def test_D3(c2pose, c3pose, c1pose):
# Spliceable: pose + splice site info
# Segment: list of spliceables
helix = Spliceable(c1pose, sites=[(':4', 'N'), ('-4:', 'C')])
dimer = Spliceable(c2pose,
sites=[('1,:2', 'N'), ('1,-1:', 'C'), ('2,:2', 'N'),
('2,-1:', 'C')])
trimer = Spliceable(c3pose,
sites=[('1,:1', 'N'), ('1,-2:', 'C'), ('2,:2', 'N'),
('2,-2:', 'C'), ('3,:1', 'N'), ('3,-2:', 'C')])
segments = [
Segment([trimer], '_C'),
Segment([helix], 'NC'),
Segment([helix], 'NC'),
Segment([helix], 'NC'),
Segment([dimer], 'N_')
]
w = grow(segments, D3(c2=-1, c3=0), thresh=1)
# vis.show_with_z_axes(w, 0)
# vis.showme(w.pose(0))
# assert 0
# print(w.scores[:5])
# print([len(s) for s in segments])
# print(w.indices[:5])
# for i in range(5):
# vis.showme(w.pose(i, join=False))
# vis.showme(w.sympose(i))
# assert 0
p = w.pose(0, only_connected=0)
assert util.no_overlapping_residues(p)
# print(len(p))
# print('foo')
# assert 0
assert 1 > residue_sym_err(p, 180, 53, 65, 6, axis=[1, 0, 0])
assert 1 > residue_sym_err(p, 120, 1, 10, 6, axis=[0, 0, 1])
# assert 0
segments = [
Segment([dimer], exit='C'),
Segment([helix], entry='N', exit='C'),
Segment([helix], entry='N', exit='C'),
Segment([helix], entry='N', exit='C'),
Segment([trimer], entry='N')
]
w = grow(segments, D3(c2=0, c3=-1), thresh=1)
# print(w.scores)
# show_with_z_axes(w, 0)
p = w.pose(4, only_connected=0)
assert util.no_overlapping_residues(p)
# vis.showme(p)
assert 1 > residue_sym_err(p, 180, 1, 13, 6, axis=[1, 0, 0])
assert 1 > residue_sym_err(p, 120, 56, 65, 6, axis=[0, 0, 1])
def test_tet33(c2pose, c3pose, c1pose):
helix = Spliceable(c1pose, [(':1', 'N'), ('-4:', 'C')])
trimer = Spliceable(c3pose, sites=[
('1,:1', 'N'),
('1,-2:', 'C'),
])
segments = ([Segment([trimer], exit='C')] +
[Segment([helix], entry='N', exit='C')] * 5 +
[Segment([trimer], entry='N')])
w = grow(segments, Tetrahedral(c3=-1, c3b=0), thresh=2)
assert len(w) == 3
p = w.pose(0, only_connected=0)
assert util.no_overlapping_residues(p)
assert 2.5 > residue_sym_err(p, 120, 2, 20, 6, axis=[1, 1, -1])
assert 2.5 > residue_sym_err(p, 120, 87, 96, 6, axis=[1, 1, 1])
def test_sym_bug(c1pose, c2pose):
helix = Spliceable(c1pose,
sites=[((1, 2, 3), "N"), ((9, 10, 11, 13), "C")])
dimer = Spliceable(c2pose,
sites=[((1, 2, 3), "N", 1), ("1,-1:", "C"),
("2,-1:", "C")])
segdimer = Segment([dimer], entry="N", exit="C")
segments = [
Segment([helix], exit="C"),
Segment([helix], entry="N", exit="C"),
Segment([dimer], entry="N", exit="C"),
Segment([helix], entry="N", exit="C"),
Segment([helix], entry="N"),
]
wnc = grow(segments, Cyclic(3, lever=200), thresh=1, verbosity=1)
assert len(wnc) == 3
print(wnc.scores)
p = wnc.pose(0, align=1, end=1)
# vis.showme(p)
# show_with_axis(wnc, 0)
# assert 0
# q = wnc.pose(4)
# vis.showme(p, name='carterr')
# vis.showme(q, name='angerr')
assert residue_sym_err(wnc.pose(0, end=True), 120, 2, 46, 6) < 1.0
def test_multichain_mixed_pol(c2pose, c3pose, c1pose):
helix = Spliceable(c1pose, [(":4", "N"), ((10, 12, 13), "C")])
dimer = Spliceable(c2pose,
sites=[("1,:2", "N"), ("1,-1:", "C"), ("2,:2", "N"),
("2,-1:", "C")])
trimer = Spliceable(
c3pose,
sites=[
("1,:1", "N"),
("1,-2:", "C"),
("2,:2", "N"),
("2,-2:", "C"),
("3,:1", "N"),
("3,-2:", "C"),
],
)
segments = [
Segment([helix], exit="C"),
Segment([dimer], entry="N", exit="N"),
Segment([helix], entry="C", exit="N"),
