backwards
|
|
if double == True:
|
|
a1 = -a1
|
|
a3 = -dir
|
|
R = R.transpose()
|
|
for i in range(bp):
|
|
rcdm = rb - CM_CENTER_DS * a1
|
|
mynewpositions.append (rcdm)
|
|
mynewa1s.append (a1)
|
|
mynewa3s.append (a3)
|
|
a1 = np.dot(R, a1)
|
|
rb += a3 * BASE_BASE
|
|
|
|
assert (len (mynewpositions) > 0)
|
|
|
|
return [mynewpositions, mynewa1s, mynewa3s]
|
|
|
|
|
|
"""
|
|
Main function for this script.
|
|
Reads a text file with the following format:
|
|
- Each line contains the sequence for a single strand (A,C,G,T)
|
|
- Lines beginning with the keyword 'DOUBLE' produce double-stranded DNA
|
|
|
|
Ex: Two ssDNA (single stranded DNA)
|
|
ATATATA
|
|
GCGCGCG
|
|
|
|
Ex: Two strands, one double stranded, the other single stranded.
|
|
DOUBLE AGGGCT
|
|
CCTGTA
|
|
|
|
"""
|
|
|
|
def read_strands(filename):
|
|
try:
|
|
infile = open (filename)
|
|
except:
|
|
print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
|
|
sys.exit(2)
|
|
|
|
# This block works out the number of nucleotides and strands by reading
|
|
# the number of non-empty lines in the input file and the number of letters,
|
|
# taking the possible DOUBLE keyword into account.
|
|
nstrands, nnucl, nbonds = 0, 0, 0
|
|
lines = infile.readlines()
|
|
for line in lines:
|
|
line = line.upper().strip()
|
|
if len(line) == 0:
|
|
continue
|
|
if line[:6] == 'DOUBLE':
|
|
line = line.split()[1]
|
|
length = len(line)
|
|
print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
|
|
nnucl += 2*length
|
|
nstrands += 2
|
|
nbonds += (2*length-2)
|
|
else:
|
|
line = line.split()[0]
|
|
length = len(line)
|
|
print( "## Found single strand of %i bases" % length, file=sys.stdout)
|
|
nnucl += length
|
|
nstrands += 1
|
|
nbonds += length-1
|
|
# rewind the sequence input file
|
|
infile.seek(0)
|
|
|
|
print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
|
|
|
|
# generate the data file in LAMMPS format
|
|
try:
|
|
out = open ("data.oxdna", "w")
|
|
except:
|
|
print( "Could not open data file for writing. Aborting.", file=sys.stderr)
|
|
sys.exit(2)
|
|
|
|
lines = infile.readlines()
|
|
nlines = len(lines)
|
|
i = 1
|
|
myns = 0
|
|
noffset = 1
|
|
|
|
for line in lines:
|
|
line = line.upper().strip()
|
|
|
|
# skip empty lines
|
|
if len(line) == 0:
|
|
i += 1
|
|
continue
|
|
|
|
# block for duplexes: last argument of the generate function
|
|
# is set to 'True'
|
|
if line[:6] == 'DOUBLE':
|
|
line = line.split()[1]
|
|
length = len(line)
|
|
seq = [(base_to_number[x]) for x in line]
|
|
|
|
myns += 1
|
|
for b in range(length):
|
|
basetype.append(seq[b])
|
|
strandnum.append(myns)
|
|
|
|
for b in range(length-1):
|
|
bondpair = [noffset + b, noffset + b + 1]
|
|
bonds.append(bondpair)
|
|
noffset += length
|
|
|
|
# create the sequence of the second strand as made of
|
|
# complementary bases
|
|
seq2 = [5-s for s in seq]
|
|
seq2.reverse()
|
|
|
|
myns += 1
|
|
for b in range(length):
|
|
basetype.append(seq2[b])
|
|
strandnum.append(myns)
|
|
|
|
for b in range(length-1):
|
|
bondpair = [noffset + b, noffset + b + 1]
|
|
bonds.append(bondpair)
|
|
noffset += length
|
|
|
|
print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
|
|
|
|
# generate random position of the first nucleotide
|
|
cdm = box_offset + np.random.random_sample(3) * box
|
|
|
|
# generate the random direction of the helix
|
|
axis = np.random.random_sample(3)
|
|
axis /= np.sqrt(np.dot(axis, axis))
|
|
|
|
# use the generate function defined above to create
|
|
# the position and orientation vector of the strand
|
|
newpositions, newa1s, newa3s = generate_strand(len(line), \
|
|
sequence=seq, dir=axis, start_pos=cdm, double=True)
|
|
|
|
# generate a new position for the strand until it does not overlap
|
|
# with anything already present
|
|
start = timer()
|
|
while not add_strands(newpositions, newa1s, newa3s):
|
|
cdm = box_offset + np.random.random_sample(3) * box
|
|
axis = np.random.random_sample(3)
|
|
axis /= np.sqrt(np.dot(axis, axis))
|
|
newpositions, newa1s, newa3s = generate_strand(len(line), \
|
|
sequence=seq, dir=axis, start_pos=cdm, double=True)
