def _format_alignment_with_ligands(self, template, aligned_template_seq):
from MDAnalysis.lib.util import convert_aa_code
sel = template.universe.select_atoms("protein and name CA")
resnames = sel.resnames.tolist()
resnames_one_letter = [convert_aa_code(x) for x in resnames]
# get the last four AAs in the aligned target sequence
end_chunk = aligned_template_seq[-4:][::-1]
aa_store = []
# loop over residues in reverse
for i, letter in enumerate(resnames_one_letter[::-1]):
# read a chunk of four AAs
current_chunk = resnames_one_letter[::-1][i : i + 4]
# if the end of the aligned target sequence is hit, stop
if current_chunk == end_chunk:
break
# otherwise store the one letter AAs that need to be added
else:
aa_store.append(letter)
# create a one element list of dashes
dashes = "".join(["-" for x in aa_store])
# create one element list of AAs in the canonical order
amino_acids = "".join(aa_store[::-1])
return amino_acids, dashes
def sequence(self):
from MDAnalysis.lib.util import convert_aa_code
pdb_seq = []
three_l_codes = [
convert_aa_code(i) for i in list(AminoAcidSequence.ALPHABET)
]
for r in self.universe.residues:
if r.resname in three_l_codes:
pdb_seq.append(convert_aa_code(r.resname))
else:
continue
s = "".join(pdb_seq)
return AminoAcidSequence(s)
def test_ValueError(self, x):
with pytest.raises(ValueError):
util.convert_aa_code(x)
def test_convert_aa_1to3(self, resname1, strings):
assert util.convert_aa_code(resname1) == strings[0]
def test_convert_aa_3to1(self, resname3, resname1):
assert util.convert_aa_code(resname3) == resname1
def check_convert_aa_1to3(resname1, resname3_canonical):
assert_equal(util.convert_aa_code(resname1), resname3_canonical)
def check_convert_aa_3to1(resname3, resname1):
assert_equal(util.convert_aa_code(resname3), resname1)
def check_convert_aa_1to3(resname1, resname3_canonical):
assert_equal(util.convert_aa_code(resname1), resname3_canonical)
def check_convert_aa_3to1(resname3, resname1):
assert_equal(util.convert_aa_code(resname3), resname1)
def convert3to1(aminoList):
from MDAnalysis.lib.util import convert_aa_code
out = []
for r in aminoList:
out.append(convert_aa_code(r))
return out
