raise Exception("Cannot determine the interface for a single PDB")
bounds = [rmsdlib.read_pdb(f) for f in boundfiles]
unbounds = [rmsdlib.read_pdb(f) for f in unboundfiles]
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)
unbound_hmask = rmsdlib.build_hydrogenmask(unbounds)
for p in unbounds + bounds:
p.remove_hydrogens()
rmsdlib.check_pdbs(unbounds, bounds)
allboundatoms = []
for p in bounds:
for c in p.coordinates():
allboundatoms.append(c)
allboundatoms = numpy.array(allboundatoms)
selmask = numpy.array([True] * len(allboundatoms))
if not opt_allresidues:
imask = rmsdlib.build_interfacemask(bounds, thresh)
initargs = [sys.argv[1], receptor] + unboundfiles
if modefile: initargs += ["--modes", modefile]
if imodefile: initargs += ["--imodes", imodefile]
ens_receptor = 0
for nr, ensfile in ensfiles:
if nr == "1": ens_receptor = 1
initargs += ["--ens", nr, ensfile]
collectlib.collect_init(initargs)
unboundsizes = [len(list(p.atoms())) for p in unbounds]
receptor_offset = collectlib.ieins[0]
collectlib.check_sizes([receptor_offset] + unboundsizes,
[receptor] + unboundfiles)
if opt_allatoms:
unbound_amask = rmsdlib.build_hydrogenmask(unbounds)
else:
unbound_amask = rmsdlib.build_atommask(unbounds, atomnames)
unbound_amasks_ligand = []
for unr, u in enumerate(unbounds):
if opt_allatoms:
uu = rmsdlib.build_hydrogenmask([u])
else:
uu = rmsdlib.build_atommask([u], atomnames)
offset = 0
if unr: offset = sum(unboundsizes[:unr])
offsetmask = numpy.zeros(offset, dtype="bool")
uu = numpy.concatenate((offsetmask, uu), axis=0)
unbound_amasks_ligand.append(uu)