From d3c6f7350811c7e410ad63eeb09a6e04f552fa6d Mon Sep 17 00:00:00 2001 From: Aliaksandr Dziarkach <18146690+AliaksandrDziarkach@users.noreply.github.com> Date: Thu, 15 Aug 2024 18:11:50 +0300 Subject: [PATCH] #2015 Import/Export of variant monomers from Fasta/Sequence (#2227) Co-authored-by: Aliakasndr Dziarkach --- api/c/indigo/src/indigo_molecule.cpp | 18 +- api/c/indigo/src/indigo_savers.cpp | 18 +- .../ref/formats/fasta_to_ket.py.out | 3 + .../ref/formats/idt_unresolved.py.out | 2 +- .../integration/ref/formats/seq_to_ket.py.out | 3 + .../tests/formats/fasta_to_fasta.py | 5 +- .../integration/tests/formats/fasta_to_ket.py | 8 +- .../tests/formats/genbank_to_seq.py | 5 +- .../integration/tests/formats/ket_to_fasta.py | 5 +- .../molecules/aminoacids_variants.fasta | 2 + .../formats/molecules/dna_variants.fasta | 2 + .../formats/molecules/rna_variants.fasta | 2 + .../tests/formats/ref/all_aminoacids.ket | 1926 +++--- .../tests/formats/ref/aminoacids_variants.ket | 4784 ++++++++++++++ .../tests/formats/ref/break_peptide.ket | 4366 ++++++------- .../integration/tests/formats/ref/comment.ket | 1362 ++-- .../tests/formats/ref/dna_acgtu.ket | 565 +- .../tests/formats/ref/dna_variants.ket | 1237 ++++ .../tests/formats/ref/monomer_library.ket | 500 ++ .../tests/formats/ref/multiseq.ket | 3242 +++++----- .../tests/formats/ref/rna_acgtu.ket | 571 +- .../tests/formats/ref/rna_variants.ket | 1251 ++++ .../integration/tests/formats/ref/spaces.ket | 1926 +++--- .../tests/formats/ref/test_1881.ket | 233 +- .../tests/formats/ref/test_dna.ket | 2696 ++++---- .../tests/formats/ref/test_peptide.ket | 5566 +++++++++-------- .../tests/formats/ref/test_rna.ket | 2696 ++++---- .../integration/tests/formats/seq_to_ket.py | 8 +- api/wasm/indigo-ketcher/test/dna_ref.ket | 2 +- .../indigo-ketcher/test/monomer_library.ket | 1136 ++++ api/wasm/indigo-ketcher/test/peptide_ref.ket | 2 +- api/wasm/indigo-ketcher/test/rna_ref.ket | 2 +- api/wasm/indigo-ketcher/test/test.js | 20 +- .../indigo-ketcher/test/test_peptide_ref.ket | 2 +- api/wasm/indigo-ketcher/test/test_rna_ref.ket | 2 +- core/indigo-core/molecule/ket_document.h | 13 +- core/indigo-core/molecule/monomer_commons.h | 13 + core/indigo-core/molecule/sequence_loader.h | 14 +- core/indigo-core/molecule/sequence_saver.h | 1 + .../indigo-core/molecule/src/ket_document.cpp | 8 +- core/indigo-core/molecule/src/ket_objects.cpp | 2 +- .../molecule/src/sequence_loader.cpp | 278 +- .../molecule/src/sequence_saver.cpp | 85 +- data/molecules/basic/monomer_library.ket | 500 ++ .../backend/service/tests/api/indigo_test.py | 24 +- .../service/tests/api/ref/dna_fasta_ref.ket | 2 +- .../backend/service/tests/api/ref/dna_ref.ket | 2 +- .../tests/api/ref/peptide_fasta_ref.ket | 2 +- .../service/tests/api/ref/peptide_ref.ket | 2 +- .../service/tests/api/ref/rna_fasta_ref.ket | 2 +- .../backend/service/tests/api/ref/rna_ref.ket | 2 +- .../tests/api/structures/monomer_library.ket | 1136 ++++ 52 files changed, 23500 insertions(+), 12754 deletions(-) create mode 100644 api/tests/integration/tests/formats/molecules/aminoacids_variants.fasta create mode 100644 api/tests/integration/tests/formats/molecules/dna_variants.fasta create mode 100644 api/tests/integration/tests/formats/molecules/rna_variants.fasta create mode 100644 api/tests/integration/tests/formats/ref/aminoacids_variants.ket create mode 100644 api/tests/integration/tests/formats/ref/dna_variants.ket create mode 100644 api/tests/integration/tests/formats/ref/rna_variants.ket diff --git a/api/c/indigo/src/indigo_molecule.cpp b/api/c/indigo/src/indigo_molecule.cpp index b58f457653..6e7d9a3ea6 100644 --- a/api/c/indigo/src/indigo_molecule.cpp +++ b/api/c/indigo/src/indigo_molecule.cpp @@ -568,11 +568,10 @@ CEXPORT int indigoLoadSequence(int source, const char* seq_type, int library) IndigoObject& lib_obj = self.getObject(library); SequenceLoader loader(IndigoScanner::get(obj), IndigoMonomerLibrary::get(lib_obj)); - std::unique_ptr molptr = std::make_unique(); + std::unique_ptr docptr = std::make_unique(); - Molecule& mol = molptr->mol; - loader.loadSequence(mol, seq_type); - return self.addObject(molptr.release()); + loader.loadSequence(docptr->get(), seq_type); + return self.addObject(docptr.release()); } INDIGO_END(-1); } @@ -619,11 +618,10 @@ CEXPORT int indigoLoadFasta(int source, const char* seq_type, int library) IndigoObject& lib_obj = self.getObject(library); SequenceLoader loader(IndigoScanner::get(obj), IndigoMonomerLibrary::get(lib_obj)); - std::unique_ptr molptr = std::make_unique(); + std::unique_ptr docptr = std::make_unique(); - Molecule& mol = molptr->mol; - loader.loadFasta(mol, seq_type); - return self.addObject(molptr.release()); + loader.loadFasta(docptr->get(), seq_type); + return self.addObject(docptr.release()); } INDIGO_END(-1); } @@ -671,11 +669,8 @@ CEXPORT int indigoLoadIdt(int source, int library) MonomerTemplateLibrary& lib = IndigoMonomerLibrary::get(lib_obj); SequenceLoader loader(IndigoScanner::get(obj), lib); - // std::unique_ptr molptr = std::make_unique(); std::unique_ptr docptr = std::make_unique(); - // Molecule& mol = molptr->mol; - // loader.loadIdt(mol); loader.loadIdt(docptr->get()); return self.addObject(docptr.release()); } @@ -3067,7 +3062,6 @@ CEXPORT int indigoAddDataSGroup(int molecule, int natoms, int* atoms, int nbonds BaseMolecule& mol = self.getObject(molecule).getBaseMolecule(); int idx = mol.sgroups.addSGroup(SGroup::SG_TYPE_DAT); DataSGroup& dsg = (DataSGroup&)mol.sgroups.getSGroup(idx); - int i; if (atoms != nullptr) dsg.atoms.concat(atoms, natoms); diff --git a/api/c/indigo/src/indigo_savers.cpp b/api/c/indigo/src/indigo_savers.cpp index 5b64344f96..257a85aaee 100644 --- a/api/c/indigo/src/indigo_savers.cpp +++ b/api/c/indigo/src/indigo_savers.cpp @@ -591,7 +591,7 @@ CEXPORT int indigoSaveSequence(int item, int output, int library) { IndigoObject& obj = self.getObject(item); Output& out = IndigoOutput::get(self.getObject(output)); - if (IndigoBaseMolecule::is(obj) || IndigoKetDocument::is(obj)) + if (IndigoBaseMolecule::is(obj)) { IndigoObject& lib_obj = self.getObject(library); SequenceSaver saver(out, IndigoMonomerLibrary::get(lib_obj)); @@ -600,6 +600,14 @@ CEXPORT int indigoSaveSequence(int item, int output, int library) out.flush(); return 1; } + else if (IndigoKetDocument::is(obj)) + { + IndigoObject& lib_obj = self.getObject(library); + SequenceSaver saver(out, IndigoMonomerLibrary::get(lib_obj)); + saver.saveKetDocument(static_cast(obj).get()); + out.flush(); + return 1; + } throw IndigoError("indigoSaveSequence(): expected molecule, got %s", obj.debugInfo()); } INDIGO_END(-1); @@ -620,6 +628,14 @@ CEXPORT int indigoSaveFasta(int item, int output, int library) out.flush(); return 1; } + else if (IndigoKetDocument::is(obj)) + { + IndigoObject& lib_obj = self.getObject(library); + SequenceSaver saver(out, IndigoMonomerLibrary::get(lib_obj)); + saver.saveKetDocument(static_cast(obj).get(), SequenceSaver::SeqFormat::FASTA); + out.flush(); + return 1; + } throw IndigoError("indigoSaveFasta(): expected molecule, got %s", obj.debugInfo()); } INDIGO_END(-1); diff --git a/api/tests/integration/ref/formats/fasta_to_ket.py.out b/api/tests/integration/ref/formats/fasta_to_ket.py.out index 0fb5130d3f..a76842a4eb 100644 --- a/api/tests/integration/ref/formats/fasta_to_ket.py.out +++ b/api/tests/integration/ref/formats/fasta_to_ket.py.out @@ -7,3 +7,6 @@ break_peptide.ket:SUCCEED break_rna.fasta:SEQUENCE loader: Invalid symbols in the sequence: * comment.ket:SUCCEED test_1881.ket:SUCCEED +aminoacids_variants.ket:SUCCEED +rna_variants.ket:SUCCEED +dna_variants.ket:SUCCEED diff --git a/api/tests/integration/ref/formats/idt_unresolved.py.out b/api/tests/integration/ref/formats/idt_unresolved.py.out index f34d33e3a2..06b4e815b3 100644 --- a/api/tests/integration/ref/formats/idt_unresolved.py.out +++ b/api/tests/integration/ref/formats/idt_unresolved.py.out @@ -1,5 +1,5 @@ *** IDT unresolved to misc. unsupported formats *** -Sequence saver: i2AmPr cannot be written in sequence/FASTA format. +Sequence saver: Can't save chem 'i2AmPr' to sequence format molecule CDXML saver: i2AmPr cannot be written in CDXML/CDX format. molfile saver: i2AmPr cannot be written in MDL Molfile format. SMILES saver: i2AmPr cannot be written in SMILES/SMARTS format. diff --git a/api/tests/integration/ref/formats/seq_to_ket.py.out b/api/tests/integration/ref/formats/seq_to_ket.py.out index 31203d76e1..92c9039030 100644 --- a/api/tests/integration/ref/formats/seq_to_ket.py.out +++ b/api/tests/integration/ref/formats/seq_to_ket.py.out @@ -3,3 +3,6 @@ all_aminoacids.ket:SUCCEED rna_acgtu.ket:SUCCEED dna_acgtu.ket:SUCCEED spaces.ket:SUCCEED +aminoacids_variants.ket:SUCCEED +rna_variants.ket:SUCCEED +dna_variants.ket:SUCCEED diff --git a/api/tests/integration/tests/formats/fasta_to_fasta.py b/api/tests/integration/tests/formats/fasta_to_fasta.py index 7c31008790..9b275f5525 100644 --- a/api/tests/integration/tests/formats/fasta_to_fasta.py +++ b/api/tests/integration/tests/formats/fasta_to_fasta.py @@ -30,8 +30,9 @@ def find_diff(a, b): {"file": "multiseq", "seq_type": "DNA"}, ] -# empty library - internal used for now -lib = indigo.loadMonomerLibrary('{"root":{}}') +lib = indigo.loadMonomerLibraryFromFile( + os.path.join(ref_path, "monomer_library.ket") +) for desc in fasta_files: filename = desc["file"] diff --git a/api/tests/integration/tests/formats/fasta_to_ket.py b/api/tests/integration/tests/formats/fasta_to_ket.py index b403a20af8..3599701565 100644 --- a/api/tests/integration/tests/formats/fasta_to_ket.py +++ b/api/tests/integration/tests/formats/fasta_to_ket.py @@ -32,6 +32,9 @@ def find_diff(a, b): {"file": "break_rna", "seq_type": "RNA"}, {"file": "comment", "seq_type": "PEPTIDE"}, {"file": "test_1881", "seq_type": "PEPTIDE"}, + {"file": "aminoacids_variants", "seq_type": "PEPTIDE"}, + {"file": "rna_variants", "seq_type": "RNA"}, + {"file": "dna_variants", "seq_type": "DNA"}, ] @@ -41,8 +44,9 @@ def remove_prefix(s, prefix="com.epam.indigo.IndigoException: "): return s -# empty library - internal used for now -lib = indigo.loadMonomerLibrary('{"root":{}}') +lib = indigo.loadMonomerLibraryFromFile( + os.path.join(ref_path, "monomer_library.ket") +) for desc in fasta_files: filename = desc["file"] diff --git a/api/tests/integration/tests/formats/genbank_to_seq.py b/api/tests/integration/tests/formats/genbank_to_seq.py index 32c4ec72ca..d41fb6e973 100644 --- a/api/tests/integration/tests/formats/genbank_to_seq.py +++ b/api/tests/integration/tests/formats/genbank_to_seq.py @@ -27,8 +27,9 @@ def find_diff(a, b): {"file": "1844-gen_pept", "seq_type": "PEPTIDE"}, ] -# empty library - internal used for now -lib = indigo.loadMonomerLibrary('{"root":{}}') +lib = indigo.loadMonomerLibraryFromFile( + os.path.join(ref_path, "monomer_library.ket") +) for infile in files: filename = infile["file"] + ".seq" diff --git a/api/tests/integration/tests/formats/ket_to_fasta.py b/api/tests/integration/tests/formats/ket_to_fasta.py index e8e22d2154..c9cda01f50 100644 --- a/api/tests/integration/tests/formats/ket_to_fasta.py +++ b/api/tests/integration/tests/formats/ket_to_fasta.py @@ -28,8 +28,9 @@ def find_diff(a, b): "1950-mixed-seq", ] -# empty library - internal used for now -lib = indigo.loadMonomerLibrary('{"root":{}}') +lib = indigo.loadMonomerLibraryFromFile( + os.path.join(ref_path, "monomer_library.ket") +) files.sort() for filename in files: diff --git a/api/tests/integration/tests/formats/molecules/aminoacids_variants.fasta b/api/tests/integration/tests/formats/molecules/aminoacids_variants.fasta new file mode 100644 index 0000000000..810968e16d --- /dev/null +++ b/api/tests/integration/tests/formats/molecules/aminoacids_variants.fasta @@ -0,0 +1,2 @@ +>Sequence1 +BJZX \ No newline at end of file diff --git a/api/tests/integration/tests/formats/molecules/dna_variants.fasta b/api/tests/integration/tests/formats/molecules/dna_variants.fasta new file mode 100644 index 