fixed indentations and ported python 2 code to python 3
This commit is contained in:
alphataubio
@ -33,7 +33,7 @@ which needs to be provided
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try:
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import numpy as np
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except:
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print >> sys.stderr, "numpy not found. Exiting."
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print("numpy not found. Exiting.", file=sys.stderr)
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sys.exit(1)
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"""
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@ -45,8 +45,8 @@ try:
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box_length = float(sys.argv[2])
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infile = sys.argv[3]
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except:
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print >> sys.stderr, "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
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"box offset", "box length", "file with sequences")
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print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
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"box offset", "box length", "file with sequences"), file=sys.stderr)
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sys.exit(1)
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box = np.array ([box_length, box_length, box_length])
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@ -57,8 +57,7 @@ try:
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inp = open (infile, 'r')
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inp.close()
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except:
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print >> sys.stderr, "Could not open file '%s' for reading. \
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Aborting." % infile
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print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
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sys.exit(2)
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# return parts of a string
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@ -174,21 +173,21 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
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# placed particles i we check whether it overlaps with any of the
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# newly created particles j
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print >> sys.stdout, "## Checking for overlaps"
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print( "## Checking for overlaps", file=sys.stdout)
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for i in xrange(len(positions)):
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for i in range(len(positions)):
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p = positions[i]
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pa1 = a1s[i]
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for j in xrange (len(mynewpositions)):
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for j in range (len(mynewpositions)):
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q = mynewpositions[j]
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qa1 = mynewa1s[j]
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# skip particles that are anyway too far away
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dr = p - q
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dr -= box * np.rint (dr / box)
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dr -= box * np.rint(dr / box)
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if np.dot(dr, dr) > RC2:
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continue
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@ -200,13 +199,13 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
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# check for no overlap between the two backbone sites
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dr = p_pos_back - q_pos_back
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dr -= box * np.rint (dr / box)
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dr -= box * np.rint(dr / box)
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if np.dot(dr, dr) < RC2_BACK:
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overlap = True
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# check for no overlap between the two base sites
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dr = p_pos_base - q_pos_base
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dr -= box * np.rint (dr / box)
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dr -= box * np.rint(dr / box)
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if np.dot(dr, dr) < RC2_BASE:
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overlap = True
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@ -238,7 +237,7 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
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for p in mynewa3s:
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a3s.append (p)
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# calculate quaternion from local body frame and append
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for ia in xrange(len(mynewpositions)):
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for ia in range(len(mynewpositions)):
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mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
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quaternions.append(mynewquaternions)
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@ -301,13 +300,12 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
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elif len(sequence) != bp:
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n = bp - len(sequence)
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sequence += np.random.randint(1, 5, n)
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print >> sys.stderr, "sequence is too short, adding %d random bases" % n
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print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
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# normalize direction
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dir_norm = np.sqrt(np.dot(dir,dir))
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if dir_norm < 1e-10:
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print >> sys.stderr, "direction must be a valid vector, \
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defaulting to (0, 0, 1)"
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print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
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dir = np.array([0, 0, 1])
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else: dir /= dir_norm
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@ -391,7 +389,7 @@ def read_strands(filename):
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try:
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infile = open (filename)
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except:
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print >> sys.stderr, "Could not open file '%s'. Aborting." % filename
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print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
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sys.exit(2)
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# This block works out the number of nucleotides and strands by reading
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@ -406,28 +404,27 @@ def read_strands(filename):
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if line[:6] == 'DOUBLE':
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line = line.split()[1]
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length = len(line)
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print >> sys.stdout, "## Found duplex of %i base pairs" % length
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print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
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nnucl += 2*length
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nstrands += 2
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nbonds += (2*length-2)
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else:
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line = line.split()[0]
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length = len(line)
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print >> sys.stdout, \
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"## Found single strand of %i bases" % length
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print( "## Found single strand of %i bases" % length, file=sys.stdout)
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nnucl += length
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nstrands += 1
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nbonds += length-1
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# rewind the sequence input file
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infile.seek(0)
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print >> sys.stdout, "## nstrands, nnucl = ", nstrands, nnucl
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print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
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# generate the data file in LAMMPS format
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try:
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out = open ("data.oxdna", "w")
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except:
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print >> sys.stderr, "Could not open data file for writing. Aborting."