Segment([trimer], entry="C", exit="C"),
Segment([helix], entry="N"),
]
w = grow(segments, Cyclic("C3"), thresh=1)
assert len(w) == 24
p = w.pose(0, end=True, cyclic_permute=0)
assert util.no_overlapping_residues(p)
# vis.show_with_axis(w, 0)
# vis.showme(p)
# print(residue_sym_err(p, 120, 2, 62, 7))
assert 0.3 > residue_sym_err(p, 120, 2, 62, 7)
def test_oct(c2pose, c3pose, c4pose, c1pose):
helix = Spliceable(c1pose, [(':1', 'N'), ('-4:', 'C')])
dimer = Spliceable(c2pose, sites=[
('1,:2', 'N'),
('1,-1:', 'C'),
])
trimer = Spliceable(c3pose, sites=[
('1,:1', 'N'),
('1,-2:', 'C'),
])
tetramer = Spliceable(c4pose, sites=[
('1,:1', 'N'),
('1,-2:', 'C'),
])
segments = ([Segment([dimer], exit='C')] +
[Segment([helix], entry='N', exit='C')] * 5 +
[Segment([trimer], entry='N')])
w = grow(segments, Octahedral(c3=-1, c2=0), thresh=1)
assert len(w) == 1
p = w.pose(0, only_connected=0)
assert util.no_overlapping_residues(p)
assert 1 > residue_sym_err(p, 120, 85, 94, 6, axis=[1, 1, 1])
assert 1 > residue_sym_err(p, 180, 1, 13, 6, axis=[1, 1, 0])
segments = ([Segment([tetramer], exit='C')] +
[Segment([helix], entry='N', exit='C')] * 5 +
[Segment([dimer], entry='N')])
w = grow(segments, Octahedral(c2=-1, c4=0), thresh=1)
assert len(w) == 5
assert np.allclose(
w.indices,
np.array([[0, 1, 1, 2, 0, 2, 1], [1, 0, 2, 3, 1, 0, 1],
[1, 0, 0, 0, 3, 2, 0], [0, 2, 0, 0, 1, 2, 0],
[1, 1, 2, 1, 1, 2, 0]]))
p = w.pose(0, only_connected=0)
assert p.sequence() == (
'AIAAALAAIAAIAAALAAIAAIAAALAAIAAIAAALAAAAAAAAAAGA' +
'AAAAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAAGAATAFLA' +
'AIPAINYTAFLAAIPAIN')
assert util.no_overlapping_residues(p)
# from socket import gethostname
# p.dump_pdb(gethostname() + '.pdb')
# assert np.allclose(p.residue(1).xyz('CA')[0], 33.0786722948)
assert 1 > residue_sym_err(p, 90, 1, 31, 6, axis=[1, 0, 0], verbose=0)
assert 1 > residue_sym_err(p, 180, 92, 104, 6, axis=[1, 1, 0], verbose=0)
def test_icos(c2pose, c3pose, c1pose):
helix = Spliceable(c1pose, [(':1', 'N'), ('-4:', 'C')])
dimer = Spliceable(c2pose, sites=[
('1,:2', 'N'),
('1,-1:', 'C'),
])
trimer = Spliceable(c3pose, sites=[
('1,:1', 'N'),
('1,-2:', 'C'),
])
segments = ([Segment([dimer], exit='C')] +
[Segment([helix], entry='N', exit='C')] * 5 +
[Segment([trimer], entry='N')])
w = grow(segments, Icosahedral(c3=-1, c2=0), thresh=2)
assert len(w) == 3
p = w.pose(2, only_connected=0)
assert util.no_overlapping_residues(p)
# vis.showme(p)
assert 2 > residue_sym_err(p, 120, 90, 99, 6, axis=IA[3])
assert 2 > residue_sym_err(p, 180, 2, 14, 6, axis=IA[2])
def test_multichain_mixed_pol(c2pose, c3pose, c1pose):
helix = Spliceable(c1pose, [(':4', 'N'), ((10, 12, 13), 'C')])
dimer = Spliceable(c2pose,
sites=[('1,:2', 'N'), ('1,-1:', 'C'), ('2,:2', 'N'),
('2,-1:', 'C')])
trimer = Spliceable(c3pose,
sites=[('1,:1', 'N'), ('1,-2:', 'C'), ('2,:2', 'N'),
('2,-2:', 'C'), ('3,:1', 'N'), ('3,-2:', 'C')])
segments = [
Segment([helix], exit='C'),
Segment([dimer], entry='N', exit='N'),
Segment([helix], entry='C', exit='N'),
Segment([trimer], entry='C', exit='C'),
Segment([helix], entry='N')
]
w = grow(segments, Cyclic('C3'), thresh=1)
assert len(w) == 24
p = w.pose(0, end=True, cyclic_permute=0)
assert util.no_overlapping_residues(p)
# vis.show_with_axis(w, 0)
# vis.showme(p)
# print(residue_sym_err(p, 120, 2, 62, 7))
assert 0.3 > residue_sym_err(p, 120, 2, 62, 7)