0000000000..80461e6f18 --- /dev/null +++ b/api/tests/integration/tests/formats/molecules/dna_variants.fasta @@ -0,0 +1,2 @@ +>Sequence1 +BN \ No newline at end of file diff --git a/api/tests/integration/tests/formats/molecules/rna_variants.fasta b/api/tests/integration/tests/formats/molecules/rna_variants.fasta new file mode 100644 index 0000000000..953114766f --- /dev/null +++ b/api/tests/integration/tests/formats/molecules/rna_variants.fasta @@ -0,0 +1,2 @@ +>Sequence1 +KN diff --git a/api/tests/integration/tests/formats/ref/all_aminoacids.ket b/api/tests/integration/tests/formats/ref/all_aminoacids.ket index 0d9b0545ae..57d743d1a0 100644 --- a/api/tests/integration/tests/formats/ref/all_aminoacids.ket +++ b/api/tests/integration/tests/formats/ref/all_aminoacids.ket @@ -303,67 +303,67 @@ ], "templates": [ { - "$ref": "monomerTemplate-Ala" + "$ref": "monomerTemplate-A___Alanine" }, { - "$ref": "monomerTemplate-Cys" + "$ref": "monomerTemplate-C___Cysteine" }, { - "$ref": "monomerTemplate-Asp" + "$ref": "monomerTemplate-D___Aspartic acid" }, { - "$ref": "monomerTemplate-Glu" + "$ref": "monomerTemplate-E___Glutamic acid" }, { - "$ref": "monomerTemplate-Phe" + "$ref": "monomerTemplate-F___Phenylalanine" }, { - "$ref": "monomerTemplate-Gly" + "$ref": "monomerTemplate-G___Glycine" }, { - "$ref": "monomerTemplate-His" + "$ref": "monomerTemplate-H___Histidine" }, { - "$ref": "monomerTemplate-Ile" + "$ref": "monomerTemplate-I___Isoleucine" }, { - "$ref": "monomerTemplate-Lys" + "$ref": "monomerTemplate-K___Lysine" }, { - "$ref": "monomerTemplate-Leu" + "$ref": "monomerTemplate-L___Leucine" }, { - "$ref": "monomerTemplate-Met" + "$ref": "monomerTemplate-M___Methionine" }, { - "$ref": "monomerTemplate-Asn" + "$ref": "monomerTemplate-N___Asparagine" }, { - "$ref": "monomerTemplate-Pyl" + "$ref": "monomerTemplate-O___Pyrrolysine" }, { - "$ref": "monomerTemplate-Pro" + "$ref": "monomerTemplate-P___Proline" }, { - "$ref": "monomerTemplate-Gln" + "$ref": "monomerTemplate-Q___Glutamine" }, { - "$ref": "monomerTemplate-Arg" + "$ref": "monomerTemplate-R___Arginine" }, { - "$ref": "monomerTemplate-Ser" + "$ref": "monomerTemplate-S___Serine" }, { - "$ref": "monomerTemplate-Sec" + "$ref": "monomerTemplate-U___Selenocysteine" }, { - "$ref": "monomerTemplate-Val" + "$ref": "monomerTemplate-V___Valine" }, { - "$ref": "monomerTemplate-Trp" + "$ref": "monomerTemplate-W___Tryptophan" }, { - "$ref": "monomerTemplate-Tyr" + "$ref": "monomerTemplate-Y___Tyrosine" } ] }, @@ -372,256 +372,255 @@ "id": "0", "seqid": 1, "position": { - "x": 0.0, - "y": -0.0 + "x": 0.000000, + "y": -0.000000 }, - "alias": "Ala", - "templateId": "Ala" + "alias": "A", + "templateId": "A___Alanine" }, "monomer1": { "type": "monomer", "id": "1", "seqid": 2, "position": { - "x": 1.600000023841858, - "y": -0.0 + "x": 1.600000, + "y": -0.000000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, "monomer2": { "type": "monomer", "id": "2", "seqid": 3, "position": { - "x": 3.200000047683716, - "y": -0.0 + "x": 3.200000, + "y": -0.000000 }, - "alias": "Asp", - "templateId": "Asp" + "alias": "D", + "templateId": "D___Aspartic acid" }, "monomer3": { "type": "monomer", "id": "3", "seqid": 4, "position": { - "x": 4.800000190734863, - "y": -0.0 + "x": 4.800000, + "y": -0.000000 }, - "alias": "Glu", - "templateId": "Glu" + "alias": "E", + "templateId": "E___Glutamic acid" }, "monomer4": { "type": "monomer", "id": "4", "seqid": 5, "position": { - "x": 6.400000095367432, - "y": -0.0 + "x": 6.400000, + "y": -0.000000 }, - "alias": "Phe", - "templateId": "Phe" + "alias": "F", + "templateId": "F___Phenylalanine" }, "monomer5": { "type": "monomer", "id": "5", "seqid": 6, "position": { - "x": 8.0, - "y": -0.0 + "x": 8.000000, + "y": -0.000000 }, - "alias": "Gly", - "templateId": "Gly" + "alias": "G", + "templateId": "G___Glycine" }, "monomer6": { "type": "monomer", "id": "6", "seqid": 7, "position": { - "x": 9.600000381469727, - "y": -0.0 + "x": 9.600000, + "y": -0.000000 }, - "alias": "His", - "templateId": "His" + "alias": "H", + "templateId": "H___Histidine" }, "monomer7": { "type": "monomer", "id": "7", "seqid": 8, "position": { - "x": 11.199999809265137, - "y": -0.0 + "x": 11.200000, + "y": -0.000000 }, - "alias": "Ile", - "templateId": "Ile" + "alias": "I", + "templateId": "I___Isoleucine" }, "monomer8": { "type": "monomer", "id": "8", "seqid": 9, "position": { - "x": 12.800000190734864, - "y": -0.0 + "x": 12.800000, + "y": -0.000000 }, - "alias": "Lys", - "templateId": "Lys" + "alias": "K", + "templateId": "K___Lysine" }, "monomer9": { "type": "monomer", "id": "9", "seqid": 10, "position": { - "x": 14.40000057220459, - "y": -0.0 + "x": 14.400001, + "y": -0.000000 }, - "alias": "Leu", - "templateId": "Leu" + "alias": "L", + "templateId": "L___Leucine" }, "monomer10": { "type": "monomer", "id": "10", "seqid": 11, "position": { - "x": 16.0, - "y": -0.0 + "x": 16.000000, + "y": -0.000000 }, - "alias": "Met", - "templateId": "Met" + "alias": "M", + "templateId": "M___Methionine" }, "monomer11": { "type": "monomer", "id": "11", "seqid": 12, "position": { - "x": 17.600000381469728, - "y": -0.0 + "x": 17.600000, + "y": -0.000000 }, - "alias": "Asn", - "templateId": "Asn" + "alias": "N", + "templateId": "N___Asparagine" }, "monomer12": { "type": "monomer", "id": "12", "seqid": 13, "position": { - "x": 19.200000762939454, - "y": -0.0 + "x": 19.200001, + "y": -0.000000 }, - "alias": "Pyl", - "templateId": "Pyl" + "alias": "O", + "templateId": "O___Pyrrolysine" }, "monomer13": { "type": "monomer", "id": "13", "seqid": 14, "position": { - "x": 20.80000114440918, - "y": -0.0 + "x": 20.800001, + "y": -0.000000 }, - "alias": "Pro", - "templateId": "Pro" + "alias": "P", + "templateId": "P___Proline" }, "monomer14": { "type": "monomer", "id": "14", "seqid": 15, "position": { - "x": 22.399999618530275, - "y": -0.0 + "x": 22.400000, + "y": -0.000000 }, - "alias": "Gln", - "templateId": "Gln" + "alias": "Q", + "templateId": "Q___Glutamine" }, "monomer15": { "type": "monomer", "id": "15", "seqid": 