'--imodes', 'flexm-' + str(nstruc + 1) + name + '.dat'
]
if not os.path.exists('flexm-' + str(nstruc + 1) + name + '.dat'):
break
collectlib.collect_iattract(newargs)
result = collectlib.collect_next()
if result: break
nstruc += 1
coor = collectlib.collect_all_coor()
coor = numpy.compress(unbound_hmask, coor, axis=0)
fcoor = numpy.compress(selmask, coor, axis=0)
U = rmsdlib.fit(fcoor, fboundatoms)[0]
rotfcoor = numpy.array([], ndmin=2)
L = len(fcoor)
COM1 = numpy.sum(fcoor, axis=0) / float(L)
COM2 = numpy.sum(fboundatoms, axis=0) / float(L)
for c in fcoor:
rotfcoor = numpy.append(rotfcoor, U.dot(c - COM1))
rotfcoor = numpy.reshape(rotfcoor, (-1, 3))
f1.write(str(nstruc))
for start, end in ligandselmask:
sel1 = rotfcoor[start:end]
sel2 = fboundatoms[start:end]
sel2 = sel2 - COM2
irmsd = rmsdlib.rmsd(sel1, sel2)
f1.write(" %.3f" % irmsd)
f1.write("\n")
if name is not None:
newargs = initargs + [
'--imodes', 'flexm-' + str(nstruc + 1) + name + '.dat'
]
if not os.path.exists('flexm-' + str(nstruc + 1) + name + '.dat'):
break
collectlib.collect_iattract(newargs)
result = collectlib.collect_next()
if result: break
nstruc += 1
l1, l2 = strucs.next()
ll = [float(v) for v in l2[0].split()[ens_receptor:ens_receptor + 6]]
for v in ll:
if abs(v) > 0.001:
raise ValueError("Structures have not yet been fitted")
f1.write("l-RMSD")
coor = collectlib.collect_all_coor()
coor = numpy.array(coor)[receptor_offset:]
fcoor = numpy.compress(unbound_amask, coor, axis=0)
rmsd = rmsdlib.rmsd(allboundatoms, fcoor)
f1.write(" %.3f" % rmsd)
if len(unbounds) > 1:
for n in range(len(unbounds)):
fcoor = numpy.compress(unbound_amasks_ligand[n], coor, axis=0)
rmsd = rmsdlib.rmsd(boundatoms[n], fcoor)
f1.write(" %.3f" % rmsd)
f1.write("\n")