xyz = np.column_stack((x.ravel(), y.ravel(), z.ravel()))
pdb = saxs.PDB(superargs.ref)
if superargs.center:
pdb.coords -= pdb.coords.mean(axis=0)
refrho = saxs.pdb2map_gauss(pdb,
xyz=xyz,
sigma=superargs.resolution)
refrho = refrho * np.sum(allrhos[0]) / np.sum(refrho)
if superargs.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(superargs.ref)
if superargs.enan:
print()
print(" Selecting best enantiomers...")
try:
allrhos, scores = saxs.select_best_enantiomers(
allrhos, cores=superargs.cores)
except KeyboardInterrupt:
sys.exit(1)
if superargs.ref is None:
print()
print(" Generating reference...")
try:
refrho = saxs.binary_average(allrhos, superargs.cores)
saxs.write_mrc(refrho, sides[0], output + "_reference.mrc")
except KeyboardInterrupt:
sys.exit(1)
print()
print(" Aligning all maps to reference...")
try:
sigma=args.resolution,
r=args.resolution * 2)
refrho = refrho * np.sum(allrhos[0]) / np.sum(refrho)
saxs.write_mrc(refrho, sides[0], filename=refbasename + '_pdb.mrc')
if args.ref.endswith('.mrc'):
refrho, refside = saxs.read_mrc(args.ref)
if (not args.ref.endswith('.mrc')) and (not args.ref.endswith('.pdb')):
print(
"Invalid reference filename given. .mrc or .pdb file required")
sys.exit(1)
if args.enan:
print(" Selecting best enantiomer(s)...")
try:
if args.ref:
allrhos, scores = saxs.select_best_enantiomers(
allrhos, refrho=refrho, cores=args.cores)
else:
allrhos, scores = saxs.select_best_enantiomers(
allrhos, refrho=allrhos[0], cores=args.cores)
except KeyboardInterrupt:
sys.exit(1)
print(" Aligning to reference...")
try:
aligned, scores = saxs.align_multiple(refrho, allrhos, args.cores)
except KeyboardInterrupt:
sys.exit(1)
for i in range(nmaps):
basename, ext = os.path.splitext(args.files[i])
output = basename + "_aligned"