def annotate(args):
stri_p = "# %s \n" % (" ".join(sys.argv[:]))
stri_p += "#%-10s %-10s %4s \n" % ("RES1","RES2","ANNO")
stri_s = "# %s \n" % (" ".join(sys.argv[:]))
stri_s += "#%-10s %-10s %4s \n" % ("RES1","RES2","ANNO")
stri_dot = "# %s \n" % (" ".join(sys.argv[:]))
if(args.top==None):
for i in range(len(args.pdbs)):
st, pair, res = bb.annotate(args.pdbs[i])
stri_p += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
stri_s += "# sequence %s\n" % "-".join(res)
stri_p += "# sequence %s\n" % "-".join(res)
stri_p += "".join([ "%-10s %-10s %4s \n" % (res[pair[0][0][e][0]],res[pair[0][0][e][1]],pair[0][1][e]) for e in range(len(pair[0][0]))])
stri_s += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
stri_s += "".join([ "%-10s %-10s %4s \n" % (res[st[0][0][e][0]],res[st[0][0][e][1]],st[0][1][e]) for e in range(len(st[0][0]))])
if(args.dotbr):
dotbr,ss = bb.dot_bracket(pair,res)
stri_dot += "# sequence %s\n" % "-".join(res)
stri_dot += "# SEQ %s" % ss
stri_dot += "%-20s %s\n" %(args.pdbs[i].split("/")[-1],dotbr[0])
else:
st,pair,res = bb.annotate(args.trj,topology=args.top)
stri_s += "# sequence %s\n" % "-".join(res)
stri_p += "# sequence %s\n" % "-".join(res)
stri_dot += "# sequence %s\n" % "-".join(res)
if(args.dotbr):
dotbr,ss = bb.dot_bracket(pair,res)
stri_dot += "# SEQ %s" % ss
stri_dot += " ".join(["%-10d %s\n" %(k,dotbr[k]) for k in range(len(pair))])
for k in range(len(st)):
stri_p += "# Frame %d \n" % k
stri_p += "".join([ "%-10s %-10s %4s \n" % (res[pair[k][0][e][0]],res[pair[k][0][e][1]],pair[k][1][e]) for e in range(len(pair[k][0]))])
stri_s += "# Frame %d \n" % k
stri_s += "".join([ "%-10s %-10s %4s \n" % (res[st[k][0][e][0]],res[st[k][0][e][1]],st[k][1][e]) for e in range(len(st[k][0]))])
fh1 = open(args.name + ".pairing.out",'w')
fh1.write(stri_p)
fh1.close()
fh2 = open(args.name + ".stacking.out",'w')
fh2.write(stri_s)
fh2.close()
if(args.dotbr):
fh3 = open(args.name + ".dotbracket.out",'w')
fh3.write(stri_dot)
fh3.close()
def annotate(args):
stri_p = "# %s \n" % (" ".join(sys.argv[:]))
stri_p += "#%-10s %-10s %4s \n" % ("RES1","RES2","ANNO")
stri_s = "# %s \n" % (" ".join(sys.argv[:]))
stri_s += "#%-10s %-10s %4s \n" % ("RES1","RES2","ANNO")
stri_dot = "# %s \n" % (" ".join(sys.argv[:]))
if(args.top==None):
for i in range(len(args.pdbs)):
st, pair, res = bb.annotate(args.pdbs[i])
stri_p += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
stri_p += "".join([ "%-10s %-10s %4s \n" % (res[pair[0][0][e][0]],res[pair[0][0][e][1]],pair[0][1][e]) for e in range(len(pair[0][0]))])
stri_s += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
stri_s += "".join([ "%-10s %-10s %4s \n" % (res[st[0][0][e][0]],res[st[0][0][e][1]],st[0][1][e]) for e in range(len(st[0][0]))])
if(args.dotbr):
dotbr = bb.dot_bracket(pair,res)
stri_dot += "%-20s %s\n" %(args.pdbs[i].split("/")[-1],dotbr[0])
else:
st,pair,res = bb.annotate(args.trj,topology=args.top)
if(args.dotbr):
dotbr = bb.dot_bracket(pair,res)
stri_dot += "".join(["%-10d %s\n" %(k,dotbr[k]) for k in range(len(pair))])
for k in range(len(st)):
stri_p += "# Frame %d \n" % k
stri_p += "".join([ "%-10s %-10s %4s \n" % (res[pair[k][0][e][0]],res[pair[k][0][e][1]],pair[k][1][e]) for e in range(len(pair[k][0]))])
stri_s += "# Frame %d \n" % k
stri_s += "".join([ "%-10s %-10s %4s \n" % (res[st[k][0][e][0]],res[st[k][0][e][1]],st[k][1][e]) for e in range(len(st[k][0]))])
fh1 = open(args.name + ".pairing.out",'w')
fh1.write(stri_p)
fh1.close()
fh2 = open(args.name + ".stacking.out",'w')
fh2.write(stri_s)
fh2.close()
if(args.dotbr):
fh3 = open(args.name + ".dotbracket.out",'w')
fh3.write(stri_dot)
fh3.close()
def test_annotate_2():
fname = "%s/test/data/1S72.pdb" % cwd
stackings, pairings, res = bb.annotate(fname)
dotbr, ss = bb.dot_bracket(pairings, res)
fh = open("%s/stackings_02.test.dat" % outdir, 'w')
