Skip to content

#3661 BILN import/export special cases #3662

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

Open
even1024 wants to merge 12 commits into
base: release/1.44
Choose a base branch
from
Open

#3661 BILN import/export special cases #3662

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
f53ec5a
biln fix
even1024 May 15, 2026
487e0a3
Fix BILN import/export
even1024 May 15, 2026
65fd079
clang fix
even1024 May 15, 2026
64e2b1f
remote fix
even1024 May 15, 2026
4c11a07
black fix
even1024 May 15, 2026
132b799
Fix BILN edge cases
even1024 May 18, 2026
8da0354
Fix BILN cap validation
even1024 May 18, 2026
64eabbf
Apply BILN clang-format
even1024 May 20, 2026
4444aa2
Address BILN review observations
even1024 May 24, 2026
f527b54
Fix BILN clang-format
even1024 May 24, 2026
07c89bb
Fix BILN integration reference order
even1024 May 24, 2026
45f3240
Limit MinGW CI parallel build
even1024 May 24, 2026
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
2 changes: 1 addition & 1 deletion .github/workflows/indigo-ci.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ jobs:
mkdir build
cd build
cmake .. -G "MinGW Makefiles" -DBUILD_INDIGO_WRAPPERS=OFF -DBUILD_BINGO=OFF -DBUILD_BINGO_ELASTIC=OFF -DPython3_ROOT_DIR=/mingw64 -DCMAKE_C_FLAGS="-Wno-error"
cmake --build . --config Release --target all --parallel
cmake --build . --config Release --target all --parallel 2
- name: Test native libs
run: |
cd build
Expand Down
49 changes: 46 additions & 3 deletions api/tests/integration/ref/formats/biln.py.out
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,53 @@
*** BILN interop ***
biln_bracketed_alias:BILN->HELM SUCCEED
biln_cap:BILN->HELM SUCCEED
biln_disulfides:BILN->HELM SUCCEED
biln_explicit_backbone:BILN->HELM SUCCEED
biln_large_bond_id:BILN->HELM SUCCEED
biln_star_alias:BILN->HELM SUCCEED
biln_three_chains:BILN->HELM SUCCEED
biln_two_backbones:BILN->HELM SUCCEED
biln_underscore_alias:BILN->HELM SUCCEED
biln_alphabetic_order:BILN->BILN SUCCEED
biln_amino_acid_count_order:BILN->BILN SUCCEED
biln_backbone_order:BILN->BILN SUCCEED
biln_bracketed_no_hyphen:BILN->BILN SUCCEED
biln_cycle_best:BILN->BILN SUCCEED
biln_cycle_reverse_rotation:BILN->BILN SUCCEED
biln_cycle_rotation:BILN->BILN SUCCEED
biln_cycle_with_external_bond_order:BILN->BILN SUCCEED
biln_cycle_with_extra_bond_order:BILN->BILN SUCCEED
biln_equal_chain_topology_order:BILN->BILN SUCCEED
biln_library_alias:BILN->BILN SUCCEED
biln_mid_chain_chem:BILN->BILN SUCCEED
biln_multi_chain_chem_cross_link:BILN->BILN SUCCEED
biln_multiple_nonbackbone_order:BILN->BILN SUCCEED
biln_short_chain_order:BILN->BILN SUCCEED
biln_valid_large_bond_ids:BILN->BILN SUCCEED
helm_alias_to_biln_alias:HELM->BILN SUCCEED
helm_bracketed_alias:HELM->BILN SUCCEED
helm_cap:HELM->BILN SUCCEED
helm_chem_backbone:HELM->BILN SUCCEED
helm_chem_with_biln_code:HELM->BILN SUCCEED
helm_cycle:HELM->BILN SUCCEED
helm_star_alias:HELM->BILN SUCCEED
helm_three_chains:HELM->BILN SUCCEED
Test 'A(1,3)-C': got expected error 'Invalid BILN bond 1: expected two endpoints but found 1.'
Test 'A--C': got expected error 'Invalid BILN string: empty monomer.'
Test 'A-C(1,4)': got expected error 'Invalid BILN bond 1: expected two endpoints but found 1.'
helm_underscore_alias:HELM->BILN SUCCEED
Test 'CHEM1{[qweqwe]}$$$$V2.0': got expected error 'Only amino acids and CHEMs with BILN codes can get exported to BILN.'
Test 'PEPTIDE1{A}|RNA1{R(A)P}$$$$V2.0': got expected error 'Only amino acids and CHEMs with BILN codes can get exported to BILN.'
Test 'PEPTIDE1{[Abu].[Sar].[NMeL].V.[NMeL].A.[DAla].[NMeL].[NMeL].[NMeV].[NMeThr4RBut2enyl]}$PEPTIDE1,PEPTIDE1,1:R1-11:R2$$$V2.0': got expected error 'Only amino acids and CHEMs with BILN codes can get exported to BILN.'
Test 'PEPTIDE1{[Ac]}|PEPTIDE2{K}$PEPTIDE1,PEPTIDE2,1:R1-1:R3$$$V2.0': got expected error 'Cannot save in BILN format - unsupported attachment point 'R1'.'
Test KET 'custom_chem_without_biln_code': got expected error 'Only amino acids and CHEMs with BILN codes can get exported to BILN.'
Test KET 'unresolved_cap_invalid_attachment': got expected error 'Cannot save in BILN format - unsupported attachment point 'R1'.'
Test 'A(1,3)-C': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'A--C': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'A-C(-1,3)-D(2,3)-E.F-G-H(-1,3)-I-K(2,3)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'A-C(1,3)-D(1,3)-E.F-G-H(1,3)-I-K(2,3)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'A-C(1,4)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'A-C(1,4)-D(2,3)-E.F-G-H(1,3)-I-K(2,3)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'A-C(1.25,3)-D(2,3)-E.F-G-H(1.25,3)-I-K(2,3)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'Ac(1,1).K(1,3)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'Ac(1,4).K(1,3)': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'Cys_SEt': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test 'D-2Thi-D-D-gGlu-meF-G-Lys-al': got expected error 'The string cannot be interpreted as a valid BILN string.'
Test '[D-Cit](1,2)-aThr(1,1)(2,2)-meS(2,1)': got expected error 'The string cannot be interpreted as a valid BILN string.'
214 changes: 207 additions & 7 deletions api/tests/integration/tests/formats/biln.py
View file
Open in desktop
Copy link
Copy Markdown
Collaborator

