bounds = [rmsdlib.read_pdb(f) for f in boundfiles]
unbounds = [rmsdlib.read_pdb(f) for f in unboundfiles]
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")
for hnr, h in enumerate(struc_header):
if not h.startswith("#pivot"): continue
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)
continue
if arg.startswith("--"): raise Exception("Unknown option '%s'" % arg)
cutoff = float(sys.argv[2])
pdbfiles = sys.argv[3:]
pdbs = [rmsdlib.read_pdb(f) for f in pdbfiles]
initargs = [sys.argv[1]] + pdbfiles
if modefile: initargs += ["--modes", modefile]
if imodefile: initargs += ["--imodes", imodefile]
for nr, ensfile in ensfiles:
initargs += ["--ens", nr, ensfile]
collectlib.collect_init(initargs)
pdbsizes = [len(list(p.atoms())) for p in pdbs]
collectlib.check_sizes(pdbsizes, pdbfiles)
resids = []
for pdb in pdbs:
cresids = []
for residue in pdb.residues():
resid = residue[0].resid
for n in range(len(residue)):
cresids.append(resid)
resids.append(cresids)
f1 = sys.stdout
if output is not None:
f1 = open(output,'w')
nstruc = 0