stri = "# STACKING \n"
for e in range(len(stackings[0][0])):
stri += "%15s " % (res[stackings[0][0][e][0]])
stri += "%15s " % (res[stackings[0][0][e][1]])
stri += " %4s \n" % (stackings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/pairings_02.test.dat" % outdir, 'w')
stri = "# PAIRING \n"
for e in range(len(pairings[0][0])):
stri += "%15s " % (res[pairings[0][0][e][0]])
stri += "%15s " % (res[pairings[0][0][e][1]])
stri += " %4s \n" % (pairings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_02.test.dat" % outdir, 'w')
fh.write(str(dotbr[0]))
fh.close()
comp("%s/stackings_02.test.dat" % refdir)
comp("%s/pairings_02.test.dat" % refdir)
comp("%s/dotbracket_02.test.dat" % refdir)
def test_annotate_2():
fname = "%s/test/data/1S72.pdb" % cwd
stackings, pairings, res = bb.annotate(fname)
dotbr,ss = bb.dot_bracket(pairings,res)
fh = open("%s/stackings_02.test.dat" % outdir,'w')
stri = "# STACKING \n"
for e in range(len(stackings[0][0])):
stri += "%15s " % (res[stackings[0][0][e][0]])
stri += "%15s " % (res[stackings[0][0][e][1]])
stri += " %4s \n" % (stackings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/pairings_02.test.dat" % outdir,'w')
stri = "# PAIRING \n"
for e in range(len(pairings[0][0])):
stri += "%15s " % (res[pairings[0][0][e][0]])
stri += "%15s " % (res[pairings[0][0][e][1]])
stri += " %4s \n" % (pairings[0][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_02.test.dat" % outdir,'w')
fh.write(str(dotbr[0]))
fh.close()
comp("%s/stackings_02.test.dat" % refdir)
comp("%s/pairings_02.test.dat" % refdir)
comp("%s/dotbracket_02.test.dat" % refdir)
def test_annotate_1():
stackings, pairings, res = bb.annotate(fname1,topology=fname)
dotbr,ss = bb.dot_bracket(pairings,res)
fh = open("%s/stackings_01.test.dat" % outdir,'w')
stri = "# STACKING \n"
for k in range(len(stackings)):
stri += "# frame %d \n" % k
for e in range(len(stackings[k][0])):
stri += "%15s " % (res[stackings[k][0][e][0]])
stri += "%15s " % (res[stackings[k][0][e][1]])
stri += " %4s \n" % (stackings[k][1][e])
stri += "\n"
fh.write(stri)
fh.close()
fh = open("%s/pairings_01.test.dat" % outdir,'w')
stri = "# PAIRING \n"
for k in range(len(pairings)):
stri += "# frame %d \n" % k
for e in range(len(pairings[k][0])):
stri += "%15s " % (res[pairings[k][0][e][0]])
stri += "%15s " % (res[pairings[k][0][e][1]])
stri += " %4s \n" % (pairings[k][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_01.test.dat" % outdir,'w')
stri = ""
for k in range(len(pairings)):
stri += " %06d " % k
stri += "%s \n" % dotbr[k]
fh.write(stri)
fh.close()
comp("%s/stackings_01.test.dat" % refdir)
comp("%s/pairings_01.test.dat" % refdir)
comp("%s/dotbracket_01.test.dat" % refdir)
def test_annotate_1():
stackings, pairings, res = bb.annotate(fname1, topology=fname)
dotbr, ss = bb.dot_bracket(pairings, res)
fh = open("%s/stackings_01.test.dat" % outdir, 'w')
stri = "# STACKING \n"
for k in range(len(stackings)):
stri += "# frame %d \n" % k
for e in range(len(stackings[k][0])):
stri += "%15s " % (res[stackings[k][0][e][0]])
stri += "%15s " % (res[stackings[k][0][e][1]])
stri += " %4s \n" % (stackings[k][1][e])
stri += "\n"
fh.write(stri)
fh.close()
fh = open("%s/pairings_01.test.dat" % outdir, 'w')
stri = "# PAIRING \n"
for k in range(len(pairings)):
stri += "# frame %d \n" % k
for e in range(len(pairings[k][0])):
stri += "%15s " % (res[pairings[k][0][e][0]])
stri += "%15s " % (res[pairings[k][0][e][1]])
stri += " %4s \n" % (pairings[k][1][e])
fh.write(stri)
fh.close()
fh = open("%s/dotbracket_01.test.dat" % outdir, 'w')
stri = ""
for k in range(len(pairings)):
stri += " %06d " % k
stri += "%s \n" % dotbr[k]
fh.write(stri)
fh.close()
comp("%s/stackings_01.test.dat" % refdir)
comp("%s/pairings_01.test.dat" % refdir)
comp("%s/dotbracket_01.test.dat" % refdir)