@AliaksandrDziarkach AliaksandrDziarkach May 25, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I don't see test for Terminal Cap aliases

Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,39 @@
)

biln_to_helm = {
# Legacy integration coverage: terminal caps must keep their explicit
# non-backbone BILN bonds during import/export roundtrip.
"biln_cap": (
"Ac(1,2).A-K(1,3)",
"PEPTIDE1{[Ac]}|PEPTIDE2{A.K}$PEPTIDE1,PEPTIDE2,1:R2-2:R3$$$V2.0",
"PEPTIDE1{[ac]}|PEPTIDE2{A.K}$PEPTIDE1,PEPTIDE2,1:R2-2:R3$$$V2.0",
),
"biln_three_chains": (
"Ac(1,2).A-K(1,3)(2,2).Me(2,1)",
"PEPTIDE1{[Ac]}|PEPTIDE2{A.K}|PEPTIDE3{[Me]}$PEPTIDE1,PEPTIDE2,1:R2-2:R3|PEPTIDE2,PEPTIDE3,2:R2-1:R1$$$V2.0",
"PEPTIDE1{[ac]}|PEPTIDE2{A.K}|PEPTIDE3{[-Me]}$PEPTIDE1,PEPTIDE2,1:R2-2:R3|PEPTIDE2,PEPTIDE3,2:R2-1:R1$$$V2.0",
),
"biln_two_backbones": (
"A-C-D.E-F-G",
"PEPTIDE1{A.C.D}|PEPTIDE2{E.F.G}$$$$V2.0",
),
"biln_underscore_alias": (
"A-1Nal-Cys_Bn-C",
"PEPTIDE1{A.[1Nal].[Cys_Bn].C}$$$$V2.0",
),
"biln_bracketed_alias": (
"A-[D-1Nal]-[Cys_Bn]-[C]",
"PEPTIDE1{A.[D-1Nal].[Cys_Bn].C}$$$$V2.0",
),
"biln_star_alias": (
"A-D*-C",
"PEPTIDE1{A.[D*].C}$$$$V2.0",
),
"biln_large_bond_id": (
"A-C(7563,3).C(7563,3)",
"PEPTIDE1{A.C}|PEPTIDE2{C}$PEPTIDE1,PEPTIDE2,2:R3-1:R3$$$V2.0",
),
"biln_explicit_backbone": (
"[D-Cit](1,2).aThr(1,1)(2,2).meS(2,1)",
"PEPTIDE1{[D-Cit].[aThr].[meS]}$$$$V2.0",
),
"biln_disulfides": (
"D-T-H-F-P-I-C(1,3)-I-F-C(2,3)-C(3,3)-G-C(2,3)-C(4,3)-H-R-S-K-C(3,3)-G-M-C(4,3)-C(1,3)-K-T",
Expand All @@ -53,6 +79,87 @@
except IndigoException as e:
print(name + ":FAILED - " + getIndigoExceptionText(e))

