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_dumb_copy_lookup():
from pyxmolpp2.polymer import Frame
frame = make_polyglycine([("A", 3),("B", 3)])
frame2 = Frame(2)
for c in frame.asChains:
frame2.emplace(c)
assert frame.asChains.size == frame2.asChains.size
assert frame.asResidues.size == frame2.asResidues.size
assert frame.asAtoms.size == frame2.asAtoms.size
for x in frame2.asAtoms:
assert x.residue[x.name] == x
for x in frame2.asResidues:
assert x.chain[x.id] == x
for x in frame2.asChains:
assert x.frame[x.name] == x
assert x.frame == frame2
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
# For sake of simplicity let's number them in reverse order
atoms = frame.asAtoms
for i, a in enumerate(atoms):
a.id = atoms.size - i
# New atom ids:
print([a.id for a in frame.asAtoms])
##############################################################################
# As you can see `atom.id` does not affect atom order.
# To change that we need to construct new Frame with desired order of atoms:
from pyxmolpp2.polymer import Frame
new_frame = Frame(0) # create empty frame with index=0
for chain in frame.asChains:
new_chain = new_frame.emplace(
chain.name) # create empty chain with same name
for residue in frame.asResidues:
new_residue = new_chain.emplace(
residue.name,
residue.id) # create empty residue with same name and id
for a in sorted(list(residue.asAtoms), key=lambda a: a.id):
new_atom = new_residue.emplace(a) # create a copy of atom `a`
# New frame atoms ids:
print([a.id for a in new_frame.asAtoms])