def show_with_axis(worms, idx=0):
"""TODO: Summary
Args:
worms (TYPE): Description
idx (int, optional): Description
"""
pose = worms.pose(idx, align=0, end=1)
x_from = worms.positions[idx][worms.criteria.from_seg]
x_to = worms.positions[idx][worms.criteria.to_seg]
x = x_to @ np.linalg.inv(x_from)
axis, ang, cen = homog.axis_ang_cen_of(x)
np.set_printoptions(precision=20)
print(x)
print(axis)
print(ang)
print(cen)
axis *= 100
showme(pose, name="unit")
util.xform_pose(x, pose)
showme(pose, name="sym1")
util.xform_pose(x, pose)
showme(pose, name="sym2")
showline(axis, cen)
showsphere(cen)
def align_pose_at_position1_sheffler(self, pose_move, pose_ref, position_move, position_ref):
stubs_ref, _ = util.get_bb_stubs(pose_ref, [position_ref])
stubs_move, _ = util.get_bb_stubs(pose_move, [position_move])
# print(stubs_ref.shape) # h**o coords numpy array n x 4 x 4
# print(stubs_move.shape)
xalign = stubs_ref @ np.linalg.inv(stubs_move)
# print(xalign.shape)
util.xform_pose(xalign[0], pose_move)
def iface_rms(self, pose0, prov, **kw):
if self.origin_seg is None:
# print('WARNING: iface_rms not implemented for simple cyclic')
return -1
else:
same_as_last = list()
for i, pr in enumerate(prov[:-1]):
if pr[2] is prov[-1][2]:
same_as_last.append(i)
if len(same_as_last) < 2:
print(
'iface_rms ERROR, not 3 merge subs! same_as_last:',
same_as_last
)
# for i, (lb, ub, src, slb, sub) in enumerate(prov):
# print(i, lb, ub, id(src), len(src), slb, sub)
return 9e9
i1, i2 = same_as_last[-2:]
i3 = -1
a1 = util.subpose(pose0, prov[i1][0], prov[i1][1])
a2 = util.subpose(pose0, prov[i2][0], prov[i2][1])
a3 = util.subpose(pose0, prov[i3][0], prov[i3][1])
b1 = util.subpose(prov[i1][2], prov[i1][3], prov[i1][4])
b2 = util.subpose(prov[i2][2], prov[i2][3], prov[i2][4])
b3 = util.subpose(prov[i3][2], prov[i3][3], prov[i3][4])
forward = hrot([0, 0, 1], 360.0 / self.nfold)
backward = hrot([0, 0, 1], -720.0 / self.nfold)
util.xform_pose(forward, a1)
# a1.dump_pdb('a3_forward.pdb')
fdist = a1.residue(1).xyz(2).distance(a3.residue(1).xyz(2))
util.xform_pose(backward, a1)
# a1.dump_pdb('a3_backward.pdb')
bdist = a1.residue(1).xyz(2).distance(a3.residue(1).xyz(2))
if bdist > fdist:
util.xform_pose(forward, a1)
util.xform_pose(forward, a1)
# pose0.dump_pdb('pose0.pdb')
# a1.dump_pdb('a1.pdb')
# a2.dump_pdb('a2.pdb')
# a3.dump_pdb('a3.pdb')
# prov[-1][2].dump_pdb('src.pdb')
# b1.dump_pdb('b1.pdb')
# b2.dump_pdb('b2.pdb')
# b3.dump_pdb('b3.pdb')
ros.core.pose.append_pose_to_pose(a1, a2, True)
ros.core.pose.append_pose_to_pose(a1, a3, True)
ros.core.pose.append_pose_to_pose(b1, b2, True)
ros.core.pose.append_pose_to_pose(b1, b3, True)
# a1.dump_pdb('a.pdb')
# b1.dump_pdb('b.pdb')
rms = ros.core.scoring.CA_rmsd(a1, b1)
# assert 0, 'debug iface rms ' + str(rms)
return rms
def _cyclic_permute_chains(chainslist, entrypol, exitpol):
"""rearrange segments in a cylic structure so chainbreak is at chain boundary
"""
n2c = 'N' == entrypol[-1]
# print('polarity', polarity)
# for ich, ch in enumerate(chainslist):
# _dump_chainlist(ch, 'before', ich)
chainslist_beg = 0
for i, cl in enumerate(chainslist):
if any(x.cyclic_entry for x in cl):
assert chainslist_beg == 0 # there can be only one
chainslist_beg = i
print('resplicing cyclic chains')
beg, end = chainslist[chainslist_beg], chainslist[-1]
# _dump_chainlist(ch, 'begend')
if n2c:
stub1 = util.get_bb_stubs(beg[0][0], [1])
stub2 = util.get_bb_stubs(end[-1][0], [1])
rm_lower_t(beg[0][0], 1)
assert len(end[-1][0]) == 1
end = end[:-1]
else:
stub1 = util.get_bb_stubs(beg[-1][0], [len(beg[-1][0])])
stub2 = util.get_bb_stubs(end[0][0], [1])
rm_upper_t(beg[-1][0], len(beg[-1][0]))
assert len(end[0][0]) == 1
end = end[1:]
xalign = stub1[0] @ np.linalg.inv(stub2[0])
all_one_chain = chainslist_beg + 1 == len(chainslist) # beg is end, all one chain
if all_one_chain:
# no no, this doesn't work
# chainslist[chainslist_beg] = end[-1:] + end[:-1] if n2c else end[1:] + end[:1]
# chainslist.append([]) # caller expects empty end, have to add
# raise NotImplementedE
print("cyclic permute chains fail, probably forming a backbone cycle")
raise ValueError('invalid cycle, involves backbone cycle with no chainbreaks')
for p in end:
util.xform_pose(xalign, p[0])
chainslist[chainslist_beg] = end + beg if n2c else beg + end
chainslist[-1] = []
def _cyclic_permute_chains(chainslist, polarity):
"""TODO: Summary
Args:
chainslist (TYPE): Description
polarity (TYPE): Description
"""
chainslist_beg = 0
for i, cl in enumerate(chainslist):
if any(x.cyclic_entry for x in cl):
assert chainslist_beg == 0
chainslist_beg = i
beg, end = chainslist[chainslist_beg], chainslist[-1]
# if chainslist_beg != 0:
# raise NotImplementedError('peace sign not working yet')
n2c = (polarity == 'N')
if n2c:
stub1 = util.get_bb_stubs(beg[0][0], [1])
stub2 = util.get_bb_stubs(end[-1][0], [1])
rm_lower_t(beg[0][0], 1)
end = end[:-1]
else:
# from . import vis
# for i, b in enumerate(beg): vis.showme(b[0], name='beg_%i' % i)
# for i, e in enumerate(end): vis.showme(e[0], name='end_%i' % i)
stub1 = util.get_bb_stubs(beg[-1][0], [len(beg[-1][0])])
stub2 = util.get_bb_stubs(end[0][0], [1])
rm_upper_t(beg[-1][0], len(beg[-1][0]))
assert len(end[0][0]) == 1
end = end[1:]
xalign = stub1[0] @ np.linalg.inv(stub2[0])
# print(xalign.shape)
for p in end:
util.xform_pose(xalign, p[0])
if n2c: chainslist[chainslist_beg] = end + beg
else: chainslist[chainslist_beg] = beg + end
chainslist[-1] = []
def contort_pose_chains(
pose,
chains,
nseg,
ir_en,
ir_ex,
pl_en,
pl_ex,
chain_start,
chain_end,
position=None,
pad=(0, 0),
iseg=None,
cyclictrim=None,
last_seg_entrypol=None,
first_seg_exitpol=None,
sym_ir=None,
sym_pol=None,
):
"""make pose chains from 'segment' info
what a monster this has become. returns (segchains, rest)
segchains elems are [enterexitchain] or, [enterchain, ..., exitchain]
rest holds other chains IFF enter and exit in same chain
each element is a pair [pose, source] where source is
(origin_pose, start_res, stop_res)
cyclictrim specifies segments which are spliced across the
symmetric interface. segments only needed if cyclictrim==True
if cyclictrim, last segment will only be a single entry residue
Args: No
"""
cyclic_entry = defaultdict(lambda: None)
if cyclictrim and cyclictrim[1] < 0:
cyclictrim = cyclictrim[0], cyclictrim[1] + nseg
if cyclictrim and iseg == cyclictrim[0]:
# assert ir_en == -1, 'paece sign not implemented yet'
sym_ch = pose.chain(sym_ir)
cyclictrim_in_rest = False
if ir_en == -1:
ir_en = sym_ir
else:
entry_chain, exit_chain = pose.chain(ir_en), pose.chain(ir_ex)
if sym_ch not in (entry_chain, exit_chain):
cyclictrim_in_rest = True
assert sym_ch != entry_chain or sym_pol != entrypol
assert sym_ch != exit_chain or sym_pol != exitpol
# annotate enex entries with cyclictrim info
cyclic_entry[pose.chain(sym_ir)] = (iseg, sym_ir, sym_pol)
if cyclictrim and iseg == cyclictrim[1]:
assert ir_ex == -1
assert iseg + 1 == nseg
i = ir_en
p = util.subpose(pose, i, i)
if position is not None: util.xform_pose(position, p)
return [AnnoPose(p, iseg, pose, i, i, None)], []
ch_en = pose.chain(ir_en) if ir_en > 0 else None
ch_ex = pose.chain(ir_ex) if ir_ex > 0 else None
if cyclictrim and iseg == 0:
pl_en = last_seg_entrypol
if cyclictrim and iseg + 1 == nseg:
assert 0, 'last segment not returned as single entry residue?!?'
pl_ex = first_seg_exitpol
if ch_en: ir_en -= chain_start[ch_en]
if ch_ex: ir_ex -= chain_start[ch_ex]
assert ch_en or ch_ex
rest = OrderedDict()
did_cyclictrim_in_rest = False
for i in range(1, len(chains) + 1):
pchain = chains[i]
lb = chain_start[i] + 1
ub = chain_end[i]
if cyclic_entry[i] is not None:
if i not in (ch_en, ch_ex):
did_cyclictrim_in_rest = True
ir = cyclic_entry[i][1] - chain_start[i]
pchain, lb, ub = util.trim_pose(pchain, ir, cyclic_entry[i][2])
lb += chain_start[i]
ub += chain_start[i]
rest[chains[i]] = AnnoPose(pchain, iseg, pose, lb, ub, cyclic_entry[i])
assert rest[chains[i]].seq() == rest[chains[i]].srcseq()
if cyclictrim and iseg == cyclictrim[0]:
if cyclictrim_in_rest != did_cyclictrim_in_rest:
print('cyclictrim_in_rest', cyclictrim_in_rest,
'did_cyclictrim_in_rest', did_cyclictrim_in_rest)
print('iseg', iseg, 'len(chains)', len(chains))
assert cyclictrim_in_rest == did_cyclictrim_in_rest
if ch_en: del rest[chains[ch_en]]
if ch_en == ch_ex:
assert len(rest) + 1 == len(chains)
p, l1, u1 = util.trim_pose(chains[ch_en], ir_en, pl_en, pad[0])
iexit1 = ir_ex - (pl_ex == 'C') * (len(chains[ch_en]) - len(p))
p, l2, u2 = util.trim_pose(p, iexit1, pl_ex, pad[1] - 1)
lb = l1 + l2 - 1 + chain_start[ch_en]
ub = l1 + u2 - 1 + chain_start[ch_en]
enex = [AnnoPose(p, iseg, pose, lb, ub, cyclic_entry[ch_en])]
assert p.sequence() == pose.sequence()[lb - 1:ub]
rest = list(rest.values())
else:
if ch_ex: del rest[chains[ch_ex]]
p_en = [chains[ch_en]] if ch_en else []
p_ex = [chains[ch_ex]] if ch_ex else []
if p_en:
p, lben, uben = util.trim_pose(p_en[0], ir_en, pl_en, pad[0])
lb = lben + chain_start[ch_en]
ub = uben + chain_start[ch_en]
p_en = [AnnoPose(p, iseg, pose, lb, ub, cyclic_entry[ch_en])]
assert p.sequence() == pose.sequence()[lb - 1:ub]
if p_ex:
p, lbex, ubex = util.trim_pose(p_ex[0], ir_ex, pl_ex, pad[1] - 1)
lb = lbex + chain_start[ch_ex]
ub = ubex + chain_start[ch_ex]
p_ex = [AnnoPose(p, iseg, pose, lb, ub, cyclic_entry[ch_ex])]
assert p.sequence() == pose.sequence()[lb - 1:ub]
enex = p_en + list(rest.values()) + p_ex
rest = []
for ap in rest:
s1 = str(ap.pose.sequence())
s2 = str(ap.srcpose.sequence()[ap.src_lb - 1:ap.src_ub])
if s1 != s2:
print('WARNING: sequence mismatch in "rest", maybe OK, but '
'proceed with caution and tell will to fix!')
# print(s1)
# print(s2)
assert s1 == s2
if position is not None:
position = util.rosetta_stub_from_numpy_stub(position)
for x in enex:
x.pose = x.pose.clone()
for x in rest:
x.pose = x.pose.clone()
for ap in it.chain(enex, rest):
ros.protocols.sic_dock.xform_pose(ap.pose, position)
for iap, ap in enumerate(it.chain(enex, rest)):
assert isinstance(ap, AnnoPose)
assert ap.iseg == iseg
assert ap.seq() == ap.srcseq()
# a = ap.seq()
# b = ap.srcseq()
# if a != b:
# print('WARNING sequence mismatch!', iap, len(enex), len(rest))
# print(a)
# print(b)
# assert a == b
return enex, rest
def make_contorted_pose(
*,
entryexits,
entrypol,
exitpol,
indices,
from_seg,
to_seg,
origin_seg,
seg_pos,
position,
is_cyclic,
align,
cryst_info,
end,
iend,
only_connected,
join,
cyclic_permute,
cyclictrim,
provenance,
make_chain_list
): # yapf: disable
"""there be dragons here"""
nseg = len(entryexits)
entryexits, rest = zip(*entryexits)
for ap in it.chain(*entryexits, *rest):
assert isinstance(ap, AnnoPose)
chainslist = reorder_spliced_as_N_to_C(entryexits, entrypol[1:iend])
if align:
for ap in it.chain(*chainslist, *rest):
util.xform_pose(position, ap.pose)
if cyclic_permute and len(chainslist) > 1:
cyclic_entry_count = 0
for ap in it.chain(*entryexits, *rest):
cyclic_entry_count += (ap.cyclic_entry is not None)
assert cyclic_entry_count == 1
_cyclic_permute_chains(chainslist, entrypol[-1])
assert len(chainslist[-1]) == 0
chainslist = chainslist[:-1]
sourcelist = [[x[1] for x in c] for c in chainslist]
chainslist = [[x[0] for x in c] for c in chainslist]
ret_chain_list = []
pose = ros.core.pose.Pose()
prov0 = []
splicepoints = []
for chains, sources in zip(chainslist, sourcelist):
if (only_connected and len(chains) is 1
and (end or chains is not chainslist[-1])):
skipsegs = ((to_seg, from_seg) if not is_cyclic else [])
skipsegs = [nseg - 1 if x is -1 else x for x in skipsegs]
if origin_seg is not None:
skipsegs.append(origin_seg)
if ((only_connected == 'auto' and sources[0][0] in skipsegs)
or only_connected != 'auto'):
continue
if make_chain_list: ret_chain_list.append(chains[0])
ros.core.pose.append_pose_to_pose(pose, chains[0], True)
prov0.append(sources[0])
for chain, source in zip(chains[1:], sources[1:]):
assert isinstance(chain, ros.core.pose.Pose)
rm_upper_t(pose, len(pose))
rm_lower_t(chain, 1)
splicepoints.append(len(pose))
if make_chain_list: ret_chain_list.append(chain)
ros.core.pose.append_pose_to_pose(pose, chain, not join)
prov0.append(source)
if not only_connected or only_connected == 'auto':
for chain, source in it.chain(*rest):
assert isinstance(chain, ros.core.pose.Pose)
if make_chain_list: ret_chain_list.append(chain)
ros.core.pose.append_pose_to_pose(pose, chain, True)
prov0.append(source)
assert util.worst_CN_connect(pose) < 0.5
assert util.no_overlapping_adjacent_residues(pose)
if cryst_info:
ci = pyrosetta.rosetta.core.io.CrystInfo()
ci.A(cryst_info[0]) #cell dimensions
ci.B(cryst_info[1])
ci.C(cryst_info[2])
ci.alpha(cryst_info[3]) #cell angles
ci.beta(cryst_info[4])
ci.gamma(cryst_info[5])
ci.spacegroup(cryst_info[6]) #sace group
pi = pyrosetta.rosetta.core.pose.PDBInfo(pose)
pi.set_crystinfo(ci)
pose.pdb_info(pi)
if not provenance and make_chain_list: return pose, ret_chain_list
if not provenance: return pose, splicepoints
prov = []
for i, pr in enumerate(prov0):
iseg, psrc, lb0, ub0 = pr
lb1 = sum(ub - lb + 1 for _, _, lb, ub in prov0[:i]) + 1
ub1 = lb1 + ub0 - lb0
if ub0 == lb0:
assert cyclic_permute
continue
assert ub0 - lb0 == ub1 - lb1
assert 0 < lb0 <= len(psrc) and 0 < ub0 <= len(psrc)
assert 0 < lb1 <= len(pose) and 0 < ub1 <= len(pose)
# if psrc.sequence()[lb0 - 1:ub0] != pose.sequence()[lb1 - 1:ub1]:
# print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
assert psrc.sequence()[lb0 - 1:ub0] == pose.sequence()[lb1 - 1:ub1]
prov.append((lb1, ub1, psrc, lb0, ub0))
if make_chain_list:
return pose, prov, ret_chain_list
return pose, prov
def make_contorted_pose(
entryexits,
entrypol,
exitpol,
indices,
from_seg,
to_seg,
origin_seg,
seg_pos,
position,
is_cyclic,
align,
cryst_info,
end,
iend,
only_connected,
join,
cyclic_permute,
cyclictrim,
provenance,
make_chain_list,
full_output_segs=[],
): # yapf: disable
"""there be dragons here"""
nseg = len(entryexits)
entryexits, rest = zip(*entryexits)
for ap in it.chain(*entryexits, *rest):
assert isinstance(ap, AnnoPose)
chainslist = reorder_spliced_as_N_to_C(entryexits, entrypol[1:iend])
if align:
for ap in it.chain(*chainslist, *rest):
util.xform_pose(position, ap.pose)
if cyclic_permute and len(chainslist) > 1:
cyclic_entry_count = 0
for ap in it.chain(*entryexits, *rest):
cyclic_entry_count += ap.cyclic_entry is not None
assert cyclic_entry_count == 1
_cyclic_permute_chains(chainslist, entrypol, exitpol)
assert len(chainslist[-1]) == 0
chainslist = chainslist[:-1]
sourcelist = [[x[1] for x in c] for c in chainslist]
chainslist = [[x[0] for x in c] for c in chainslist]
ret_chain_list = []
pose = ros.core.pose.Pose()
prov0 = []
splicepoints = []
for i, (chains, sources) in enumerate(zip(chainslist, sourcelist)):
if (only_connected and len(chains) is 1 and (end or chains is not chainslist[-1])):
skipsegs = (to_seg, from_seg) if not is_cyclic else []
skipsegs = [nseg - 1 if x is -1 else x for x in skipsegs]
skipsegs = [s for s in skipsegs if s not in full_output_segs]
if origin_seg is not None:
skipsegs.append(origin_seg)
if (only_connected == "auto" and sources[0][0] in skipsegs) or only_connected != "auto":
# print('skip', i, skipsegs, len(chains), len(sources))
continue
if make_chain_list:
ret_chain_list.append(chains[0])
ros.core.pose.append_pose_to_pose(pose, chains[0], True)
prov0.append(sources[0])
prev_source, prev_chain = sources[0], chains[0]
for chain, source in zip(chains[1:], sources[1:]):
assert isinstance(chain, ros.core.pose.Pose)
rm_upper_t(pose, len(pose))
rm_lower_t(chain, 1)
splicepoints.append(len(pose))
if make_chain_list:
ret_chain_list.append(chain)
fixres = len(pose)
####################################################
# tim look here!
# pose: overall output structure
# chain: new thing to splice on, already truncated
# prev_chain: the last thing spliced on, already truncated
# pose_source_before: untruncated pose of previous BB
# pose_source_after: untruncated pose of this BB
# lb/ub_before/after residue range in source poses in truncated 'chain's
ros.core.pose.append_pose_to_pose(pose, chain, not join)
iseg_before, pose_source_before, lb_before, ub_before = prev_source
iseg_after, pose_source_after, lb_after, ub_after = source
#
######################################################
# this dosen't work correctly
# util.fix_bb_o(pose, fixres)
# util.fix_bb_h(pose, fixres + 1)
prov0.append(source)
prev_source, prev_chain = source, chain
if not only_connected or only_connected == "auto":
for chain, source in it.chain(*rest):
assert isinstance(chain, ros.core.pose.Pose)
if make_chain_list:
ret_chain_list.append(chain)
ros.core.pose.append_pose_to_pose(pose, chain, True)
prov0.append(source)
assert util.worst_CN_connect(pose) < 0.5
assert util.no_overlapping_adjacent_residues(pose)
if cryst_info:
ci = pyrosetta.rosetta.core.io.CrystInfo()
ci.A(cryst_info[0]) # cell dimensions
ci.B(cryst_info[1])
ci.C(cryst_info[2])
ci.alpha(cryst_info[3]) # cell angles
ci.beta(cryst_info[4])
ci.gamma(cryst_info[5])
ci.spacegroup(cryst_info[6]) # sace group
pi = pyrosetta.rosetta.core.pose.PDBInfo(pose)
pi.set_crystinfo(ci)
pose.pdb_info(pi)
ros.core.scoring.dssp.Dssp(pose).insert_ss_into_pose(pose)
if not provenance and make_chain_list:
return pose, ret_chain_list
if not provenance:
return pose, splicepoints
prov = []
for i, pr in enumerate(prov0):
iseg, psrc, lb0, ub0 = pr
lb1 = sum(ub - lb + 1 for _, _, lb, ub in prov0[:i]) + 1
ub1 = lb1 + ub0 - lb0
if ub0 == lb0:
assert cyclic_permute
continue
assert ub0 - lb0 == ub1 - lb1
assert 0 < lb0 <= len(psrc) and 0 < ub0 <= len(psrc)
assert 0 < lb1 <= len(pose) and 0 < ub1 <= len(pose)
# if psrc.sequence()[lb0 - 1:ub0] != pose.sequence()[lb1 - 1:ub1]:
# print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
assert psrc.sequence()[lb0 - 1:ub0] == pose.sequence()[lb1 - 1:ub1]
prov.append((lb1, ub1, psrc, lb0, ub0))
if make_chain_list:
return pose, prov, ret_chain_list
return pose, prov