def test_sugar_3():
resi = ["RG_69_0", "RU_37_0"]
na = ["Phase", "tm"]
angles, rr = bb.pucker_angles(fname, residues=resi)
stri = "".join([" %10s " % pp for pp in na])
stri += "\n"
for e in range(angles.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles.shape[2]):
stri += " %10.4f " % angles[0, e, k]
stri += "\n"
fh = open("%s/sugar_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/sugar_03.test.dat" % refdir)
def test_sugar_3():
resi = ["RG_69_0","RU_37_0"]
na = ["Phase","tm"]
angles,rr = bb.pucker_angles(fname,residues=resi,altona=True)
stri = "".join([" %10s " % pp for pp in na])
stri += "\n"
for e in range(angles.shape[1]):
stri += "%20s " % (rr[e])
for k in range(angles.shape[2]):
stri += " %10.4f " % angles[0,e,k]
stri += "\n"
fh = open("%s/sugar_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/sugar_03.test.dat" % refdir)
def test_sugar_4():
resi = ["RC5_1_0","RG_69_0","RU_37_0"]
na = ["Phase","tm"]
angles_b,rr = bb.pucker_angles(fname,residues=resi)
stri = "%20s " % "#"
for pp in na:
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/sugar_04.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/sugar_04.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()