16, "position": { - "x": 24.0, - "y": -0.0 + "x": 24.000000, + "y": -0.000000 }, - "alias": "Arg", - "templateId": "Arg" + "alias": "R", + "templateId": "R___Arginine" }, "monomer16": { "type": "monomer", "id": "16", "seqid": 17, "position": { - "x": 25.600000381469728, - "y": -0.0 + "x": 25.600000, + "y": -0.000000 }, - "alias": "Ser", - "templateId": "Ser" + "alias": "S", + "templateId": "S___Serine" }, "monomer17": { "type": "monomer", "id": "17", "seqid": 18, "position": { - "x": 27.200000762939454, - "y": -0.0 + "x": 27.200001, + "y": -0.000000 }, - "alias": "Arg", - "templateId": "Arg" + "alias": "R", + "templateId": "R___Arginine" }, "monomer18": { "type": "monomer", "id": "18", "seqid": 19, "position": { - "x": 28.80000114440918, - "y": -0.0 + "x": 28.800001, + "y": -0.000000 }, - "alias": "Sec", - "templateId": "Sec" + "alias": "U", + "templateId": "U___Selenocysteine" }, "monomer19": { "type": "monomer", "id": "19", "seqid": 20, "position": { - "x": 30.399999618530275, - "y": -0.0 + "x": 30.400000, + "y": -0.000000 }, - "alias": "Val", - "templateId": "Val" + "alias": "V", + "templateId": "V___Valine" }, "monomer20": { "type": "monomer", "id": "20", "seqid": 21, "position": { - "x": 32.0, - "y": -0.0 + "x": 32.000000, + "y": -0.000000 }, - "alias": "Trp", - "templateId": "Trp" + "alias": "W", + "templateId": "W___Tryptophan" }, "monomer21": { "type": "monomer", "id": "21", "seqid": 22, "position": { - "x": 33.60000228881836, - "y": -0.0 + "x": 33.600002, + "y": -0.000000 }, - "alias": "Tyr", - "templateId": "Tyr" + "alias": "Y", + "templateId": "Y___Tyrosine" }, - "monomerTemplate-Ala": { + "monomerTemplate-A___Alanine": { "type": "monomerTemplate", - "id": "Ala", + "id": "A___Alanine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "A", - "name": "Ala", "fullName": "Alanine", + "alias": "A", "naturalAnalogShort": "A", - "naturalAnalog": "Ala", "attachmentPoints": [ { "attachmentAtom": 0, + "type": "left", "leavingGroup": { "atoms": [ 6 @@ -630,6 +629,7 @@ }, { "attachmentAtom": 3, + "type": "right", "leavingGroup": { "atoms": [ 5 @@ -641,58 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a/api/tests/integration/tests/formats/ref/break_peptide.ket b/api/tests/integration/tests/formats/ref/break_peptide.ket index 900318f856..05c4414bbd 100644 --- a/api/tests/integration/tests/formats/ref/break_peptide.ket +++ b/api/tests/integration/tests/formats/ref/break_peptide.ket @@ -4884,64 +4884,64 @@ ], "templates": [ { - "$ref": "monomerTemplate-Met" + "$ref": "monomerTemplate-M___Methionine" }, { - "$ref": "monomerTemplate-Asp" + "$ref": "monomerTemplate-D___Aspartic acid" }, { - "$ref": "monomerTemplate-Gln" + "$ref": "monomerTemplate-Q___Glutamine" }, { - "$ref": "monomerTemplate-Ser" + "$ref": "monomerTemplate-S___Serine" }, { - "$ref": "monomerTemplate-Pro" + "$ref": "monomerTemplate-P___Proline" }, { - "$ref": "monomerTemplate-Ala" + "$ref": "monomerTemplate-A___Alanine" }, { - "$ref": "monomerTemplate-Glu" + "$ref": "monomerTemplate-E___Glutamic acid" }, { - "$ref": "monomerTemplate-Lys" + "$ref": "monomerTemplate-K___Lysine" }, { - "$ref": "monomerTemplate-Gly" + "$ref": 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}, - "alias": "Thr", - "templateId": "Thr" + "alias": "T", + "templateId": "T___Threonine" }, "monomer126": { "type": "monomer", "id": "126", "seqid": 57, "position": { - "x": 89.5999984741211, - "y": -1.600000023841858 + "x": 89.599998, + "y": -1.600000 }, - "alias": "Gly", - "templateId": "Gly" + "alias": "G", + "templateId": "G___Glycine" }, "monomer127": { "type": "monomer", "id": "127", "seqid": 58, "position": { - "x": 91.20000457763672, - "y": -1.600000023841858 + "x": 91.200005, + "y": -1.600000 }, - "alias": "Gly", - "templateId": "Gly" + "alias": "G", + "templateId": "G___Glycine" }, "monomer128": { "type": "monomer", "id": "128", "seqid": 59, "position": { - "x": 92.80000305175781, - "y": -1.600000023841858 + "x": 92.800003, + "y": -1.600000 }, - "alias": "Gly", - "templateId": "Gly" + "alias": "G", + "templateId": "G___Glycine" }, "monomer129": { "type": "monomer", "id": "129", "seqid": 60, "position": { - "x": 94.4000015258789, - "y": -1.600000023841858 + "x": 94.400002, + "y": -1.600000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, "monomer130": { "type": "monomer", "id": "130", "seqid": 61, "position": { - "x": 96.0, - "y": -1.600000023841858 + "x": 96.000000, + "y": -1.600000 }, - "alias": "Gly", - "templateId": "Gly" + "alias": "G", + "templateId": "G___Glycine" }, "monomer131": { "type": "monomer", "id": "131", "seqid": 62, "position": { - "x": 97.5999984741211, - "y": -1.600000023841858 + "x": 97.599998, + "y": -1.600000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, "monomer132": { "type": "monomer", "id": "132", "seqid": 63, "position": { - "x": 99.20000457763672, - "y": -1.600000023841858 + "x": 99.200005, + "y": -1.600000 }, - "alias": "Ala", - "templateId": "Ala" + "alias": "A", + "templateId": "A___Alanine" }, "monomer133": { "type": "monomer", "id": "133", "seqid": 64, "position": { - "x": 100.80000305175781, - "y": -1.600000023841858 + "x": 100.800003, + "y": -1.600000 }, - "alias": "Gly", - "templateId": "Gly" + "alias": "G", + "templateId": "G___Glycine" }, "monomer134": { "type": "monomer", "id": "134", "seqid": 65, "position": { - "x": 102.4000015258789, - "y": -1.600000023841858 + "x": 102.400002, + "y": -1.600000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, "monomer135": { "type": "monomer", "id": "135", "seqid": 66, "position": { - "x": 104.0, - "y": -1.600000023841858 + "x": 104.000000, + "y": -1.600000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, "monomer136": { "type": "monomer", "id": "136", "seqid": 67, "position": { - "x": 105.5999984741211, - "y": -1.600000023841858 + "x": 105.599998, + "y": -1.600000 }, - "alias": "Thr", - "templateId": "Thr" + "alias": "T", + "templateId": "T___Threonine" }, "monomer137": { "type": "monomer", "id": "137", "seqid": 