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rpextractsink #49

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2bbbe77
fix(rpextractsink): handle cmpd info not found from URL
breakthewall Dec 17, 2025
579c441
feat: --forward + integrate new rrCache
breakthewall Feb 20, 2026
47e4f33
feat (rpviz): Toggle panels
breakthewall Feb 20, 2026
706b6c4
chore: new rrCache
breakthewall Feb 20, 2026
2a7d7cb
fix(rpscore): consider None value for molecule
breakthewall Feb 20, 2026
cc07263
fix(rpthermo): rm exit()
breakthewall Feb 20, 2026
465c57e
fix(rpthermo): rm debug exit()
breakthewall Feb 20, 2026
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5 changes: 5 additions & 0 deletions rptools/rpcompletion/Args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,11 @@ def add_arguments(parser: ArgumentParser) -> ArgumentParser:
help='Name of the file containing the list of cofactors to ignore (default: None)',
default=None
)
parser.add_argument(
'--forward', dest='forward',
help='Consider reactions in the forward direction',
required=False, action='store_true'
)
# parser.add_argument('--pathway_id', type=str, default='rp_pathway')
# parser.add_argument('--compartment_id', type=str, default='MNXC3')
# parser.add_argument('--species_group_id', type=str, default='rp_trunk_species')
Expand Down
4 changes: 3 additions & 1 deletion rptools/rpcompletion/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,15 +66,17 @@ def _cli():
lower_flux_bound=int(args.lower_flux_bound),
maxsubpaths=args.maxsubpaths,
cofile=args.cofactors,
forward=args.forward,
logger=logger
)

# WRITE OUT
if not os_path.exists(args.outdir):
os_mkdir(args.outdir)
# Write out selected pathways
local_cache = {}
for pathway in pathways:
pathway.to_rpSBML().write_to_file(
pathway.to_rpSBML(cache=cache, local_cache=local_cache).write_to_file(
os_path.join(
args.outdir,
pathway.get_id()
Expand Down
101 changes: 67 additions & 34 deletions rptools/rpcompletion/rpcompletion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ def rp_completion(
lower_flux_bound: float = default_lower_flux_bound,
maxsubpaths: int = default_maxsubpaths,
cofile: str = default_cofactors,
forward: bool = False,
logger: Logger = getLogger(__name__)
) -> List[rpPathway]:
"""Process to the completion of metabolic pathways
Expand Down Expand Up @@ -140,6 +141,7 @@ def rp_completion(
ec_numbers=ec_numbers,
cache=cache,
cofactors=cofactors,
forward=forward,
logger=logger
)

Expand All @@ -159,8 +161,7 @@ def rp_completion(
pathways=pathway_combinatorics,
transfos=full_transfos,
sink_molecules=sink_molecules,
rr_reactions=cache.get('rr_reactions'),
compounds_cache=cache.get('cid_strc'),
cache=cache,
maxsubpaths=maxsubpaths,
lower_flux_bound=lower_flux_bound,
upper_flux_bound=upper_flux_bound,
Expand All @@ -175,6 +176,7 @@ def __complete_transformations(
ec_numbers: Dict,
cache: rrCache,
cofactors: List[str] = [],
forward: bool = False,
logger: Logger = getLogger(__name__)
) -> Dict:
"""From template reactions, put back chemical species
Expand Down Expand Up @@ -206,15 +208,8 @@ def __complete_transformations(
# For each transformation
for transfo_id, transfo in transfos.items():
logger.debug(f'transfo_id: {transfo_id}, transfo: {transfo}')

full_transfos[transfo_id] = {}
full_transfos[transfo_id]['ec'] = ec_numbers[transfo_id]['ec']
# Convert transformation into SMILES
transfo_smi = '{left}>>{right}'.format(
left=__build_smiles(transfo['left']),
right=__build_smiles(transfo['right'])
)
logger.debug(f'transfo_smi: {transfo_smi}')

