def test_angles_4():
resi = ["RG_69_0","RU_37_0"]
angles = ["gamma","alpha"]
angles_b,rr = bb.backbone_angles(fname1,topology=fname,residues=resi,angles=angles)
stri = ""
for p in range(angles_b.shape[0]):
for k in range(angles_b.shape[2]):
stri += " %10.4f %10.4f " % (angles_b[p,0,k],angles_b[p,1,k])
stri += "\n"
fh = open("%s/angles_04.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/angles_04.test.dat" % refdir)
def test_angles_1():
angles_b,rr = bb.backbone_angles(fname)
fh = open("%s/angles_01.test.dat" % outdir,'w')
stri = "%20s " % "#"
for pp in dd.bb_angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0,e,k]
stri += "\n"
fh.write(stri)
fh.close()
comp("%s/angles_01.test.dat" % refdir)
def test_angles_1():
angles_b, rr = bb.backbone_angles(fname)
fh = open("%s/angles_01.test.dat" % outdir, 'w')
stri = "%20s " % "#"
for pp in dd.bb_angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0, e, k]
stri += "\n"
fh.write(stri)
fh.close()
comp("%s/angles_01.test.dat" % refdir)
def test_angles_4():
resi = ["RG_69_0", "RU_37_0"]
angles = ["gamma", "alpha"]
angles_b, rr = bb.backbone_angles(fname1,
topology=fname,
residues=resi,
angles=angles)
stri = ""
for p in range(angles_b.shape[0]):
for k in range(angles_b.shape[2]):
stri += " %10.4f %10.4f " % (angles_b[p, 0, k], angles_b[p, 1, k])
stri += "\n"
fh = open("%s/angles_04.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/angles_04.test.dat" % refdir)
def test_angles_3():
resi = ["RG_69_0","RU_37_0"]
angles = ["gamma","alpha"]
angles_b,rr = bb.backbone_angles(fname,residues=resi,angles=angles)
stri = "%20s " % "#"
for pp in angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0,e,k]
stri += "\n"
fh = open("%s/angles_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/angles_03.test.dat" % refdir)
def test_angles_3():
resi = ["RG_69_0", "RU_37_0"]
angles = ["gamma", "alpha"]
angles_b, rr = bb.backbone_angles(fname, residues=resi, angles=angles)
stri = "%20s " % "#"
for pp in angles:
stri += " %10s " % pp
stri += "\n"
for e in range(angles_b.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles_b.shape[2]):
stri += " %10.4f " % angles_b[0, e, k]
stri += "\n"
fh = open("%s/angles_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/angles_03.test.dat" % refdir)
def torsion(args):
assert args.backbone or args.sugar or args.pucker, "# ERROR. choose --backbone/sugar/pucker"
if(args.backbone):
stri_b = "# %s \n" % (" ".join(sys.argv[:]))
stri_b += "#%-12s %11s %11s %11s %11s %11s %11s %11s\n" % ("RESIDUE","alpha","beta","gamma","delta","eps","zeta","chi")
if(args.top==None):
for i in range(len(args.pdbs)):
stri_b += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
angles_b,rr = bb.backbone_angles(args.pdbs[i],residues=args.res)
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[0,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
else:
angles_b,rr = bb.backbone_angles(args.trj,topology=args.top,residues=args.res)
for i in range(angles_b.shape[0]):
stri_b += "# Frame %d \n" % i
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[i,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
fh = open(args.name + ".backbone.out",'w')
fh.write(stri_b)
fh.close()
if(args.sugar):
stri_b = "# %s \n" % (" ".join(sys.argv[:]))
stri_b += "#%-12s %11s %11s %11s %11s %11s \n" % ("RESIDUE","nu0","nu1","nu2","nu3","nu4")
if(args.top==None):
for i in range(len(args.pdbs)):
stri_b += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
angles_b,rr = bb.sugar_angles(args.pdbs[i],residues=args.res)
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[0,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
else:
angles_b,rr = bb.sugar_angles(args.trj,topology=args.top,residues=args.res)
for i in range(angles_b.shape[0]):
stri_b += "# Frame %d \n" % i
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[i,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
fh = open(args.name + ".sugar.out",'w')
fh.write(stri_b)
fh.close()
if(args.pucker):
stri_b = "# %s \n" % (" ".join(sys.argv[:]))
stri_b += "#%-12s %11s %11s \n" % ("RESIDUE","Phase","Amplitude")
if(args.top==None):
for i in range(len(args.pdbs)):
stri_b += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
angles_b,rr = bb.pucker_angles(args.pdbs[i],residues=args.res,altona=args.altona)
stri_b += "".join(["%-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[0,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
else:
angles_b,rr = bb.pucker_angles(args.trj,topology=args.top,residues=args.res,altona=args.altona)
for i in range(angles_b.shape[0]):
stri_b += "# Frame %d \n" % i
stri_b += "".join(["%-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[i,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
fh = open(args.name + ".pucker.out",'w')
fh.write(stri_b)
fh.close()
def torsion(args):
assert args.backbone or args.sugar or args.pucker, "# ERROR. choose --backbone/sugar/pucker"
if(args.backbone):
stri_b = "# %s \n" % (" ".join(sys.argv[:]))
stri_b += "#%-12s %11s %11s %11s %11s %11s %11s %11s\n" % ("RESIDUE","alpha","beta","gamma","delta","eps","zeta","chi")
if(args.top==None):
for i in range(len(args.pdbs)):
stri_b += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
angles_b,rr = bb.backbone_angles(args.pdbs[i],residues=args.res)
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[0,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
else:
angles_b,rr = bb.backbone_angles(args.trj,topology=args.top,residues=args.res)
for i in range(angles_b.shape[0]):
stri_b += "# Frame %d \n" % i
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[i,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
fh = open(args.name + ".backbone.out",'w')
fh.write(stri_b)
fh.close()
if(args.sugar):
stri_b = "# %s \n" % (" ".join(sys.argv[:]))
stri_b += "#%-12s %11s %11s %11s %11s %11s \n" % ("RESIDUE","nu0","nu1","nu2","nu3","nu4")
if(args.top==None):
for i in range(len(args.pdbs)):
stri_b += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
angles_b,rr = bb.sugar_angles(args.pdbs[i],residues=args.res)
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[0,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
else:
angles_b,rr = bb.sugar_angles(args.trj,topology=args.top,residues=args.res)
for i in range(angles_b.shape[0]):
stri_b += "# Frame %d \n" % i
stri_b += "".join([" %-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[i,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
fh = open(args.name + ".sugar.out",'w')
fh.write(stri_b)
fh.close()
if(args.pucker):
stri_b = "# %s \n" % (" ".join(sys.argv[:]))
stri_b += "#%-12s %11s %11s \n" % ("RESIDUE","Phase","Amplitude")
if(args.top==None):
for i in range(len(args.pdbs)):
stri_b += "# PDB %s \n" % args.pdbs[i].split("/")[-1]
angles_b,rr = bb.pucker_angles(args.pdbs[i],residues=args.res)
stri_b += "".join(["%-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[0,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
else:
angles_b,rr = bb.pucker_angles(args.trj,topology=args.top,residues=args.res)
for i in range(angles_b.shape[0]):
stri_b += "# Frame %d \n" % i
stri_b += "".join(["%-12s %s \n" % (rr[e], "".join([" %11.3e" % angles_b[i,e,k] for k in range(angles_b.shape[2])])) for e in range(angles_b.shape[1])])
fh = open(args.name + ".pucker.out",'w')
fh.write(stri_b)
fh.close()