def get_residue(self, seq):
"""Get the residue in ``seq`` that is at this alignment position,
or None if a gap is present."""
aln = self.__aln
if not isinstance(seq, alnsequence.Sequence):
raise TypeError("Expected an alignment 'Sequence' object for seq")
if seq.aln != aln:
raise ValueError("seq must be a sequence in the same alignment")
ialn = _modeller.mod_alignment_ialn_get(aln.modpt)
ires = _modeller.mod_int2_get(ialn, self.__indx, seq._num)
if ires == 0:
return None
else:
return seq.residues[ires-1]
def get_residue(self, seq):
"""Get the residue in C{seq} that is at this profile position, or None
if a gap is present."""
prf = self.__prf
if not isinstance(seq, Sequence):
raise TypeError("Expected a profile 'Sequence' object for seq")
if seq._prf != prf:
raise ValueError("seq must be a sequence in the same profile")
sprofile = _modeller.mod_profile_sprofile_get(prf.modpt)
irestyp = _modeller.mod_int2_get(sprofile, self.__indx, seq._num)
if irestyp == 21: # 21 = gap
return None
else:
return Residue(prf, 0, irestyp)
def _getfunc(self, indx):
indarray = self.__getfunc(self.__mtp)
inds = [_modeller.mod_int2_get(indarray, i, indx) \
for i in range(self.__natm)]
ats = self.__mdl.atoms
return [ats[i - 1] for i in inds]
def get_position(self):
"""Get the position in the alignment of this residue"""
invaln = _modeller.mod_alignment_invaln_get(self.mdl.aln.modpt)
num = _modeller.mod_int2_get(invaln, self._num, self.mdl._num)
return self.mdl.aln.positions[num - 1]