def rmsd(args):
if(args.top==None):
if(args.dump==True):
dd = [bb.rmsd(args.reference,pdb,out="%s_%06d.pdb" % (args.name,i),heavy_atom=args.heavy_atom) for i,pdb in enumerate(args.pdbs)]
else:
dd = [bb.rmsd(args.reference,pdb,heavy_atom=args.heavy_atom) for i,pdb in enumerate(args.pdbs)]
else:
if(args.dump==True):
out = "%s.%s" % (args.name, (args.trj).split(".")[-1])
dd = bb.rmsd(args.reference,args.trj,topology=args.top,out=out,heavy_atom=args.heavy_atom)
else:
dd = bb.rmsd(args.reference,args.trj,topology=args.top,heavy_atom=args.heavy_atom)
fh = open(args.name + ".out",'w')
fh.write("# %s \n" % (" ".join(sys.argv[:])))
fh.write("#%10s %10s\n" % ("Frame","RMSD"))
fh.write("".join([ " %10d %10.4e \n" % (i,d) for i,d in enumerate(dd)]))
fh.close()
def rmsd(args):
if(args.top==None):
if(args.dump==True):
dd = [bb.rmsd(args.reference,pdb,out="%s_%06d.pdb" % (args.name,i)) for i,pdb in enumerate(args.pdbs)]
else:
dd = [bb.rmsd(args.reference,pdb) for i,pdb in enumerate(args.pdbs)]
else:
if(args.dump==True):
out = "%s.%s" % (args.name, (args.trj).split(".")[-1])
dd = bb.rmsd(args.reference,args.trj,topology=args.top,out=out)
else:
dd = bb.rmsd(args.reference,args.trj,topology=args.top)
fh = open(args.name + ".out",'w')
fh.write("# %s \n" % (" ".join(sys.argv[:])))
fh.write("#%10s %10s\n" % ("Frame","RMSD"))
fh.write("".join([ " %10d %10.4e \n" % (i,d) for i,d in enumerate(dd)]))
fh.close()
def test_rmsd_2():
# align pdb to pdb with different sequence
fname = "%s/test/data/4v7t-pdb-bundle3_G521_00006.align.pdb" % cwd
fname1 = "%s/test/data/centroid_10.pdb" % cwd
dist = bb.rmsd(fname,fname1,out='%s/aligned_2.pdb' % outdir)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_02.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_02.test.dat" % refdir)
comp("%s/aligned_2.pdb" % refdir)
def test_rmsd_2():
# align pdb to pdb with different sequence
fname = "%s/test/data/4v7t-pdb-bundle3_G521_00006.align.pdb" % cwd
fname1 = "%s/test/data/centroid_10.pdb" % cwd
dist = bb.rmsd(fname, fname1, out='%s/aligned_2.pdb' % outdir)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_02.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_02.test.dat" % refdir)
comp("%s/aligned_2.pdb" % refdir)
def test_rmsd_1():
# align pdb to pdb with the same sequence
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/sample2.pdb" % cwd
dist = bb.rmsd(fname,fname1,out='%s/aligned_1.pdb' % outdir,heavy_atom=True)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_01.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_01.test.dat" % refdir)
comp("%s/aligned_1.pdb" % refdir)
def test_rmsd_1():
# align pdb to pdb with the same sequence
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/sample2.pdb" % cwd
dist = bb.rmsd(fname, fname1, out='%s/aligned_1.pdb' % outdir)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_01.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_01.test.dat" % refdir)
comp("%s/aligned_1.pdb" % refdir)
def test_rmsd_3():
# align trajectory to pdb
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/samples.xtc" % cwd
dist = bb.rmsd(fname,fname1,topology=fname,out='%s/aligned_3.xtc' % outdir,heavy_atom=True)
stri = "".join([ "%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_03.test.dat" % outdir,'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_03.test.dat" % refdir)
def test_rmsd_3():
# align trajectory to pdb
fname = "%s/test/data/sample1.pdb" % cwd
fname1 = "%s/test/data/samples.xtc" % cwd
dist = bb.rmsd(fname,
fname1,
topology=fname,
out='%s/aligned_3.xtc' % outdir)
stri = "".join(["%14e \n" % (dd) for dd in dist])
fh = open("%s/rmsd_03.test.dat" % outdir, 'w')
fh.write(stri)
fh.close()
comp("%s/rmsd_03.test.dat" % refdir)