def serialize_efm(S, efm_id, model, path):
efm_txt = os.path.join(path, '%s.txt' % efm_id)
initial_r_ids = {r_id for r_id in S.r_id2i.keys() if r_id not in S.gr_id2r_id2c}
r_id2c = S.pws.get_r_id2coeff(efm_id, r_ids=initial_r_ids)
with open(efm_txt, 'w+') as f:
f.write('EFM %s of length %d\n\n' % (efm_id, len(r_id2c)))
write_inputs_outputs(f, model, S.get_boundary_inputs_outputs(efm_id))
f.write(THIN_DELIMITER)
write_detailed_r_id2c(model, r_id2c, f)
return efm_txt
def write_pathway(model, pathway_id, S, get_key, f):
write_inputs_outputs(f, model, S.get_boundary_inputs_outputs(pathway_id))
if pathway_id not in S.pathways:
write_folded_efm(f_efm_id=pathway_id, S=S, get_key=get_key, f=f)
return
f.write('%s of length %d:\n\n\t%s\n\n'
% (pathway_id, S.get_len(pathway_id),
r_id2c_to_string(S.pws.get_r_id2coeff(pathway_id, r_ids=S.r_ids), get_key=get_key)))
folded_efm_ids = S.gr_id2efm_ids[pathway_id]
f.write('\tContains %d elements:\n\n' % len(folded_efm_ids))
started = False
for f_efm_id in folded_efm_ids:
if started:
f.write('\t\t%s' % THIN_DELIMITER)
else:
started = True
write_folded_efm(f_efm_id=f_efm_id, S=S, get_key=get_key, f=f, tab='\t\t')
def serialize_coupled_reaction_groups(model, path, **kwargs):
S = kwargs["S"]
coupled_r_ids = S.coupled_rs
r_types = S.r_types
initial_efm_ids = [efm_id for efm_id in S.efm_id2i.keys() if efm_id not in S.gr_id2efm_ids]
def write_coupled_rn_group(cr_id, inverted=False, tab=""):
r_id2c = S.gr_id2r_id2c[cr_id]
f.write(
"%sCoupled reaction group %s of length %d%s:\n\n\t\t%s\n\n"
% (
tab,
cr_id,
len(r_id2c),
" (Inputs and Outputs are inverted)" if inverted else "",
r_id2c_to_string(r_id2c),
)
)
efm_ids = sorted(S.get_efm_ids_by_r_id(cr_id, efm_ids=initial_efm_ids))
f.write("%sFound in %d EFMs: %s.\n\n" % (tab, len(efm_ids), ", ".join((str(efm_id) for efm_id in efm_ids))))
rgroups_txt = os.path.join(path, "coupled_reactions.txt")
with open(rgroups_txt, "w+") as f:
f.write("Found %d coupled reaction groups.\n\n" % len(coupled_r_ids))
f.write(THICK_DELIMITER)
# types that include coupled reactions
for rtype_id in sorted(
(rtype_id for rtype_id in r_types if set(S.gr_id2r_id2c[rtype_id].keys()) & coupled_r_ids),
key=lambda rtype_id: (-len(S.gr_id2r_id2c[rtype_id]), rtype_id),
):
r_id2c = S.gr_id2r_id2c[rtype_id]
cur_r_ids = set(r_id2c.keys())
cur_coupled_ids = cur_r_ids & coupled_r_ids
cur_simple_ids = cur_r_ids - coupled_r_ids
write_inputs_outputs(f, model, S.st_matrix.get_inputs_outputs(rtype_id))
f.write(
"Type %s common to %d reaction group%s%s:\n\n"
% (
rtype_id,
len(cur_coupled_ids),
"s" if len(cur_coupled_ids) != 1 else "",
(" and %d reaction%s" % (len(cur_simple_ids), "s" if len(cur_simple_ids) > 1 else ""))
if cur_simple_ids
else "",
)
)
f.write(THIN_DELIMITER)
for cr_id in sorted(cur_coupled_ids, key=lambda lr_id: (-len(S.gr_id2r_id2c[lr_id]), lr_id)):
write_coupled_rn_group(cr_id, inverted=r_id2c[cr_id] < 0, tab="\t")
f.write("\t%s" % THIN_DELIMITER)
if cur_simple_ids:
f.write(
"\tReaction%s %s also ha%s the same structure.\n\n"
% (
"s" if len(cur_simple_ids) != 1 else "",
", ".join((("-%s" % r_id) if r_id2c[r_id] < 0 else r_id for r_id in sorted(cur_simple_ids))),
"s" if len(cur_simple_ids) == 1 else "ve",
)
)
f.write(THICK_DELIMITER)
# coupled reaction that form an unique type
for cr_id in sorted(S.coupled_rs & S.r_ids, key=lambda lr_id: (-len(S.gr_id2r_id2c[lr_id]), lr_id)):
write_inputs_outputs(f, model, S.st_matrix.get_inputs_outputs(cr_id))
write_coupled_rn_group(cr_id)
f.write(THICK_DELIMITER)
# non-coupled reaction groups
f.write(THICK_DELIMITER)
for rtype_id in sorted(
(rtype_id for rtype_id in r_types if not set(S.gr_id2r_id2c[rtype_id].keys()) & coupled_r_ids),
key=lambda rtype_id: (-len(S.gr_id2r_id2c[rtype_id]), rtype_id),
):
write_inputs_outputs(f, model, S.st_matrix.get_inputs_outputs(rtype_id))
r_id2c = S.gr_id2r_id2c[rtype_id]
f.write(
"Type %s is common to reaction%s %s.\n\n"
% (
rtype_id,
"s" if len(r_id2c) != 1 else "",
", ".join((("-%s" % r_id) if r_id2c[r_id] < 0 else r_id for r_id in sorted(r_id2c.keys()))),
)
)
f.write(THICK_DELIMITER)
return rgroups_txt, len(coupled_r_ids)