68, "position": { - "x": 107.20000457763672, - "y": -1.600000023841858 + "x": 107.200005, + "y": -1.600000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, "monomer138": { "type": "monomer", "id": "138", "seqid": 69, "position": { - "x": 108.80000305175781, - "y": -1.600000023841858 + "x": 108.800003, + "y": -1.600000 }, - "alias": "Ala", - "templateId": "Ala" + "alias": "A", + "templateId": "A___Alanine" }, "monomer139": { "type": "monomer", "id": "139", "seqid": 70, "position": { - "x": 110.4000015258789, - "y": -1.600000023841858 + "x": 110.400002, + "y": -1.600000 }, - "alias": "Ala", - "templateId": "Ala" + "alias": "A", + "templateId": "A___Alanine" }, - "monomerTemplate-Gly": { + "monomerTemplate-G___Glycine": { "type": "monomerTemplate", - "id": "Gly", + "id": "G___Glycine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "G", - "name": "Gly", "fullName": "Glycine", + "alias": "G", "naturalAnalogShort": "G", - "naturalAnalog": "Gly", "attachmentPoints": [ { "attachmentAtom": 4, + "type": "left", "leavingGroup": { "atoms": [ 5 @@ -3518,6 +3517,7 @@ }, { "attachmentAtom": 1, + "type": "right", "leavingGroup": { "atoms": [ 3 @@ -3529,49 +3529,49 @@ { "label": "C", "location": [ - -0.33629998564720156, - 0.534600019454956, - 0.0 + -0.336300, + 0.534600, + 0.000000 ] }, { "label": "C", "location": [ - 0.992900013923645, - -0.11069999635219574, - 0.0 + 0.992900, + -0.110700, + 0.000000 ] }, { "label": "O", "location": [ - 1.0781999826431275, - -1.2890000343322755, - 0.0 + 1.078200, + -1.289000, + 0.000000 ] }, { "label": "O", "location": [ - 1.970900058746338, - 0.5519999861717224, - 0.0 + 1.970900, + 0.552000, + 0.000000 ] }, { "label": "N", "location": [ - -1.3259999752044678, - -0.11069999635219574, - 0.0 + -1.326000, + -0.110700, + 0.000000 ] }, { "label": "H", "location": [ - -2.379699945449829, - 0.423799991607666, - 0.0 + -2.379700, + 0.423800, + 0.000000 ] } ], @@ -3613,19 +3613,18 @@ } ] }, - "monomerTemplate-Cys": { + "monomerTemplate-C___Cysteine": { "type": "monomerTemplate", - "id": "Cys", + "id": "C___Cysteine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "C", - "name": "Cys", "fullName": "Cysteine", + "alias": "C", "naturalAnalogShort": "C", - "naturalAnalog": "Cys", "attachmentPoints": [ { "attachmentAtom": 4, + "type": "left", "leavingGroup": { "atoms": [ 7 @@ -3634,6 +3633,7 @@ }, { "attachmentAtom": 0, + "type": "right", "leavingGroup": { "atoms": [ 6 @@ -3642,6 +3642,7 @@ }, { "attachmentAtom": 3, + "type": "side", "leavingGroup": { "atoms": [ 8 @@ -3653,74 +3654,74 @@ { "label": "C", "location": [ - 1.4457000494003297, - -1.1332999467849732, - 0.0 + 1.445700, + -1.133300, + 0.000000 ] }, { "label": "C", "location": [ - 0.1453000009059906, - -0.3840000033378601, - 0.0 + 0.145300, + -0.384000, + 0.000000 ], "stereoLabel": "abs" }, { "label": "C", "location": [ - 0.14300000667572022, - 1.1167999505996705, - 0.0 + 0.143000, + 1.116800, + 0.000000 ] }, { "label": "S", "location": [ - -1.1572999954223633, - 1.8660999536514283, - 0.0 + -1.157300, + 1.866100, + 0.000000 ] }, { "label": "N", "location": [ - -1.1550999879837037, - -1.1332999467849732, - 0.0 + -1.155100, + -1.133300, + 0.000000 ] }, { "label": "O", "location": [ - 1.4474999904632569, - -2.3333001136779787, - 0.0 + 1.447500, + -2.333300, + 0.000000 ] }, { "label": "O", "location": [ - 2.4842000007629396, - -0.5320000052452087, - 0.0 + 2.484200, + -0.532000, + 0.000000 ] }, { "label": "H", "location": [ - -2.194200038909912, - -0.5331000089645386, - 0.0 + -2.194200, + -0.533100, + 0.000000 ] }, { "label": "H", "location": [ - -1.15910005569458, - 3.0660998821258547, - 0.0 + -1.159100, + 3.066100, + 0.000000 ] } ], @@ -3784,19 +3785,18 @@ } ] }, - "monomerTemplate-Ala": { + "monomerTemplate-A___Alanine": { "type": "monomerTemplate", - "id": "Ala", + "id": "A___Alanine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "A", - "name": "Ala", "fullName": "Alanine", + "alias": "A", "naturalAnalogShort": "A", - "naturalAnalog": "Ala", "attachmentPoints": [ { "attachmentAtom": 0, + "type": "left", "leavingGroup": { "atoms": [ 6 @@ -3805,6 +3805,7 @@ }, { "attachmentAtom": 3, + "type": "right", "leavingGroup": { "atoms": [ 5 @@ -3816,58 +3817,58 @@ { "label": "N", "location": [ - -0.9805331230163574, - -0.3062945008277893, - 0.0 + -1.254900, + -0.392000, + 0.000000 ] }, { "label": "C", "location": [ - -0.21253088116645814, - 0.2057330161333084, - 0.0 + -0.272000, + 0.263300, + 0.000000 ], "stereoLabel": "abs" }, { "label": "C", "location": [ - -0.24245710670948029, - 1.3590255975723267, - 0.0 + -0.310300, + 1.739300, + 0.000000 ] }, { "label": "C", "location": [ - 0.8222288489341736, - -0.3062945008277893, - 0.0 + 1.052300, + -0.392000, + 0.000000 ] }, { "label": "O", "location": [ - 0.846138596534729, - -1.2284597158432007, - 0.0 + 1.082900, + -1.572200, + 0.000000 ] }, { "label": "O", "location": [ - 1.5903092622756959, - 0.2057330161333084, - 0.0 + 2.035300, + 0.263300, + 0.000000 ] }, { "label": "H", "location": [ - -1.823233723640442, - 0.07071340084075928, - 0.0 + -2.333400, + 0.090500, + 0.000000 ] } ], @@ -3917,19 +3918,18 @@ } ] }, - "monomerTemplate-Thr": { + "monomerTemplate-T___Threonine": { "type": "monomerTemplate", - "id": "Thr", + "id": "T___Threonine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "T", - "name": "Thr", "fullName": "Threonine", + "alias": "T", "naturalAnalogShort": "T", - "naturalAnalog": "Thr", "attachmentPoints": [ { "attachmentAtom": 3, + "type": "left", "leavingGroup": { "atoms": [ 4 @@ -3938,6 +3938,7 @@ }, { "attachmentAtom": 0, + "type": "right", "leavingGroup": { "atoms": [ 8 @@ -3946,6 +3947,7 @@ }, { "attachmentAtom": 6, + "type": "side", "leavingGroup": { "atoms": [ 9 @@ -3957,83 +3959,83 @@ { "label": "C", "location": [ - 0.8195480108261108, - -0.9813008904457092, - 0.0 + 1.048800, + -1.255800, + 0.000000 ] }, { "label": "O", "location": [ - 0.8190010190010071, - -1.9042301177978516, - 0.0 + 1.048100, + -2.436900, + 