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print( "Could not open data file for writing. Aborting.", file=sys.stderr)
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sys.exit(2)
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lines = infile.readlines()
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@ -452,11 +449,11 @@ def read_strands(filename):
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seq = [(base_to_number[x]) for x in line]
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myns += 1
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for b in xrange(length):
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for b in range(length):
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basetype.append(seq[b])
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strandnum.append(myns)
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for b in xrange(length-1):
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for b in range(length-1):
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bondpair = [noffset + b, noffset + b + 1]
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bonds.append(bondpair)
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noffset += length
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@ -467,16 +464,16 @@ def read_strands(filename):
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seq2.reverse()
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myns += 1
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for b in xrange(length):
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for b in range(length):
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basetype.append(seq2[b])
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strandnum.append(myns)
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for b in xrange(length-1):
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for b in range(length-1):
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bondpair = [noffset + b, noffset + b + 1]
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bonds.append(bondpair)
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noffset += length
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print >> sys.stdout, "## Created duplex of %i bases" % (2*length)
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print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
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# generate random position of the first nucleotide
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cdm = box_offset + np.random.random_sample(3) * box
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@ -499,10 +496,10 @@ def read_strands(filename):
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axis /= np.sqrt(np.dot(axis, axis))
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newpositions, newa1s, newa3s = generate_strand(len(line), \
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sequence=seq, dir=axis, start_pos=cdm, double=True)
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print >> sys.stdout, "## Trying %i" % i
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print( "## Trying %i" % i, file=sys.stdout)
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end = timer()
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print >> sys.stdout, "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
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(2*length, i, nlines, end-start, len(positions), nnucl)
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print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
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(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
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# block for single strands: last argument of the generate function
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# is set to 'False'
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@ -511,11 +508,11 @@ def read_strands(filename):
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seq = [(base_to_number[x]) for x in line]
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myns += 1
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for b in xrange(length):
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for b in range(length):
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basetype.append(seq[b])
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strandnum.append(myns)
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for b in xrange(length-1):
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for b in range(length-1):
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bondpair = [noffset + b, noffset + b + 1]
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bonds.append(bondpair)
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noffset += length
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@ -527,8 +524,7 @@ def read_strands(filename):
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axis = np.random.random_sample(3)
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axis /= np.sqrt(np.dot(axis, axis))
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print >> sys.stdout, \
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"## Created single strand of %i bases" % length
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print("## Created single strand of %i bases" % length, file=sys.stdout)
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newpositions, newa1s, newa3s = generate_strand(length, \
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sequence=seq, dir=axis, start_pos=cdm, double=False)
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@ -541,14 +537,14 @@ def read_strands(filename):
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sequence=seq, dir=axis, start_pos=cdm, double=False)
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print >> sys.stdout, "## Trying %i" % (i)
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end = timer()
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print >> sys.stdout, "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
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(length, i, nlines, end-start,len(positions), nnucl)
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print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
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(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
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i += 1
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# sanity check
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if not len(positions) == nnucl:
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print len(positions), nnucl
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print( len(positions), nnucl )
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raise AssertionError
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out.write('# LAMMPS data file\n')
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@ -580,18 +576,16 @@ def read_strands(filename):
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out.write('Atoms\n')
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out.write('\n')
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for i in xrange(nnucl):
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for i in range(nnucl):
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out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
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% (i+1, basetype[i], \
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positions[i][0], positions[i][1], positions[i][2], \
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strandnum[i]))
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% (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
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out.write('\n')
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out.write('# Atom-ID, translational, rotational velocity\n')
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out.write('Velocities\n')
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out.write('\n')
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for i in xrange(nnucl):
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for i in range(nnucl):
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out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
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% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
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@ -600,9 +594,8 @@ def read_strands(filename):
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out.write('Ellipsoids\n')
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out.write('\n')
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for i in xrange(nnucl):
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out.write(\
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"%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
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for i in range(nnucl):
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out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
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% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
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quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
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@ -611,13 +604,13 @@ def read_strands(filename):
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out.write('Bonds\n')
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out.write('\n')
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for i in xrange(nbonds):
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for i in range(nbonds):
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out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
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out.close()
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print >> sys.stdout, "## Wrote data to 'data.oxdna'"
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print >> sys.stdout, "## DONE"
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print("## Wrote data to 'data.oxdna'", file=sys.stdout)
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print("## DONE", file=sys.stdout)
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# call the above main() function, which executes the program
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read_strands (infile)
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@ -627,4 +620,6 @@ runtime = end_time-start_time
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hours = runtime/3600
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minutes = (runtime-np.rint(hours)*3600)/60
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seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
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print >> sys.stdout, "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds)
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print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
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