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)