def _cmp_atm(r0: Residue, r1: Residue, a0: Atom, a1: Atom, verbose: bool,
cmpdict: Dict) -> None:
cmpdict["aCount"] += 1
if a0 is None:
if verbose:
print(r1.get_full_id(), "None !=", a1.get_full_id(),
a1.parent.resname)
elif a1 is None:
if verbose:
print(r0.get_full_id(), a0.get_full_id(), a0.parent.resname,
"!= None")
else:
if a0.get_full_id() == a1.get_full_id():
cmpdict["aFullIdMatchCount"] += 1
elif verbose:
print(
r0.get_full_id(),
a0.get_full_id(),
a0.parent.resname,
"!=",
a1.get_full_id(),
)
a0c = a0.get_coord()
a1c = a1.get_coord()
if numpy.allclose(a0c, a1c, rtol=1e-05, atol=1e-08):
cmpdict["aCoordMatchCount"] += 1
elif verbose:
print(
"atom coords disagree:",
r0.get_full_id(),
a0.get_full_id(),
a1.get_full_id(),
a0c,
"!=",
a1c,
)
def _cmp_atm(
r0: Residue,
r1: Residue,
a0: Atom,
a1: Atom,
verbose: bool,
cmpdict: Dict,
rtol: float = None,
atol: float = None,
) -> None:
cmpdict["aCount"] += 1
if a0 is None:
if verbose:
print(
r1.get_full_id(),
"None !=",
a1.get_full_id(),
a1.parent.resname,
)
elif a1 is None:
if verbose:
print(
r0.get_full_id(),
a0.get_full_id(),
a0.parent.resname,
"!= None",
)
else:
if a0.get_full_id() == a1.get_full_id() or _atmfid_d2h(
a0) == a1.get_full_id():
cmpdict["aFullIdMatchCount"] += 1
elif verbose:
print(
r0.get_full_id(),
a0.get_full_id(),
a0.parent.resname,
"!=",
a1.get_full_id(),
)
ac_rslt = False
if rtol is None and atol is None:
a0c = numpy.round(a0.get_coord(), 3)
a1c = numpy.round(a1.get_coord(), 3)
ac_rslt = numpy.array_equal(a0c, a1c)
else:
a0c = a0.get_coord()
a1c = a1.get_coord()
ac_rslt = numpy.allclose(a0c, a1c, rtol=rtol, atol=atol)
if ac_rslt:
cmpdict["aCoordMatchCount"] += 1
elif verbose:
print(
"atom coords disagree:",
r0.get_full_id(),
a0.get_full_id(),
a1.get_full_id(),
a0c,
"!=",
a1c,
)
def _atmfid_d2h(atm: Atom) -> Tuple:
afid = list(atm.get_full_id())
afid4 = list(afid[4])
afid40 = re.sub("D", "H", afid4[0], count=1)
new_afid = (afid[0], afid[1], afid[2], afid[3], (afid40, afid4[1]))
return tuple(new_afid)