a.add_argument("pdblist")
a.add_argument("--np", type=int)
a.add_argument("--allatoms", action="store_true")
a.add_argument("--ca", action="store_true")
args = a.parse_args()
#structures
pdbfiles = [
l.strip().strip("\n") for l in open(args.pdblist)
if len(l.strip().strip("\n"))
]
#read atoms
pdbs = [rmsdlib.read_pdb(f) for f in pdbfiles]
for pdb in pdbs:
rmsdlib.check_pdbs((pdb, ), pdbs)
coors = np.array([list(pdb.coordinates()) for pdb in pdbs])
#select backbone
if args.allatoms:
assert not args.ca
else:
if args.ca:
atomnames = ("CA", )
else:
atomnames = ("CA", "C", "O", "N")
amask = np.array([a.name in atomnames for a in pdbs[0].atoms()])
coors = coors[:, amask]
def run(index):
hh = h.split()
assert len(hh) == 5 and hh[1] == str(hnr + 1), h
pivot = numpy.array([float(v) for v in hh[2:5]])
pivots.append(pivot)
initargs = [sys.argv[1]] + unboundfiles
if modefile: initargs += ["--modes", modefile]
if imodefile: initargs += ["--imodes", imodefile]
for nr, ensfile in ensfiles:
initargs += ["--ens", nr, ensfile]
collectlib.collect_init(initargs)
unboundsizes = [len(list(p.atoms())) for p in unbounds]
collectlib.check_sizes(unboundsizes, unboundfiles)
rmsdlib.check_pdbs(unbounds, bounds)
allboundatoms = []
for p in bounds:
for c in p.coordinates():
allboundatoms.append(c)
allboundatoms = numpy.array(allboundatoms)
sel = numpy.array([True] * len(allboundatoms))
if not opt_allresidues:
imask = rmsdlib.build_interfacemask(bounds, thresh)
sel = (sel & imask)
if not opt_allatoms:
amask = rmsdlib.build_atommask(bounds, atomnames)
sel = (sel & amask)
allboundatoms = numpy.array(allboundatoms)