def pack_sequences(structure, lines):
try:
for chain in sorted(structure.chains(), key=lambda c: c.id):
residues = valerius.from_string(chain.sequence).codes
length = len(residues)
line_count = ceil(length / 13)
for line_num in range(line_count):
lines += ["SEQRES {:>3} {} {:>4} {}".format(
line_num + 1, chain.id, length,
" ".join(residues[line_num * 13: (line_num + 1) * 13])
)]
except AttributeError: pass
def pack_sequences(structure, lines):
"""Adds SEQRES lines from polymer sequence data.
:param AtomStructure structure: the structure to convert.
:param list lines: the string lines to update."""
try:
for chain in sorted(structure.chains(), key=lambda c: c.id):
residues = valerius.from_string(chain.sequence).codes
length = len(residues)
line_count = ceil(length / 13)
for line_num in range(line_count):
lines += [
"SEQRES {:>3} {} {:>4} {}".format(
line_num + 1, chain.id, length,
" ".join(residues[line_num * 13:(line_num + 1) * 13]))
]
except AttributeError:
pass
def update_lines_with_entities(lines, entities):
"""Updates a list of .cif lines with relevant information about entities.
:param list lines: the list of lines to update.
:param list entities: the entities to pack."""
lines += ["#", "loop_", "_entity.id", "_entity.type"]
for i, entity in enumerate(entities, start=1):
lines.append("{} {}".format(i, "polymer" if isinstance(entity, Chain)
else "water" if entity.water else "non-polymer"))
if any(isinstance(entity, Chain) for entity in entities):
lines += ["#", "loop_", "_entity_poly_seq.entity_id",
"_entity_poly_seq.num", "_entity_poly_seq.mon_id"]
for ei, entity in enumerate(entities, start=1):
if isinstance(entity, Chain):
for ci, code in enumerate(
valerius.from_string(entity.sequence).codes, start=1
):
lines.append("{} {} {}".format(ei, ci, code))
def update_lines_with_entities(lines, entities):
"""Updates a list of .cif lines with relevant information about entities.
:param list lines: the list of lines to update.
:param list entities: the entities to pack."""
lines += ["#", "loop_", "_entity.id", "_entity.type"]
for i, entity in enumerate(entities, start=1):
lines.append("{} {}".format(i, "polymer" if isinstance(entity, Chain)
else "water" if entity.is_water else "non-polymer"))
if any(isinstance(entity, Chain) for entity in entities):
lines += ["#", "loop_", "_entity_poly_seq.entity_id",
"_entity_poly_seq.num", "_entity_poly_seq.mon_id"]
for ei, entity in enumerate(entities, start=1):
if isinstance(entity, Chain):
for ci, code in enumerate(
valerius.from_string(entity.sequence).codes, start=1
):
lines.append("{} {} {}".format(ei, ci, code))