biln_to_biln = {
"biln_cycle_best": (
"A(1,1)-C-D-E(1,2)",
"A(1,1)-C-D-E(1,2)",
),
"biln_cycle_rotation": (
"C(1,1)-D-E-A(1,2)",
"A(1,1)-C-D-E(1,2)",
),
"biln_cycle_reverse_rotation": (
"D(1,2)-C-A-E(1,1)",
"A(1,1)-C-D-E(1,2)",
),
"biln_bracketed_no_hyphen": (
"[D-2Thi]-[D]-[D-gGlu]-[meF]-[G]-[Lys-al]",
"[D-2Thi]-D-[D-gGlu]-meF-G-[Lys-al]",
),
"biln_backbone_order": (
"A-A-A-A-A-A.C-C-C-C.[PEG-2]-C-C-C-C-[PEG-2]",
"A-A-A-A-A-A.[PEG-2]-C-C-C-C-[PEG-2].C-C-C-C",
),
"biln_short_chain_order": (
"A-A-A6OH-A6OH-A6OH.C-C-C-C-C",
"A-A-A6OH-A6OH-A6OH.C-C-C-C-C",
),
"biln_amino_acid_count_order": (
"C-C-A6OH-A6OH-C-C.C-C-C-C-C-A6OH",
"C-C-C-C-C-A6OH.C-C-A6OH-A6OH-C-C",
),
"biln_alphabetic_order": (
"C-D-E-F-G-A6OH.A-C-D-E-F-A6OH",
"A-C-D-E-F-A6OH.C-D-E-F-G-A6OH",
),
"biln_multiple_nonbackbone_order": (
"A-[Test-6-Ch](1,4)(2,3)-C.D(2,1).E(1,2)",
"A-[Test-6-Ch](1,3)(2,4)-C.D(1,1).E(2,2)",
),
"biln_cycle_with_extra_bond_order": (
"C(1,1)(2,3)-C-C(2,3)-C(1,2)",
"C(1,1)-C(2,3)-C-C(1,2)(2,3)",
),
"biln_cycle_with_external_bond_order": (
"C(1,1)-C(2,3)-C(1,2).C(2,3)",
"C(1,1)(2,3)-C-C(1,2).C(2,3)",
),
"biln_equal_chain_topology_order": (
"C(1,3).C(1,1)",
"C(1,1).C(1,3)",
),
"biln_library_alias": (
"Edc",
"Edc",
),
"biln_mid_chain_chem": (
"A-[PEG-2]-A",
"A-[PEG-2]-A",
),
"biln_multi_chain_chem_cross_link": (
"A-[PEG-2]-C(1,3).D-[PEG-2]-E(1,3)",
"A-[PEG-2]-C(1,3).D-[PEG-2]-E(1,3)",
),
"biln_valid_large_bond_ids": (
"A-C(7563,3)-D(3,3)-E.F-G-H(7563,3)-I-K(3,3)",
"F-G-H(1,3)-I-K(2,3).A-C(1,3)-D(2,3)-E",
),
}

