def load_cached_bblock_into_memory(self, pdbkey, cache_replace=True):
assert not isinstance(pdbkey, (str, bytes))
if not isinstance(pdbkey, (int, str)):
success = True
for f in pdbkey:
success &= self.load_cached_bblock_into_memory(f)
return success
bblockfile = self.bblockfile(pdbkey)
if not os.path.exists(bblockfile):
# print(f'warning: bblock cachefile not found {bblockfile}')
return False
with open(bblockfile, 'rb') as f:
bbstate = list(pickle.load(f))
entry = self._dictdb[self._key_to_pdbfile[pdbkey]]
newjson = json.dumps(entry).encode()
if bytes(bbstate[0]) == newjson:
self._bblock_cache[pdbkey] = _BBlock(*bbstate)
return True
print('!!! database entry updated for key', pdbkey, entry['file'])
if cache_replace:
print(' removing cachefile', bblockfile)
os.remove(bblockfile)
print(' reloading info cache', entry['file'])
self.load_pdbs_multiprocess([entry['file']], parallel=0)
return self.load_cached_bblock_into_memory(pdbkey,
cache_replace=False)
return False
def worms_main_protocol(criteria, bbs_states=None, **kw):
try:
if bbs_states is not None:
kw['bbs'] = [tuple(_BBlock(*s) for s in bb) for bb in bbs_states]
ssdag, result1, log = search_func(criteria, **kw)
if result1 is None: return []
result2 = prune_clashes(ssdag, criteria, result1, **kw)
result3 = check_geometry(ssdag, criteria, result2, **kw)
log = []
if True: # len(result3.idx) > 0:
msg = f'nresults after clash/geom check {len(result3.idx):,}'
log.append(' ' + msg)
print(log[-1])
log += filter_and_output_results(criteria, ssdag, result3, **kw)
if not kw['pbar']:
print(f'completed: mbb{kw["merge_bblock"]:04}')
sys.stdout.flush()
return log
except Exception as e:
print('error on mbb' + str(kw['merge_bblock']))
print(type(e))
print(traceback.format_exc())
print(e)
sys.stdout.flush()
return []
def __setstate__(self, state):
self.bbspec = state[0]
self.bbs = tuple(tuple(_BBlock(*x) for x in bb) for bb in state[1])
self.verts = tuple(_Vertex(*x) for x in state[2])
self.edges = tuple(_Edge(*x) for x in state[3])
_validate_bbs_verts(self.bbs, self.verts)
assert len(self.bbs) == len(self.verts) == len(self.edges) + 1
def load_cached_bblock_into_memory(self, pdbfile):
"""TODO: Summary
Args:
pdbfile (TYPE): Description
Returns:
TYPE: Description
"""
if not isinstance(pdbfile, str):
success = True
for f in pdbfile:
success &= self.load_cached_bblock_into_memory(f)
return success
bblockfile = self.bblockfile(pdbfile)
try:
with open(bblockfile, 'rb') as f:
bbstate = list(pickle.load(f))
self._bblock_cache[pdbfile] = _BBlock(*bbstate)
return True
except FileNotFound:
return False
def vertex_single(bbstate, bbid, din, dout, min_seg_len):
"""Summary
Args:
bb (TYPE): Description
bbid (TYPE): Description
din (TYPE): Description
dout (TYPE): Description
min_seg_len (TYPE): Description
Returns:
TYPE: Description
"""
bb = _BBlock(*bbstate)
ires0, ires1 = [], []
isite0, isite1 = [], []
for i in range(bb.n_connections):
ires = bb.conn_resids(i)
if bb.conn_dirn(i) == din:
ires0.append(ires)
isite0.append(np.repeat(i, len(ires)))
if bb.conn_dirn(i) == dout:
ires1.append(ires)
isite1.append(np.repeat(i, len(ires)))
if (din < 2 and not ires0 or dout < 2 and not ires1):
dirn = 'NC_'[din] + 'NC_'[dout]
warning('invalid vertex ' + dirn + ' ' + bytes(bb.file).decode())
return None
dummy = [np.array([-1], dtype='i4')]
ires0 = np.concatenate(ires0 or dummy)
ires1 = np.concatenate(ires1 or dummy)
isite0 = np.concatenate(isite0 or dummy)
isite1 = np.concatenate(isite1 or dummy)
chain0 = chain_of_ires(bb, ires0)
chain1 = chain_of_ires(bb, ires1)
if ires0[0] == -1: assert len(ires0) is 1
