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()
result = collectlib.collect_next()
if result: break
nstruc += 1
coor = collectlib.collect_all_coor()
coor = numpy.array(coor)
fcoor = coor[sel]
irotmat, ipivot = align_interface(fboundatoms, fcoor)
print >> f1, "#" + str(nstruc)
if len(structure[0]):
print >> f1, "\n".join(structure[0])
for lignr, lig in enumerate(ligands):
ll = lig.split()
if str(lignr + 1) in ensembles:
ens = ll[0] + " "
dofs = ll[1:]
sigma = sqrt(varmap / 3.0)
emdata_gaussian = scipy.ndimage.filters.gaussian_filter(emdata,
sigma,
mode="constant")
initargs = [datfile] + pdbfiles
if modefile: initargs += ["--modes", modefile]
if imodefile: initargs += ["--imodes", imodefile]
for nr, ensfile in ensfiles:
initargs += ["--ens", nr, ensfile]
collectlib.collect_init(initargs)
blocksize0 = 100
poolsize = multiprocessing.cpu_count()
blocksize = max(poolsize * int(blocksize0 / poolsize), 1)
pool = multiprocessing.Pool(poolsize)
while 1:
coors = []
for nstruc in range(blocksize):
eof = collectlib.collect_next()
if eof: break
coor = collectlib.collect_coor(copy=True)
coors.append(coor)
if eof and not nstruc: break
#corr = [calc_emcorr(coor) for coor in coors]
corr = pool.map(calc_emcorr, coors)
for c in corr:
print "%.6f" % c
if eof: break