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0.786600, + 2.731800, + 0.000000 ] } ], diff --git a/api/tests/integration/tests/formats/ref/dna_acgtu.ket b/api/tests/integration/tests/formats/ref/dna_acgtu.ket index e42daa1072..c552b4e07f 100644 --- a/api/tests/integration/tests/formats/ref/dna_acgtu.ket +++ b/api/tests/integration/tests/formats/ref/dna_acgtu.ket @@ -191,25 +191,25 @@ ], "templates": [ { - "$ref": "monomerTemplate-Ade" + "$ref": "monomerTemplate-A___Adenine" }, { - "$ref": "monomerTemplate-dRib" + "$ref": "monomerTemplate-dR___Deoxy-Ribose" }, { - "$ref": "monomerTemplate-Cyt" + "$ref": "monomerTemplate-C___Cytosine" }, { - "$ref": "monomerTemplate-P" + "$ref": "monomerTemplate-P___Phosphate" }, { - "$ref": "monomerTemplate-Gua" + "$ref": "monomerTemplate-G___Guanine" }, { - "$ref": "monomerTemplate-Thy" + "$ref": "monomerTemplate-T___Thymine" }, { - "$ref": "monomerTemplate-Ura" + "$ref": "monomerTemplate-U___Uracil" } ] }, @@ -218,168 +218,167 @@ "id": "0", "seqid": 1, "position": { - "x": 0.0, - "y": -0.0 + "x": 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}, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 10 + ] + }, + { + "type": 2, + "atoms": [ + 7, + 8 + ] + } + ] + }, + "monomerTemplate-P___Phosphate": { + "type": "monomerTemplate", + "id": "P___Phosphate", + "class": "Phosphate", + "classHELM": "RNA", + "fullName": "Phosphate", + "alias": "P", + "naturalAnalogShort": "P", + "attachmentPoints": [ + { + "attachmentAtom": 0, + "type": "left", + "leavingGroup": { + "atoms": [ + 1 + ] + } + }, + { + "attachmentAtom": 0, + "type": "right", + "leavingGroup": { + "atoms": [ + 3 + ] + } + } + ], + "atoms": [ + { + "label": "P", + "location": [ + -0.239900, + 0.000000, + 0.000000 + ] + }, + { + "label": "O", + "location": [ + -1.439900, + 0.000000, + 0.000000 + ] + }, + { + "label": "O", + "location": [ + 0.359800, + -1.039400, + 0.000000 + ] + }, + { + "label": "O", + "location": [ + 0.960100, + 0.000000, + 0.000000 + ] + }, + { + "label": "O", + "location": [ + 0.359800, + 1.039400, + 0.000000 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 2, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 4 + ] + } + ] + }, + "variantMonomerTemplate-B": { + "type": "variantMonomerTemplate", + "subtype": "mixture", + "id": "B", + "name": "B", + "options": [ + { + "templateId": "C___Cytosine" + }, + { + "templateId": "G___Guanine" + }, + { + "templateId": "T___Thymine" + } + ] + }, + "variantMonomerTemplate-N": { + "type": "variantMonomerTemplate", + "subtype": "mixture", + "id": "N", + "name": "N", + "options": [ + { + "templateId": "A___Adenine" + }, + { + "templateId": "C___Cytosine" + }, + { + "templateId": "G___Guanine" + }, + { + "templateId": "T___Thymine" + } + ] + } +} \ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/monomer_library.ket b/api/tests/integration/tests/formats/ref/monomer_library.ket index c4c3b1d280..5dab2bcfc5 100644 --- a/api/tests/integration/tests/formats/ref/monomer_library.ket +++ b/api/tests/integration/tests/formats/ref/monomer_library.ket @@ -561,6 +561,9 @@ { "$ref": "monomerTemplate-pnT___PNA Thymine" }, + { + "$ref": "monomerTemplate-U___Selenocysteine" + }, { "$ref": "monomerTemplate-seC___SelenoCysteine" }, @@ -609,6 +612,9 @@ { "$ref": "monomerTemplate-NMe___C-Terminal NMe" }, + { + "$ref": "monomerTemplate-O___Pyrrolysine" + }, { "$ref": "monomerTemplate-OMe___C-Terminal OMe" }, @@ -42537,6 +42543,178 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-U___Selenocysteine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "N", + "location": [ + 14.558974596215561, + -10.200000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -9.700000000000001, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 16.291025403784438, + -10.200000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 17.15705080756888, + -9.700000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 16.291025403784438, + -11.200000000000003, + 0 + ] + }, + { + "label": "H", + "location": [ + 13.692949192431122, + -9.700000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -8.700000000000001, + 0 + ] + }, + { + "label": "Se", + "location": [ + 14.558974596215563, + -8.2, + 0 + ] + }, + { + "label": "H", + "location": [ + 14.558974596215563, + -7.2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "U___Selenocysteine", + "fullName": "Selenocysteine", + "alias": "U", + "attachmentPoints": [ + { + "attachmentAtom": 0, + "leavingGroup": { + "atoms": [ + 5 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 2, + "leavingGroup": { + "atoms": [ + 3 + ] + }, + "type": "right" + }, + { + "attachmentAtom": 7, + "leavingGroup": { + "atoms": [ + 8 + ] + }, + "type": "side" + } + ], + "naturalAnalogShort": "U" + }, "monomerTemplate-seC___SelenoCysteine": { "type": "monomerTemplate", "atoms": [ @@ -46248,6 +46426,328 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-O___Pyrrolysine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "H", + "location": [ + -2.0487, + -3.86, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.0256, + -4.4508, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.0024, + -3.86, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.0208, + -4.4508, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.0439, + -3.86, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.0208, + -5.6322, + 0 + ] 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"templateId": "T___Thymine" + } + ] + } +} \ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/spaces.ket b/api/tests/integration/tests/formats/ref/spaces.ket index 140940f008..4599a4c408 100644 --- a/api/tests/integration/tests/formats/ref/spaces.ket +++ b/api/tests/integration/tests/formats/ref/spaces.ket @@ -292,67 +292,67 @@ ], "templates": [ { - "$ref": "monomerTemplate-Ala" + "$ref": "monomerTemplate-A___Alanine" }, { - "$ref": "monomerTemplate-Cys" + "$ref": "monomerTemplate-C___Cysteine" }, { - "$ref": "monomerTemplate-Asp" + "$ref": "monomerTemplate-D___Aspartic