def make_polyglycine( chain_lengths, no_reserve=True):
from pyxmolpp2.polymer import Frame
from pyxmolpp2.polymer import ChainName
from pyxmolpp2.polymer import AtomName
from pyxmolpp2.polymer import ResidueName, ResidueId
from pyxmolpp2.geometry import XYZ
aid=1
rid=1
frame = Frame(0)
for chainId, N in chain_lengths:
if no_reserve:
c = frame.emplace(ChainName(chainId))
else:
c = frame.emplace(ChainName(chainId),N)
for i in range(N):
if no_reserve:
r = c.emplace(ResidueName("GLY"),ResidueId(rid))
else:
r = c.emplace(ResidueName("GLY"),ResidueId(rid),7)
rid+=1
for aname in ["N","H","CA","HA2","HA3","C","O"]:
r.emplace(AtomName(aname),aid,XYZ(1,2,3))
aid+=1
return frame
def test_Residue_setters():
from pyxmolpp2.polymer import ResidueName, ResidueId
frame = make_polyglycine([("A", 1)])
r = frame.asResidues[0]
r.name = ResidueName("X")
assert r.name == ResidueName("X")
r.rName = ResidueName("Y")
assert r.rName == ResidueName("Y")
r.id = ResidueId(5)
assert r.id == ResidueId(5)
r.rId = ResidueId(7)
assert r.rId == ResidueId(7)
def test_lookup_by_name():
from pyxmolpp2.polymer import ChainName, ResidueId, AtomName, \
OutOfRangeResidue, OutOfRangeFrame, OutOfRangeChain
frame = make_polyglycine([("A",2)])
frame[ChainName("A")] # does not throw
frame[ChainName("A")][ResidueId(2)] # does not throw
frame[ChainName("A")][ResidueId(2)][AtomName("CA")] # does not throw
frame[ChainName("A")][ResidueId(2)][AtomName("N")] # does not throw
with pytest.raises(OutOfRangeFrame):
frame[ChainName("B")] # does throw
with pytest.raises(OutOfRangeChain):
frame[ChainName("A")][ResidueId(3)] # does throw
with pytest.raises(OutOfRangeResidue):
frame[ChainName("A")][ResidueId(2)][AtomName("CX")] # does not throw
def test_residue_id():
from pyxmolpp2.polymer import rId, ResidueId, ResidueInsertionCode
frame = make_polyglycine([("A", 10)])
assert frame.asAtoms.filter(rId == 5).size == 1 * 7
assert frame.asAtoms.filter(rId.is_in({1, 2, 3})).size == 3 * 7
assert frame.asAtoms.filter(~rId.is_in({1, 2, 3})).size == 7 * 7
assert frame.asAtoms.filter((rId == 2) | (rId == 3)).size == 2 * 7
assert frame.asResidues.filter(rId == 5).size == 1
assert frame.asResidues.filter(rId.is_in({1, 2, 3})).size == 3
assert frame.asResidues.filter(~rId.is_in({1, 2, 3})).size == 7
assert frame.asResidues.filter((rId == 2) | (rId == 3)).size == 2
assert frame.asResidues.filter(
rId == ResidueId(5, ResidueInsertionCode("A"))).size == 0
def test_lookup_after_rename():
from pyxmolpp2.polymer import ChainName, ResidueId, AtomName, \
OutOfRangeResidue, OutOfRangeFrame, OutOfRangeChain
frame = make_polyglycine([("A",2)])
frame[ChainName("A")] # does not throw
frame[ChainName("A")][ResidueId(2)] # does not throw
frame[ChainName("A")][ResidueId(2)][AtomName("CA")] # does not throw
frame[ChainName("A")][ResidueId(2)][AtomName("CA")].name = AtomName("CX")
frame[ChainName("A")][ResidueId(2)].id = ResidueId(99)
frame[ChainName("A")].name = ChainName("X")
frame[ChainName("X")] # does not throw
frame[ChainName("X")][ResidueId(99)] # does not throw
frame[ChainName("X")][ResidueId(99)][AtomName("CX")] # does not throw
def test_Frame():
from pyxmolpp2.polymer import Frame
from pyxmolpp2.polymer import ChainName
from pyxmolpp2.polymer import AtomName
from pyxmolpp2.polymer import ResidueName, ResidueId
from pyxmolpp2.geometry import XYZ
f = Frame(5)
c = f.emplace(ChainName("A"), 1)
r = c.emplace(ResidueName("LYS"), ResidueId(1))
a = r.emplace(AtomName("CA"), 1, XYZ(1,2,3))
assert a.residue == r
assert a.chain == c
assert a.frame == f
assert r.asAtoms[0] == a
assert c.asAtoms[0] == a
assert f.asAtoms[0] == a
assert r.asAtoms.asResidues[0] == r
assert c.asAtoms.asResidues[0] == r
assert f.asAtoms.asResidues[0] == r
assert r.asAtoms.asResidues.asChains[0] == c
assert c.asAtoms.asResidues.asChains[0] == c
assert f.asAtoms.asResidues.asChains[0] == c
assert r.chain == c
assert r.frame == f
assert c.frame == f
assert c.asResidues[0] == r
assert f.asResidues[0] == r
assert f.asChains[0] == c