else: assert np.all(ires0 >= 0)
if ires1[0] == -1: assert len(ires1) is 1
else: assert np.all(ires1 >= 0)
if ires0[0] == -1: stub0inv = np.eye(4).reshape(1, 4, 4)
else: stub0inv = np.linalg.inv(bb.stubs[ires0])
if ires1[0] == -1: stub1 = np.eye(4).reshape(1, 4, 4)
else: stub1 = bb.stubs[ires1]
stub0inv, stub1 = np.broadcast_arrays(stub0inv[:, None], stub1)
ires = np.stack(np.broadcast_arrays(ires0[:, None], ires1), axis=-1)
isite = np.stack(np.broadcast_arrays(isite0[:, None], isite1), axis=-1)
chain = np.stack(np.broadcast_arrays(chain0[:, None], chain1), axis=-1)
x2exit = stub0inv @ stub1
x2orig = stub0inv
assert is_homog_xform(x2exit) # this could be slowish
assert is_homog_xform(x2orig)
# min chain len, not same site
not_same_chain = chain[..., 0] != chain[..., 1]
not_same_site = isite[..., 0] != isite[..., 1]
seqsep = np.abs(ires[..., 0] - ires[..., 1])
# remove invalid in/out pairs (+ is or, * is and)
valid = not_same_site
valid *= (not_same_chain + (seqsep >= min_seg_len))
valid = valid.reshape(-1)
if sum(valid) == 0: return None
return (
x2exit.reshape(-1, 4, 4)[valid],
x2orig.reshape(-1, 4, 4)[valid],
ires.reshape(-1, 2)[valid].astype('i4'),
isite.reshape(-1, 2)[valid].astype('i4'),
chain.reshape(-1, 2)[valid].astype('i4'),
np.repeat(bbid, sum(valid)).astype('i4'),
)
def vertex_single(bbstate, bbid, din, dout, min_seg_len, verbosity=0):
"""build on bblock's worth of vertex"""
bb = _BBlock(*bbstate)
ires0, ires1 = [], []
isite0, isite1 = [], []
for i in range(bb.n_connections):
ires = bb.conn_resids(i)
if bb.conn_dirn(i) == din:
ires0.append(ires)
isite0.append(np.repeat(i, len(ires)))
if bb.conn_dirn(i) == dout:
ires1.append(ires)
isite1.append(np.repeat(i, len(ires)))
dirn = "NC_"[din] + "NC_"[dout]
if din < 2 and not ires0 or dout < 2 and not ires1:
if verbosity > 0:
warning("invalid vertex " + dirn + " " + bytes(bb.file).decode())
return None
dummy = [np.array([-1], dtype="i4")]
ires0 = np.concatenate(ires0 or dummy)
ires1 = np.concatenate(ires1 or dummy)
isite0 = np.concatenate(isite0 or dummy)
isite1 = np.concatenate(isite1 or dummy)
chain0 = chain_of_ires(bb, ires0)
chain1 = chain_of_ires(bb, ires1)
if ires0[0] == -1:
assert len(ires0) is 1
else:
assert np.all(ires0 >= 0)
if ires1[0] == -1:
assert len(ires1) is 1
else:
assert np.all(ires1 >= 0)
if ires0[0] == -1:
stub0inv = np.eye(4).reshape(1, 4, 4)
else:
stub0inv = np.linalg.inv(bb.stubs[ires0])
if ires1[0] == -1:
stub1 = np.eye(4).reshape(1, 4, 4)
else:
stub1 = bb.stubs[ires1]
assert _check_inorder(ires0)
assert _check_inorder(ires1)
stub0inv, stub1 = np.broadcast_arrays(stub0inv[:, None], stub1)
ires = np.stack(np.broadcast_arrays(ires0[:, None], ires1), axis=-1)
isite = np.stack(np.broadcast_arrays(isite0[:, None], isite1), axis=-1)
chain = np.stack(np.broadcast_arrays(chain0[:, None], chain1), axis=-1)
x2exit = stub0inv @ stub1
x2orig = stub0inv
# assert is_homog_xform(x2exit) # this could be slowish
# assert is_homog_xform(x2orig)
# min chain len, not same site
not_same_chain = chain[..., 0] != chain[..., 1]
not_same_site = isite[..., 0] != isite[..., 1]
seqsep = np.abs(ires[..., 0] - ires[..., 1])
# remove invalid in/out pairs (+ is or, * is and)
valid = not_same_site
valid *= not_same_chain + (seqsep >= min_seg_len)
valid = valid.reshape(-1)
if np.sum(valid) == 0:
return None
return (
x2exit.reshape(-1, 4, 4)[valid],
x2orig.reshape(-1, 4, 4)[valid],
ires.reshape(-1, 2)[valid].astype("i4"),
isite.reshape(-1, 2)[valid].astype("i4"),
chain.reshape(-1, 2)[valid].astype("i4"),
np.repeat(bbid, np.sum(valid)).astype("i4"),
)