acid" }, { - "$ref": "monomerTemplate-Glu" + "$ref": "monomerTemplate-E___Glutamic acid" }, { - "$ref": "monomerTemplate-Phe" + "$ref": "monomerTemplate-F___Phenylalanine" }, { - "$ref": "monomerTemplate-Gly" + "$ref": "monomerTemplate-G___Glycine" }, { - "$ref": "monomerTemplate-His" + "$ref": "monomerTemplate-H___Histidine" }, { - "$ref": "monomerTemplate-Ile" + "$ref": "monomerTemplate-I___Isoleucine" }, { - "$ref": "monomerTemplate-Lys" + "$ref": "monomerTemplate-K___Lysine" }, { - "$ref": "monomerTemplate-Leu" + "$ref": "monomerTemplate-L___Leucine" }, { - "$ref": "monomerTemplate-Met" + "$ref": "monomerTemplate-M___Methionine" }, { - "$ref": "monomerTemplate-Asn" + "$ref": "monomerTemplate-N___Asparagine" }, { - "$ref": "monomerTemplate-Pyl" + "$ref": "monomerTemplate-O___Pyrrolysine" }, { - "$ref": "monomerTemplate-Pro" + "$ref": "monomerTemplate-P___Proline" }, { - "$ref": "monomerTemplate-Gln" + "$ref": "monomerTemplate-Q___Glutamine" }, { - "$ref": "monomerTemplate-Arg" + "$ref": "monomerTemplate-R___Arginine" }, { - "$ref": "monomerTemplate-Ser" + "$ref": "monomerTemplate-S___Serine" }, { - "$ref": "monomerTemplate-Sec" + "$ref": "monomerTemplate-U___Selenocysteine" }, { - "$ref": "monomerTemplate-Val" + "$ref": "monomerTemplate-V___Valine" }, { - "$ref": "monomerTemplate-Trp" + "$ref": "monomerTemplate-W___Tryptophan" }, { - "$ref": 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"O", "location": [ - 3.1133999824523927, - -1.4767999649047852, - 0.0 + 3.113400, + -1.476800, + 0.000000 ] }, { "label": "H", "location": [ - -2.6319000720977785, - 3.238100051879883, - 0.0 + -2.631900, + 3.238100, + 0.000000 ] } ], diff --git a/api/tests/integration/tests/formats/ref/test_1881.ket b/api/tests/integration/tests/formats/ref/test_1881.ket index d920dfc642..dc338a6571 100644 --- a/api/tests/integration/tests/formats/ref/test_1881.ket +++ b/api/tests/integration/tests/formats/ref/test_1881.ket @@ -14,16 +14,15 @@ "$ref": "monomer3" } ], - "connections": [], "templates": [ { - "$ref": "monomerTemplate-Ala" + "$ref": "monomerTemplate-A___Alanine" }, { - "$ref": "monomerTemplate-Asp" + "$ref": "monomerTemplate-D___Aspartic acid" }, { - "$ref": "monomerTemplate-Cys" + "$ref": "monomerTemplate-C___Cysteine" } ] }, @@ -32,58 +31,57 @@ "id": "0", "seqid": 1, "position": { - "x": 0.0, - "y": -0.0 + "x": 0.000000, + "y": -0.000000 }, - "alias": "Ala", - "templateId": "Ala" + "alias": "A", + "templateId": "A___Alanine" }, "monomer1": { "type": "monomer", "id": "1", "seqid": 1, "position": { - "x": 0.0, - "y": -1.600000023841858 + "x": 0.000000, + "y": -1.600000 }, - "alias": "Ala", - "templateId": "Ala" + "alias": "A", + "templateId": "A___Alanine" }, "monomer2": { "type": "monomer", "id": "2", "seqid": 1, "position": { - "x": 0.0, - "y": -3.200000047683716 + "x": 0.000000, + "y": -3.200000 }, - "alias": "Asp", - "templateId": "Asp" + "alias": "D", + "templateId": "D___Aspartic acid" }, "monomer3": { "type": "monomer", "id": "3", "seqid": 1, "position": { - "x": 0.0, - "y": -4.800000190734863 + "x": 0.000000, + "y": -4.800000 }, - "alias": "Cys", - "templateId": "Cys" + "alias": "C", + "templateId": "C___Cysteine" }, - "monomerTemplate-Ala": { + "monomerTemplate-A___Alanine": { "type": "monomerTemplate", - "id": "Ala", + "id": "A___Alanine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "A", - "name": "Ala", "fullName": "Alanine", + "alias": "A", "naturalAnalogShort": "A", - "naturalAnalog": "Ala", "attachmentPoints": [ { "attachmentAtom": 0, + "type": "left", "leavingGroup": { "atoms": [ 6 @@ -92,6 +90,7 @@ }, { "attachmentAtom": 3, + "type": "right", "leavingGroup": { "atoms": [ 5 @@ -103,58 +102,58 @@ { "label": "N", "location": [ - -0.9805331230163574, - -0.3062945008277893, - 0.0 + -1.254900, + -0.392000, + 0.000000 ] }, { "label": "C", "location": [ - -0.21253088116645814, - 0.2057330161333084, - 0.0 + -0.272000, + 0.263300, + 0.000000 ], "stereoLabel": "abs" }, { "label": "C", "location": [ - -0.24245710670948029, - 1.3590255975723267, - 0.0 + -0.310300, + 1.739300, + 0.000000 ] }, { "label": "C", "location": [ - 0.8222288489341736, - -0.3062945008277893, - 0.0 + 1.052300, + -0.392000, + 0.000000 ] }, { "label": "O", "location": [ - 0.846138596534729, - -1.2284597158432007, - 0.0 + 1.082900, + -1.572200, + 0.000000 ] }, { "label": "O", "location": [ - 1.5903092622756959, - 0.2057330161333084, - 0.0 + 2.035300, + 0.263300, + 0.000000 ] }, { "label": "H", "location": [ - -1.823233723640442, - 0.07071340084075928, - 0.0 + -2.333400, + 0.090500, + 0.000000 ] } ], @@ -204,19 +203,18 @@ } ] }, - "monomerTemplate-Asp": { + "monomerTemplate-D___Aspartic acid": { "type": "monomerTemplate", - "id": "Asp", + "id": "D___Aspartic acid", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "D", - "name": "Asp", "fullName": "Aspartic acid", + "alias": "D", "naturalAnalogShort": "D", - "naturalAnalog": "Asp", "attachmentPoints": [ { "attachmentAtom": 3, + "type": "left", "leavingGroup": { "atoms": [ 4 @@ -225,6 +223,7 @@ }, { "attachmentAtom": 0, + "type": "right", "leavingGroup": { "atoms": [ 9 @@ -233,6 +232,7 @@ }, { "attachmentAtom": 8, + "type": "side", "leavingGroup": { "atoms": [ 10 @@ -244,90 +244,90 @@ { "label": "C", "location": [ - 1.63100004196167, - -1.557800054550171, - 0.0 + 1.631000, + -1.557800, + 0.000000 ] }, { "label": "O", "location": [ - 1.632699966430664, - -2.7392001152038576, - 0.0 + 1.632700, + -2.739200, + 0.000000 ] }, { "label": "C", "location": [ - 0.3506999909877777, - -0.8201000094413757, - 0.0 + 0.350700, + -0.820100, + 0.000000 ], "stereoLabel": "abs" }, { "label": "N", "location": [ - -0.9294999837875366, - -1.557800054550171, - 0.0 + -0.929500, + -1.557800, + 0.000000 ] }, { "label": "H", "location": [ - -1.9524999856948853, - -0.9668999910354614, - 0.0 + -1.952500, + -0.966900, + 0.000000 ] }, { "label": "C", "location": [ - 0.34850001335144045, - 0.6575000286102295, - 0.0 + 0.348500, + 0.657500, + 0.000000 ] }, { "label": "C", "location": [ - -0.9316999912261963, - 