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Backmerge: #2615 - Export to three letter amino acid codes cause convert error. #2619

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Nov 7, 2024
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Backmerge: #2615 - Export to three letter amino acid codes cause convert error. #2619

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2 changes: 1 addition & 1 deletion api/c/indigo/src/indigo_savers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -630,7 +630,7 @@ CEXPORT int indigoSaveSequence3Letter(int item, int output, int library)
out.flush();
return 1;
}
throw IndigoError("indigoSaveSequence(): expected molecule, got %s", obj.debugInfo());
throw IndigoError("indigoSaveSequence3Letter(): expected document, got %s", obj.debugInfo());
}
INDIGO_END(-1);
}
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9 changes: 5 additions & 4 deletions api/wasm/indigo-ketcher/indigo-ketcher.cpp
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Expand Up @@ -144,7 +144,7 @@ namespace indigo
{
result = _checkResultString(indigoSequence(id(), library));
}
else if (outputFormat == "sequence-3-letter" || outputFormat == "chemical/x-sequence-3-letter")
else if (outputFormat == "peptide-sequence-3-letter" || outputFormat == "chemical/x-peptide-sequence-3-letter")
{
result = _checkResultString(indigoSequence3Letter(id(), library));
}
Expand Down Expand Up @@ -540,9 +540,10 @@ namespace indigo
input_format = it->second;

bool use_document = false;
if (input_format == "ket" && outputFormat.size() > 0 &&
(outputFormat == "sequence" || outputFormat == "chemical/x-sequence" || outputFormat == "fasta" || outputFormat == "chemical/x-fasta" ||
outputFormat == "idt" || outputFormat == "chemical/x-idt" || outputFormat == "helm" || outputFormat == "chemical/x-helm"))
if ((input_format == "ket" || input_format == "application/json") && outputFormat.size() > 0 &&
(outputFormat == "sequence" || outputFormat == "chemical/x-sequence" || "chemical/x-peptide-sequence-3-letter" || outputFormat == "fasta" ||
outputFormat == "chemical/x-fasta" || outputFormat == "idt" || outputFormat == "chemical/x-idt" || outputFormat == "helm" ||
outputFormat == "chemical/x-helm"))
use_document = true;
IndigoKetcherObject iko = loadMoleculeOrReaction(data, options_copy, library, use_document);

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1 change: 1 addition & 0 deletions api/wasm/indigo-ketcher/test/peptide_ref_3_letter.ket
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26 changes: 24 additions & 2 deletions api/wasm/indigo-ketcher/test/test.js
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Expand Up @@ -480,8 +480,8 @@ M END
var fs = require('fs');
const cdx_data = fs.readFileSync("test64.cdx");
const ket = indigo.convert(cdx_data, "ket", options);
const ket_data = indigo.convert(fs.readFileSync("test64.ket"), "ket", options);
fs.writeFileSync("test64a.ket", ket);
const ket_data = fs.readFileSync("test64.ket").toString();
fs.writeFileSync("test64a1.ket", ket_data);
assert.equal(ket, ket_data);
options.delete();
});
Expand Down Expand Up @@ -839,6 +839,28 @@ M END
});
}

{
test("PEPTIDE-3-LETTER", "basic", () => {
var fs = require('fs');
let options = new indigo.MapStringString();
const monomersLib = fs.readFileSync("monomer_library.ket");
options.set("monomerLibrary", monomersLib);
options.set("output-content-type", "application/json");
options.set("input-format", "chemical/x-peptide-sequence-3-letter");
const peptide_seq_ref = "AlaCysAspGluPheGlyHisIleLysLeuMetAsnPylProGlnArgSerArgSecValTrpTyr";
const peptide_ket = JSON.parse(indigo.convert(peptide_seq_ref, "ket", options)).struct;
// fs.writeFileSync("peptide_ref_3_letter.ket", peptide_ket);
const peptide_ket_ref = fs.readFileSync("peptide_ref_3_letter.ket");
assert.equal(peptide_ket, peptide_ket_ref.toString());

options.set("input-format", "application/json");
options.set("output-content-type", "chemical/x-peptide-sequence-3-letter");
const peptide_seq = indigo.convert(peptide_ket_ref.toString(), "chemical/x-peptide-sequence-3-letter", options);
assert.equal(peptide_seq, peptide_seq_ref);
options.delete();
});
}

