def __init__(self, res:Residue):
fullid = list( res.get_full_id() )
self.structure = fullid[0]
self.model = fullid[1]
self.strand_id = fullid[2]
self.chemicalName = res.get_resname()
self.residue_id = [*fullid[3]][1]
def __init__(self, res: Residue):
fid = list(res.get_full_id())
self.model: int = fid[1]
self.resname: str = fid[3][0]
self.struct: str = fid[0]
self.chemicalName: str = res.get_resname()
self.strand_id: str = fid[2]
self.residue_id: int = [*fid[3]][1]
self.banClass: str = ""
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_res(r0: Residue, r1: Residue, verbose: bool, cmpdict: Dict) -> None:
r0id, r0fid, r1fid = r0.id, r0.full_id, r1.full_id
chn = r0.parent.id
if chn not in cmpdict["chains"]:
cmpdict["chains"].append(chn)
cmpdict["rCount"] += 1
if r0fid == r1fid:
cmpdict["rMatchCount"] += 1
elif verbose:
print(r0fid, "!=", r1fid)
if " " == r0id[0] and not (" " == r0.resname[0] or 2 == len(r0.resname)):
# skip water, DNA (' ' == [0] for pdb, 2 == len() for mmcif)
cmpdict["residues"] += 1
longer = r0 if len(r0.child_dict) >= len(r1.child_dict) else r1
for ak in longer.child_dict:
a0 = r0.child_dict.get(ak, None)
if a0 is None:
aknd = re.sub("D", "H", ak, count=1)
a0 = r0.child_dict.get(aknd, None)
a1 = r1.child_dict.get(ak, None)
if a1 is None:
aknd = re.sub("D", "H", ak, count=1)
a1 = r1.child_dict.get(aknd, None)
if (a0 is None or a1 is None
or 0 == a0.is_disordered() == a1.is_disordered()):
_cmp_atm(r0, r1, a0, a1, verbose, cmpdict)
elif 2 == a0.is_disordered() == a1.is_disordered():
cmpdict["disAtmCount"] += 1
for da0k in a0.child_dict:
_cmp_atm(
r0,
r1,
a0.child_dict.get(da0k, None),
a1.child_dict.get(da0k, None),
verbose,
cmpdict,
)
else:
if verbose:
print("disorder disagreement:", r0.get_full_id(), ak)
cmpdict["aCount"] += 1
def __init__(self, res:Residue):
fid = list(res.get_full_id())
self.resn = fid[3][0]
self.struct = fid[0]
self.strand_id = fid[2]
self.residue_id = [*fid[3]][1]
def _cmp_res(
r0: Residue,
r1: Residue,
verbose: bool,
cmpdict: Dict,
rtol: float = None,
atol: float = None,
) -> None:
r0id, r0fid, r1fid = r0.id, r0.full_id, r1.full_id
chn = r0.parent.id
if chn not in cmpdict["chains"]:
cmpdict["chains"].append(chn)
cmpdict["rCount"] += 1
if r0fid == r1fid:
cmpdict["rMatchCount"] += 1
elif verbose:
print(r0fid, "!=", r1fid)
if hasattr(r0, "internal_coord") and r0.internal_coord is not None:
ric0 = r0.internal_coord
ric1 = r1.internal_coord
r0prev = sorted((ric.rbase for ric in ric0.rprev))
r1prev = sorted((ric.rbase for ric in ric1.rprev))
r0next = sorted((ric.rbase for ric in ric0.rnext))
r1next = sorted((ric.rbase for ric in ric1.rnext))
if r0prev != r1prev:
if verbose:
print(r0, "rprev error:", r0prev, "!=", r1prev)
cmpdict["rpnMismatchCount"] += 1
if r0next != r1next:
if verbose:
print(r0, "rnext error", r0next, "!=", r1next)
cmpdict["rpnMismatchCount"] += 1
if " " == r0id[0] and not (" " == r0.resname[0] or 2 == len(r0.resname)):
# skip water, DNA (' ' == [0] for pdb, 2 == len() for mmcif)
cmpdict["residues"] += 1
longer = r0 if len(r0.child_dict) >= len(r1.child_dict) else r1
for ak in longer.child_dict:
a0 = r0.child_dict.get(ak, None)
if a0 is None:
aknd = re.sub("D", "H", ak, count=1)
a0 = r0.child_dict.get(aknd, None)
a1 = r1.child_dict.get(ak, None)
if a1 is None:
aknd = re.sub("D", "H", ak, count=1)
a1 = r1.child_dict.get(aknd, None)
if (a0 is None or a1 is None
or 0 == a0.is_disordered() == a1.is_disordered()):
_cmp_atm(r0,
r1,
a0,
a1,
verbose,
cmpdict,
rtol=rtol,
atol=atol)
elif 2 == a0.is_disordered() == a1.is_disordered():
cmpdict["disAtmCount"] += 1
for da0k in a0.child_dict:
_cmp_atm(
r0,
r1,
a0.child_dict.get(da0k, None),
a1.child_dict.get(da0k, None),
verbose,
cmpdict,
rtol=rtol,
atol=atol,
)
else:
if verbose:
print("disorder disagreement:", r0.get_full_id(), ak)
cmpdict["aCount"] += 1
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,
)