Skip to content

fix(rp2erxn.py): skips without failure transformation having dot-cont… #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
tduigou merged 1 commit into from
Oct 29, 2025
Merged

fix(rp2erxn.py): skips without failure transformation having dot-cont… #8

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 28 additions & 5 deletions rp2paths/rp2erxn.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@ def compute(infile, cmpdfile='compounds.txt', rxnfile='reactions.txt',

# 1) Check consistency and 2) Populate compounds
all_cmpds = dict()
banished_trs = set()
for tid in sorted(content.keys()): # Order determine CMPD IDs
first = True
for row in content[tid]:
Expand Down Expand Up @@ -228,20 +229,42 @@ def compute(infile, cmpdfile='compounds.txt', rxnfile='reactions.txt',
sys.exit(0)
try:
assert prods_from_rxn == prods_from_cmpd
except BaseException:
print('Assertion error: differences in products')
print(tid)
print(prods_from_rxn, prods_from_cmpd)
sys.exit(0)
except AssertionError:
if any("." in smi for smi in prods_from_cmpd):
print(
"Unexpected multiple products detected in 'Product "
"SMILES' column from RetroPath2.0 result file. This "
"is likely due to a sanitization issue from "
"RetroPath2.0 result file."
)
print(f" L Transformation skipped: {tid}")
print(f" L Products from reaction: {prods_from_rxn}")
print(f" L Products from 'Product SMILES' column: {prods_from_cmpd}")
banished_trs.add(tid)
continue
else:
print('Assertion error: differences in products')
print(tid)
print(prods_from_rxn, prods_from_cmpd)
sys.exit(0)
# Populate
for smi in sorted(list(subs_from_rxn | prods_from_rxn)):
if smi not in all_cmpds.keys():
cmpd = Compound(smi)
all_cmpds[smi] = cmpd

# Debug info
if len(banished_trs) > 0:
print(f"Total transformations skipped: {len(banished_trs)}")
for tid in sorted(banished_trs):
print(f" - {tid}")

# Populate transformations
all_trs = dict()
for tid in content.keys():
# Skip transformations that were marked as banished
if tid in banished_trs:
continue
first = True
for row in content[tid]:
if first:
Expand Down
Loading