{
test("RNA", "basic", () => {
var fs = require('fs');
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33 changes: 31 additions & 2 deletions utils/indigo-service/backend/service/tests/api/indigo_test.py
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Expand Up @@ -478,8 +478,9 @@ def test_headers_wrong(self):
chemical/x-daylight-smiles, chemical/x-cml, chemical/x-inchi, chemical/x-inchi-key, \
chemical/x-iupac, chemical/x-daylight-smarts, chemical/x-inchi-aux, chemical/x-chemaxon-cxsmiles, \
chemical/x-cdxml, chemical/x-cdx, chemical/x-sdf, chemical/x-rdf, chemical/x-peptide-sequence, \
chemical/x-rna-sequence, chemical/x-dna-sequence, chemical/x-sequence, chemical/x-peptide-fasta, \
chemical/x-rna-fasta, chemical/x-dna-fasta, chemical/x-fasta, chemical/x-idt, chemical/x-helm."
chemical/x-peptide-sequence-3-letter, chemical/x-rna-sequence, chemical/x-dna-sequence, chemical/x-sequence, \
chemical/x-peptide-fasta, chemical/x-rna-fasta, chemical/x-dna-fasta, chemical/x-fasta, \
chemical/x-idt, chemical/x-helm."
expected_text = (
"ValidationError: {'input_format': ['Must be one of: %s']}"
% formats
Expand Down Expand Up @@ -3277,6 +3278,33 @@ def test_convert_sequences(self):
self.url_prefix + "/convert", headers=headers, data=data
)

peptide_3 = "AlaCysGlyThrSec"
headers, data = self.get_headers(
{
"struct": peptide_3,
"options": {"monomerLibrary": monomer_library},
"input_format": "chemical/x-peptide-sequence-3-letter",
"output_format": "chemical/x-indigo-ket",
}
)
result_ket_3 = requests.post(
self.url_prefix + "/convert", headers=headers, data=data
)

headers, data = self.get_headers(
{
"struct": json.loads(result_ket_3.text)["struct"],
"options": {"monomerLibrary": monomer_library},
"output_format": "chemical/x-peptide-sequence-3-letter",
}
)
result_peptide_3 = requests.post(
self.url_prefix + "/convert", headers=headers, data=data
)
self.assertEqual(
json.loads(result_peptide_3.text)["struct"], peptide_3
)

headers, data = self.get_headers(
{
"struct": "ACDEFGHIKLMNOPQRSRUVWY",
Expand Down Expand Up @@ -3314,6 +3342,7 @@ def test_convert_sequences(self):
with open(os.path.join(ref_path, "peptide_ref") + ".ket", "r") as file:
peptide_ref = file.read()
self.assertEqual(result_peptide.text, peptide_ref)
self.assertEqual(result_ket_3.text, peptide_ref)

def test_convert_fasta(self):
ref_path = joinPathPy("ref/", __file__)
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7 changes: 7 additions & 0 deletions utils/indigo-service/backend/service/v2/indigo_api.py
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Expand Up @@ -335,6 +335,10 @@ def load_moldata(
md.struct = indigo.loadSequence(molstr, "PEPTIDE", library)
md.is_rxn = False
md.is_query = False
elif input_format == "chemical/x-peptide-sequence-3-letter":
md.struct = indigo.loadSequence(molstr, "PEPTIDE-3-LETTER", library)
md.is_rxn = False
md.is_query = False
elif input_format == "chemical/x-rna-sequence":
md.struct = indigo.loadSequence(molstr, "RNA", library)
md.is_rxn = False
Expand Down Expand Up @@ -431,6 +435,8 @@ def save_moldata(
return md.struct.json()
elif output_format == "chemical/x-sequence":
return md.struct.sequence(library)
elif output_format == "chemical/x-peptide-sequence-3-letter":
return md.struct.sequence3Letter(library)
elif output_format == "chemical/x-fasta":
return md.struct.fasta(library)
elif output_format == "chemical/x-idt":
Expand Down Expand Up @@ -928,6 +934,7 @@ def convert():
"chemical/x-fasta",
"chemical/x-idt",
"chemical/x-helm",
"chemical/x-peptide-sequence-3-letter",
):
try_document = True

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1 change: 1 addition & 0 deletions utils/indigo-service/backend/service/v2/validation.py
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Expand Up @@ -26,6 +26,7 @@ class InputFormatSchema(Schema):
"chemical/x-sdf",
"chemical/x-rdf",
"chemical/x-peptide-sequence",
"chemical/x-peptide-sequence-3-letter",
"chemical/x-rna-sequence",
"chemical/x-dna-sequence",
"chemical/x-sequence",
Expand Down
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