# Add compounds of the current transformation
full_transfos[transfo_id]['left'] = dict(transfos[transfo_id]['left'])
Expand All @@ -226,25 +221,39 @@ def __complete_transformations(

# MULTIPLE RR FOR ONE TRANSFO
for rule_id in transfo['rule_ids']:
logger.debug(f'rule_id: {rule_id}')

# MULTIPLE TEMPLATE REACTIONS FOR ONE RR
# If 'tmpl_rxn_id' is not given,
# the transformation will be completed
# for each template reaction from reaction rule was built from
try:
full_transfos[transfo_id]['complement'][rule_id] = rebuild_rxn(
# Convert transformation into SMILES
left_smiles = __build_smiles(transfo['left'])
right_smiles = __build_smiles(transfo['right'])
logger.debug(f'transfo_smi: {left_smiles}>>{right_smiles}')
if forward:
transfo_smi = f'{left_smiles}>>{right_smiles}'
else:
transfo_smi = f'{right_smiles}>>{left_smiles}'
full_transfo = rebuild_rxn(
cache=cache,
rxn_rule_id=rule_id,
transfo=transfo_smi,
direction='forward',
cmpds_to_ignore=cofactors,
cspace=cache.get('cspace'),
# tmpl_rxn_id=tmpl_rxn_id,
cspace=cache.get_cspace(),
cspace_type=cache.get_type(),
logger=logger
)
if not forward:
for rxn_id, _transfo in full_transfo.items():
_transfo['full_transfo']['right'], _transfo['full_transfo']['left'] = _transfo['full_transfo']['left'], _transfo['full_transfo']['right']
_transfo['added_cmpds']['right'], _transfo['added_cmpds']['left'] = _transfo['added_cmpds']['left'], _transfo['added_cmpds']['right']
full_transfos[transfo_id]['complement'][rule_id] = deepcopy(full_transfo)
logger.debug(f'full_transfos[{transfo_id}]["complement"][{rule_id}]: {full_transfos[transfo_id]["complement"][rule_id]}')
except KeyError as e:
logger.error(f'Could not find reaction rule {rule_id} in the cache. Are you in the right data type space?')
# logger.error(f'Could not find reaction rule {rule_id} in the cache. Are you in the right chemical space (mnx3.1, mnx4.4, rr2026...)?')
logger.error(e)
exit(1)

return full_transfos
Expand Down Expand Up @@ -292,14 +301,24 @@ def __build_smiles(
Parameters
----------
side: Dict
Stoichiometric chemical reaction side
Stoichiometric chemical reaction side with species IDs as keys
and stoichiometric coefficients as values
logger: Logger, optional

Returns
-------
SMILES string
"""
return '.'.join([Cache.get(spe_id).get_smiles() for spe_id in side.keys()])
logger.debug(f'side: {side}')
smiles_list = []
for spe_id, stoichio_coeff in side.items():
logger.debug(f'spe_id: {spe_id}, sto_coeff: {stoichio_coeff}')
spe_smiles = Cache.get(spe_id).get_smiles()
# Repeat SMILES based on stoichiometric coefficient
smiles_list.extend([spe_smiles] * int(stoichio_coeff))

result = '.'.join(smiles_list)
return result


def __build_reader(
Expand Down Expand Up @@ -426,7 +445,8 @@ def __get_compound_from_cache(
resConv = cache._convert_depiction(
idepic=smiles,
itype='smiles',
otype={'inchi'}
otype={'inchi'},
logger=logger
)
inchi = resConv['inchi']
except NotImplementedError as e:
Expand All @@ -440,7 +460,8 @@ def __get_compound_from_cache(
resConv = cache._convert_depiction(
idepic=smiles,
itype='smiles',
otype={'inchikey'}
otype={'inchikey'},
logger=logger
)
inchikey = resConv['inchikey']
except NotImplementedError as e:
Expand Down Expand Up @@ -581,6 +602,8 @@ def __read_pathways(
for compound in compounds:
sto, spe = compound.split('.')
transfos[transfo_id][side][spe] = int(sto)
# if sto != '1':
# print(transfos[transfo_id])