|
|
print( "## Trying %i" % i, file=sys.stdout)
|
|
end = timer()
|
|
print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
|
(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
|
|
|
|
# block for single strands: last argument of the generate function
|
|
# is set to 'False'
|
|
else:
|
|
length = len(line)
|
|
seq = [(base_to_number[x]) for x in line]
|
|
|
|
myns += 1
|
|
for b in range(length):
|
|
basetype.append(seq[b])
|
|
strandnum.append(myns)
|
|
|
|
for b in range(length-1):
|
|
bondpair = [noffset + b, noffset + b + 1]
|
|
bonds.append(bondpair)
|
|
noffset += length
|
|
|
|
# generate random position of the first nucleotide
|
|
cdm = box_offset + np.random.random_sample(3) * box
|
|
|
|
# generate the random direction of the helix
|
|
axis = np.random.random_sample(3)
|
|
axis /= np.sqrt(np.dot(axis, axis))
|
|
|
|
print("## Created single strand of %i bases" % length, file=sys.stdout)
|
|
|
|
newpositions, newa1s, newa3s = generate_strand(length, \
|
|
sequence=seq, dir=axis, start_pos=cdm, double=False)
|
|
start = timer()
|
|
while not add_strands(newpositions, newa1s, newa3s):
|
|
cdm = box_offset + np.random.random_sample(3) * box
|
|
axis = np.random.random_sample(3)
|
|
axis /= np.sqrt(np.dot(axis, axis))
|
|
newpositions, newa1s, newa3s = generate_strand(length, \
|
|
sequence=seq, dir=axis, start_pos=cdm, double=False)
|
|
print >> sys.stdout, "## Trying %i" % (i)
|
|
end = timer()
|
|
print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
|
(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
|
|
|
|
i += 1
|
|
|
|
# sanity check
|
|
if not len(positions) == nnucl:
|
|
print( len(positions), nnucl )
|
|
raise AssertionError
|
|
|
|
out.write('# LAMMPS data file\n')
|
|
out.write('%d atoms\n' % nnucl)
|
|
out.write('%d ellipsoids\n' % nnucl)
|
|
out.write('%d bonds\n' % nbonds)
|
|
out.write('\n')
|
|
out.write('4 atom types\n')
|
|
out.write('1 bond types\n')
|
|
out.write('\n')
|
|
out.write('# System size\n')
|
|
out.write('%f %f xlo xhi\n' % (box_offset,box_offset+box_length))
|
|
out.write('%f %f ylo yhi\n' % (box_offset,box_offset+box_length))
|
|
out.write('%f %f zlo zhi\n' % (box_offset,box_offset+box_length))
|
|
|
|
out.write('\n')
|
|
out.write('Masses\n')
|
|
out.write('\n')
|
|
out.write('1 3.1575\n')
|
|
out.write('2 3.1575\n')
|
|
out.write('3 3.1575\n')
|
|
out.write('4 3.1575\n')
|
|
|
|
# for each nucleotide print a line under the headers
|
|
# Atoms, Velocities, Ellipsoids and Bonds
|
|
out.write('\n')
|
|
out.write(\
|
|
'# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
|
|
out.write('Atoms\n')
|
|
out.write('\n')
|
|
|
|
for i in range(nnucl):
|
|
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
|
|
% (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
|
|
|
|
out.write('\n')
|
|
out.write('# Atom-ID, translational, rotational velocity\n')
|
|
out.write('Velocities\n')
|
|
out.write('\n')
|
|
|
|
for i in range(nnucl):
|
|
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
|
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
|
|
|
|
out.write('\n')
|
|
out.write('# Atom-ID, shape, quaternion\n')
|
|
out.write('Ellipsoids\n')
|
|
out.write('\n')
|
|
|
|
for i in range(nnucl):
|
|
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
|
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
|
|
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
|
|
|
|
out.write('\n')
|
|
out.write('# Bond topology\n')
|
|
out.write('Bonds\n')
|
|
out.write('\n')
|
|
|
|
for i in range(nbonds):
|
|
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
|
|
|
|
out.close()
|
|
|
|
print("## Wrote data to 'data.oxdna'", file=sys.stdout)
|
|
print("## DONE", file=sys.stdout)
|
|
|
|
# call the above main() function, which executes the program
|
|
read_strands (infile)
|
|
|
|
end_time=timer()
|
|
runtime = end_time-start_time
|
|
hours = runtime/3600
|
|
minutes = (runtime-np.rint(hours)*3600)/60
|
|
seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
|
|
print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
|
|
|
|
|