for name in sorted(biln_to_biln.keys()):
biln, biln_ref = biln_to_biln[name]
try:
doc = indigo.loadBiln(biln, lib)
canonical_biln = doc.biln(lib)
diff = find_diff(biln_ref, canonical_biln)
if diff:
print(name + ":FAILED")
print(diff)
else:
print(name + ":BILN->BILN SUCCEED")
except IndigoException as e:
print(name + ":FAILED - " + getIndigoExceptionText(e))

helm_to_biln = {
"helm_cap": (
"PEPTIDE1{[Ac]}|PEPTIDE2{A.K}$PEPTIDE1,PEPTIDE2,1:R2-2:R3$$$V2.0",
Expand All @@ -62,9 +169,33 @@
"PEPTIDE1{[Ac]}|PEPTIDE2{A.K}|PEPTIDE3{[Me]}$PEPTIDE1,PEPTIDE2,1:R2-2:R3|PEPTIDE2,PEPTIDE3,2:R2-1:R1$$$V2.0",
"Ac(1,2).A-K(1,3)(2,2).Me(2,1)",
),
"helm_underscore_alias": (
"PEPTIDE1{A.[1Nal].[Cys_Bn].C}$$$$V2.0",
"A-1Nal-Cys_Bn-C",
),
"helm_bracketed_alias": (
"PEPTIDE1{A.[D-1Nal].[Cys_Bn].C}$$$$V2.0",
"A-[D-1Nal]-Cys_Bn-C",
),
"helm_star_alias": (
"PEPTIDE1{A.[D*].C}$$$$V2.0",
"A-D*-C",
),
"helm_cycle": (
"PEPTIDE1{[Abu].[Sar].[NMeL].V.[NMeL].A.[DAla].[NMeL].[NMeL].[NMeV].[NMeThr4RBut2enyl]}$PEPTIDE1,PEPTIDE1,1:R1-11:R2$$$V2.0",
"Abu(1,1)-Sar-NMeL-V-NMeL-A-DAla-NMeL-NMeL-NMeV-NMeThr4RBut2enyl(1,2)",
"PEPTIDE1{A.C.D.E}$PEPTIDE1,PEPTIDE1,1:R1-4:R2$$$V2.0",
"A(1,1)-C-D-E(1,2)",
),
"helm_chem_backbone": (
"PEPTIDE1{A.A.A.A.A.A}|CHEM1{[PEG-2]}|PEPTIDE2{C.C.C.C}|CHEM2{[PEG-2]}$PEPTIDE1,CHEM1,6:R2-1:R1|CHEM1,PEPTIDE2,1:R2-1:R1|PEPTIDE2,CHEM2,4:R2-1:R1$$$V2.0",
"A-A-A-A-A-A-[PEG-2]-C-C-C-C-[PEG-2]",
),
"helm_chem_with_biln_code": (
"CHEM1{[PEG-2]}$$$$V2.0",
"[PEG-2]",
),
"helm_alias_to_biln_alias": (
"PEPTIDE1{[Cys_SEt]}$$$$V2.0",
"Edc",
),
}

Expand All @@ -82,10 +213,79 @@
except IndigoException as e:
print(name + ":FAILED - " + getIndigoExceptionText(e))

helm_errors = {
"CHEM1{[qweqwe]}$$$$V2.0": "Only amino acids and CHEMs with BILN codes can get exported to BILN.",
# Unresolved HELM aliases that map to real BILN terminal caps must still be
# validated against the resolved library template attachment points.
"PEPTIDE1{[Ac]}|PEPTIDE2{K}$PEPTIDE1,PEPTIDE2,1:R1-1:R3$$$V2.0": "Cannot save in BILN format - unsupported attachment point 'R1'.",
"PEPTIDE1{A}|RNA1{R(A)P}$$$$V2.0": "Only amino acids and CHEMs with BILN codes can get exported to BILN.",
# Legacy integration input retained as an error expectation. #3541 export
# requirement 1 forbids exporting PEPTIDE monomers without BILN codes.
"PEPTIDE1{[Abu].[Sar].[NMeL].V.[NMeL].A.[DAla].[NMeL].[NMeL].[NMeV].[NMeThr4RBut2enyl]}$PEPTIDE1,PEPTIDE1,1:R1-11:R2$$$V2.0": "Only amino acids and CHEMs with BILN codes can get exported to BILN.",
}

