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)
fboundatoms = numpy.array(allboundatoms[sel])
icom = numpy.sum(fboundatoms, axis=0) / float(len(fboundatoms))
fboundatoms = fboundatoms - icom
nstruc = 0
f1 = sys.stdout
if output is not None:
f1 = open(output, 'w')
print >> f1, "\n".join(struc_header)
for structure in structures:
ligands = structure[1]
assert len(ligands) == len(pivots), (len(ligands), len(pivots))
sys.stdout.flush()
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)
for p in unbounds + bounds:
if opt_allatoms: