def align_pose_at_position1_sheffler(self, pose_move, pose_ref,
position_move, position_ref):
stubs_ref = rcl.bbstubs(
pose_ref, [position_ref])['raw'] # gets 'stub' for reslist
stubs_move = rcl.bbstubs(
pose_move, [position_move])['raw'] # raw field is position matrix
# PRINTDBG(stubs_ref.shape) # h**o coords numpy array n x 4 x 4
# PRINTDBG(stubs_move.shape)
# a @ b is np.matmul(a, b)
xalign = stubs_ref @ np.linalg.inv(stubs_move)
# PRINTDBG(xalign.shape)
rcl.xform_pose(xalign[0], pose_move)
def main():
pose1 = poselib.c1
pose2 = poselib.c2
stubs1 = rcl.bbstubs(pose1, [len(pose1)])['raw'] # gets 'stub' for reslist
stubs2 = rcl.bbstubs(pose2, [1])['raw'] # raw field is position matrix
print(stubs1.shape) # h**o coords numpy array n x 4 x 4
print(stubs2.shape)
xalign = stubs1 @ np.linalg.inv(stubs2) # a @ b is np.matmul(a, b)
print(xalign.shape)
rcl.xform_pose(xalign[0], pose2)
# append residues 2-7 of pose2 to pose1
# note: O and H positions may be f****d up...
# not sure easiest way to fix... cart min?
rosetta.core.pose.remove_upper_terminus_type_from_pose_residue(
pose1, len(pose1))
rosetta.core.pose.append_subpose_to_pose(pose1, pose2, 2, 7)
def _cyclic_permute_chains(chainslist, polarity, spliceres):
rm_lower_t = ros.core.pose.remove_lower_terminus_type_from_pose_residue
rm_upper_t = ros.core.pose.remove_upper_terminus_type_from_pose_residue
beg, end = chainslist[0], chainslist[-1]
n2c = polarity == 'N'
if n2c:
stub1 = rcl.bbstubs(beg[0], [spliceres])
stub2 = rcl.bbstubs(end[-1], [len(end[-1])])
beg[0] = rcl.subpose(beg[0], spliceres + 1, len(beg[0]))
rm_lower_t(beg[0], 1)
rm_upper_t(end[-1], len(end[-1]))
else:
stub1 = rcl.bbstubs(beg[-1], [spliceres])
stub2 = rcl.bbstubs(end[0], [1])
beg[-1] = rcl.subpose(beg[-1], 1, spliceres - 1)
rm_lower_t(beg[-1], len(beg[-1]))
rm_upper_t(end[0], 1)
xalign = stub1['raw'][0] @ np.linalg.inv(stub2['raw'][0])
for p in end: rcl.xform_pose(xalign, p)
if n2c: chainslist[0] = end + beg
else: chainslist[0] = beg + end
chainslist = chainslist[:-1]
def pose(self, which, *, align=True, end=None, join=True,
only_connected=None, cyclic_permute=False, provenance=False,
**kw):
"makes a pose for the ith worm"
if isinstance(which, Iterable): return (
self.pose(w, align=align, end=end, join=join,
only_connected=only_connected, **kw)
for w in which)
# print("Will needs to fix bb O/H position!")
rm_lower_t = ros.core.pose.remove_lower_terminus_type_from_pose_residue
rm_upper_t = ros.core.pose.remove_upper_terminus_type_from_pose_residue
if end is None:
end = not self.criteria.is_cyclic
if only_connected is None:
only_connected = not self.criteria.is_cyclic
if cyclic_permute is None:
cyclic_permute = self.criteria.is_cyclic
elif cyclic_permute and not self.criteria.is_cyclic:
raise ValueError('cyclic_permute should only be used for Cyclic')
iend = None if end else -1
entryexits = [seg.make_pose_chains(self.indices[which][iseg],
self.positions[which][iseg])
for iseg, seg in enumerate(self.segments[:iend])]
entryexits, rest = zip(*entryexits)
chainslist = reorder_spliced_as_N_to_C(
entryexits, [s.entrypol for s in self.segments[1:iend]])
if align:
x = self.criteria.alignment(segpos=self.positions[which], **kw)
for p in it.chain(*chainslist, *rest): rcl.xform_pose(x, p[0])
if cyclic_permute and len(chainslist) > 1:
# todo: this is only correct if 1st seg is one chain
spliceres = self.segments[-1].entryresid[self.indices[which, -1]]
bodyid = self.segments[0].bodyid[self.indices[which, 0]]
origlen = len(self.segments[0].spliceables[bodyid].body)
i = -1 if self.segments[-1].entrypol == 'C' else 0
spliceres -= origlen - len(chainslist[0][0][i])
_cyclic_permute_chains(chainslist, self.segments[-1].entrypol,
spliceres + 1)
sourcelist = [[x[1] for x in c] for c in chainslist]
chainslist = [[x[0] for x in c] for c in chainslist]
pose = ros.core.pose.Pose()
prov0 = []
splicepoints = []
for chains, sources in zip(chainslist, sourcelist):
if only_connected and len(chains) is 1: continue
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))
ros.core.pose.append_pose_to_pose(pose, chain, not join)
prov0.append(source)
self.splicepoint_cache[which] = splicepoints
if not only_connected:
for chain, source in it.chain(*rest):
assert isinstance(chain, ros.core.pose.Pose)
ros.core.pose.append_pose_to_pose(pose, chain, True)
prov0.append(source)
assert rcl.worst_CN_connect(pose) < 0.5
if not provenance: return pose
prov = []
for i, pr in enumerate(prov0):
psrc, lb0, ub0 = pr
lb1 = sum(ub - lb + 1 for _, lb, ub in prov0[:i]) + 1
ub1 = lb1 + ub0 - lb0
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)
assert psrc.sequence()[lb0 - 1:ub0] == pose.sequence()[lb1 - 1:ub1]
prov.append((lb1, ub1, psrc, lb0, ub0))
return pose, prov