return pathways, transfos

Expand Down Expand Up @@ -655,7 +678,7 @@ def __build_pathway_combinatorics(
'left': dict(full_transfos[transfo_id]['left'])
}
except KeyError as e:
logger.error(f'Could not find transformation {transfo_id} in the cache. Are you in the right data type space?')
logger.error(f'Could not find transformation {transfo_id} in the cache. Are you in the right chemical space (mnx3.1, mnx4.4, rr2026...)?')
exit(1)
# Build list of transformations
# where each transfo can correspond to multiple reactions
Expand Down Expand Up @@ -696,8 +719,7 @@ def __build_all_pathways(
pathways: Dict,
transfos: Dict,
sink_molecules: List,
rr_reactions: Dict,
compounds_cache: Dict,
cache: rrCache,
maxsubpaths: int,
lower_flux_bound: float,
upper_flux_bound: float,
Expand All @@ -719,10 +741,8 @@ def __build_all_pathways(
Full chemical transformations
sink_molecules: List
Sink chemical species IDs
rr_reactions: Dict
Reaction rules cache
compounds_cache: Dict
Compounds cache
cache: rrCache
Cache that contains reaction rules, reactions and compounds data
maxsubpaths: int
Number of pathways (best) kept per master pathway, after completion
lower_flux_bound: float
Expand All @@ -736,6 +756,17 @@ def __build_all_pathways(
Set of ranked rpPathway objects
"""

logger.debug(f'pathways: {pathways}')
logger.debug(f'transfos: {transfos}')
logger.debug(f'sink_molecules: {sink_molecules}')
logger.debug(f'cache: {cache}')
logger.debug(f'maxsubpaths: {maxsubpaths}')
logger.debug(f'lower_flux_bound: {lower_flux_bound}')
logger.debug(f'upper_flux_bound: {upper_flux_bound}')

rr_reactions=cache.get('rr_reactions')
compounds_cache=cache.get('cid_strc')

res_pathways = {}

nb_pathways = 0
Expand Down Expand Up @@ -771,8 +802,10 @@ def __build_all_pathways(
## COMPOUNDS
# Template reaction compounds
added_cmpds = transfo['complement'][rule_ids][tmpl_rxn_id]['added_cmpds']

# Add missing compounds to the cache
for side in added_cmpds.keys():
# Compounds with no structure are in '<side>_nostruct'
for spe_id in added_cmpds[side].keys():
logger.debug(f'Add missing compound {spe_id}')
if spe_id not in Cache.get_objects():
Expand Down Expand Up @@ -937,17 +970,17 @@ def __add_compounds(
return _compounds
for side in ['right', 'left']:
# added compounds with struct
for cmpd_id, cmpd in compounds_to_add[side].items():
if cmpd_id in _compounds[side]:
_compounds[side][cmpd_id] += cmpd['stoichio']
else:
_compounds[side][cmpd_id] = cmpd['stoichio']
# added compounds with no struct
for cmpd_id, cmpd in compounds_to_add[side+'_nostruct'].items():
for cmpd_id, cmpd_sto in compounds_to_add[side].items():
if cmpd_id in _compounds[side]:
_compounds[side][cmpd_id] += cmpd['stoichio']
_compounds[side][cmpd_id] += cmpd_sto
else:
_compounds[side][cmpd_id] = cmpd['stoichio']
_compounds[side][cmpd_id] = cmpd_sto
# # added compounds with no struct
# for cmpd_id, cmpd in compounds_to_add[side+'_nostruct'].items():
# if cmpd_id in _compounds[side]:
# _compounds[side][cmpd_id] += cmpd['stoichio']
# else:
# _compounds[side][cmpd_id] = cmpd['stoichio']
return _compounds


Expand Down
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