for helm in sorted(helm_errors.keys()):
error = helm_errors[helm]
try:
doc = indigo.loadHelm(helm, lib)
doc.biln(lib)
print("Test %s failed: exception expected." % helm)
except IndigoException as e:
text = getIndigoExceptionText(e)
if error in text:
print("Test '%s': got expected error '%s'" % (helm, error))
else:
print(
"Test '%s': expected error '%s' but got '%s'"
% (helm, error, text)
)

ket_errors = {
"custom_chem_without_biln_code": (
"CHEM1{[qweqwe]}$$$$V2.0",
"Only amino acids and CHEMs with BILN codes can get exported to BILN.",
),
"unresolved_cap_invalid_attachment": (
"PEPTIDE1{[Ac]}|PEPTIDE2{K}$PEPTIDE1,PEPTIDE2,1:R1-1:R3$$$V2.0",
"Cannot save in BILN format - unsupported attachment point 'R1'.",
),
}

for name in sorted(ket_errors.keys()):
helm, error = ket_errors[name]
try:
doc = indigo.loadHelm(helm, lib)
doc = indigo.loadKetDocument(doc.json())
doc.biln(lib)
print("Test KET %s failed: exception expected." % name)
except IndigoException as e:
text = getIndigoExceptionText(e)
if error in text:
print("Test KET '%s': got expected error '%s'" % (name, error))
else:
print(
"Test KET '%s': expected error '%s' but got '%s'"
% (name, error, text)
)

biln_errors = {
"A(1,3)-C": "Invalid BILN bond 1: expected two endpoints but found 1.",
"A--C": "Invalid BILN string: empty monomer.",
"A-C(1,4)": "Invalid BILN bond 1: expected two endpoints but found 1.",
# #3541 import requirement 1: any invalid BILN string must return the
# generic error text below. This intentionally replaces older detailed
# error expectations for the pre-existing invalid integration cases.
"A(1,3)-C": "The string cannot be interpreted as a valid BILN string.",
"A--C": "The string cannot be interpreted as a valid BILN string.",
"A-C(1,4)": "The string cannot be interpreted as a valid BILN string.",
"[D-Cit](1,2)-aThr(1,1)(2,2)-meS(2,1)": "The string cannot be interpreted as a valid BILN string.",
"D-2Thi-D-D-gGlu-meF-G-Lys-al": "The string cannot be interpreted as a valid BILN string.",
"A-C(-1,3)-D(2,3)-E.F-G-H(-1,3)-I-K(2,3)": "The string cannot be interpreted as a valid BILN string.",
"A-C(1.25,3)-D(2,3)-E.F-G-H(1.25,3)-I-K(2,3)": "The string cannot be interpreted as a valid BILN string.",
"A-C(1,3)-D(1,3)-E.F-G-H(1,3)-I-K(2,3)": "The string cannot be interpreted as a valid BILN string.",
"A-C(1,4)-D(2,3)-E.F-G-H(1,3)-I-K(2,3)": "The string cannot be interpreted as a valid BILN string.",
# Terminal caps must be resolved against their real templates, not imported
# as unresolved monomers with synthetic R1..R4 attachment points.
"Ac(1,1).K(1,3)": "The string cannot be interpreted as a valid BILN string.",
"Ac(1,4).K(1,3)": "The string cannot be interpreted as a valid BILN string.",
"Cys_SEt": "The string cannot be interpreted as a valid BILN string.",
}

for biln in sorted(biln_errors.keys()):
Expand Down
Loading
Loading