1.3952000141143799, - 0.0 + -0.931700, + 1.395200, + 0.000000 ] }, { "label": "O", "location": [ - -1.954200029373169, - 0.8032000064849854, - 0.0 + -1.954200, + 0.803200, + 0.000000 ] }, { "label": "O", "location": [ - -0.9334999918937683, - 2.5766000747680666, - 0.0 + -0.933500, + 2.576600, + 0.000000 ] }, { "label": "O", "location": [ - 2.65339994430542, - -0.9657999873161316, - 0.0 + 2.653400, + -0.965800, + 0.000000 ] }, { "label": "H", "location": [ - 0.08510000258684159, - 3.175100088119507, - 0.0 + 0.085100, + 3.175100, + 0.000000 ] } ], @@ -405,19 +405,18 @@ } ] }, - "monomerTemplate-Cys": { + "monomerTemplate-C___Cysteine": { "type": "monomerTemplate", - "id": "Cys", + "id": "C___Cysteine", "class": "AminoAcid", "classHELM": "PEPTIDE", - "alias": "C", - "name": "Cys", "fullName": "Cysteine", + "alias": "C", "naturalAnalogShort": "C", - "naturalAnalog": "Cys", "attachmentPoints": [ { "attachmentAtom": 4, + "type": "left", "leavingGroup": { "atoms": [ 7 @@ -426,6 +425,7 @@ }, { "attachmentAtom": 0, + "type": "right", "leavingGroup": { "atoms": [ 6 @@ -434,6 +434,7 @@ }, { "attachmentAtom": 3, + "type": "side", "leavingGroup": { "atoms": [ 8 @@ -445,74 +446,74 @@ { "label": "C", "location": [ - 1.4457000494003297, - -1.1332999467849732, - 0.0 + 1.445700, + -1.133300, + 0.000000 ] }, { "label": "C", "location": [ - 0.1453000009059906, - -0.3840000033378601, - 0.0 + 0.145300, + -0.384000, + 0.000000 ], "stereoLabel": "abs" }, { "label": "C", "location": [ - 0.14300000667572022, - 1.1167999505996705, - 0.0 + 0.143000, + 1.116800, + 0.000000 ] }, { "label": "S", "location": [ - -1.1572999954223633, - 1.8660999536514283, - 0.0 + -1.157300, + 1.866100, + 0.000000 ] }, { "label": "N", "location": [ - -1.1550999879837037, - -1.1332999467849732, - 0.0 + -1.155100, + -1.133300, + 0.000000 ] }, { "label": "O", "location": [ - 1.4474999904632569, - -2.3333001136779787, - 0.0 + 1.447500, + -2.333300, + 0.000000 ] }, { "label": "O", "location": [ - 2.4842000007629396, - -0.5320000052452087, - 0.0 + 2.484200, + -0.532000, + 0.000000 ] }, { "label": "H", "location": [ - -2.194200038909912, - -0.5331000089645386, - 0.0 + -2.194200, + -0.533100, + 0.000000 ] }, { "label": "H", "location": [ - -1.15910005569458, - 3.0660998821258547, - 0.0 + -1.159100, + 3.066100, + 0.000000 ] } ], diff --git a/api/tests/integration/tests/formats/ref/test_dna.ket b/api/tests/integration/tests/formats/ref/test_dna.ket index 814045c433..b8404aaa60 100644 --- a/api/tests/integration/tests/formats/ref/test_dna.ket +++ b/api/tests/integration/tests/formats/ref/test_dna.ket @@ -5315,22 +5315,22 @@ ], "templates": [ { - "$ref": "monomerTemplate-Thy" + "$ref": "monomerTemplate-T___Thymine" }, { - "$ref": "monomerTemplate-dRib" + "$ref": "monomerTemplate-dR___Deoxy-Ribose" }, { - "$ref": "monomerTemplate-Cyt" + "$ref": "monomerTemplate-C___Cytosine" }, { - "$ref": "monomerTemplate-P" + "$ref": "monomerTemplate-P___Phosphate" }, { - "$ref": "monomerTemplate-Ade" + "$ref": "monomerTemplate-A___Adenine" }, { - "$ref": "monomerTemplate-Gua" + "$ref": "monomerTemplate-G___Guanine" } ] }, @@ -5339,4194 +5339,4193 @@ "id": "0", "seqid": 1, "position": { - "x": 0.0, - "y": -0.0 + "x": 0.000000, + "y": -0.000000 }, "alias": "dR", - "templateId": "dRib" + "templateId": "dR___Deoxy-Ribose" }, "monomer1": { "type": "monomer", "id": "1", "seqid": 1, "position": { - 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a/api/tests/integration/tests/formats/ref/test_peptide.ket +++ b/api/tests/integration/tests/formats/ref/test_peptide.ket @@ -6995,64 +6995,64 @@ ], "templates": [ { - "$ref": "monomerTemplate-Met" + "$ref": "monomerTemplate-M___Methionine" }, { - "$ref": "monomerTemplate-Ile" + "$ref": "monomerTemplate-I___Isoleucine" }, { - "$ref": "monomerTemplate-Gly" + "$ref": "monomerTemplate-G___Glycine" }, { - "$ref": "monomerTemplate-Tyr" + "$ref": "monomerTemplate-Y___Tyrosine" }, { - "$ref": "monomerTemplate-Val" + "$ref": "monomerTemplate-V___Valine" }, { - "$ref": "monomerTemplate-Gln" + "$ref": "monomerTemplate-Q___Glutamine" }, { - "$ref": "monomerTemplate-Ala" + "$ref": "monomerTemplate-A___Alanine" }, { - "$ref": "monomerTemplate-Thr" + "$ref": "monomerTemplate-T___Threonine" }, { - "$ref": "monomerTemplate-Glu" + "$ref": "monomerTemplate-E___Glutamic acid" }, { - "$ref": "monomerTemplate-Leu" + "$ref": "monomerTemplate-L___Leucine" }, { - "$ref": "monomerTemplate-Arg" + "$ref": 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2.180400, + 0.000000 ] }, { "label": "N", "location": [ - 0.4990125596523285, - 1.1842495203018189, - 0.0 + 0.723500, + 1.717000, + 0.000000 ] }, { "label": "N", "location": [ - -1.6464310884475709, - -1.0369253158569337, - 0.0 + -2.387100, + -1.503400, + 0.000000 ] }, { "label": "C", "location": [ - -1.0382357835769654, - -1.8738317489624024, - 0.0 + -1.505300, + -2.716800, + 0.000000 ] }, { "label": "N", "location": [ - -0.054280977696180347, - -1.5540775060653687, - 0.0 + -0.078700, + -2.253200, + 0.000000 ] }, { "label": "N", "location": [ - 1.5013829469680787, - -0.08338717371225357, - 0.0 + 2.176800, + -0.120900, + 0.000000 ] }, { "label": "H", "location": [ - -2.474095344543457, - -1.0369253158569337, - 0.0 + -3.587100, + -1.503400, + 0.000000 ] } ], @@ -10360,19 +10359,18 @@ } ] }, - "monomerTemplate-Gua": { + "monomerTemplate-G___Guanine": { "type": "monomerTemplate", - "id": "Gua", + "id": "G___Guanine", "class": "Base", "classHELM": "RNA", - "alias": "G", - "name": "Gua", "fullName": "Guanine", + "alias": "G", "naturalAnalogShort": "G", - "naturalAnalog": "Gua", "attachmentPoints": [ { "attachmentAtom": 6, + "type": "left", "leavingGroup": { "atoms": [ 11 @@ -10384,97 +10382,97 @@ { "label": "C", "location": [ - 1.0354000329971314, - 0.24979999661445619, - 0.0 + 1.035400, + 0.249800, + 0.000000 ] }, { "label": "C", "location": [ - -0.07919999957084656, - -0.7540000081062317, - 0.0 + -0.079200, + -0.754000, + 0.000000 ] }, { "label": "C", "location": [ - -1.5056999921798707, - -0.2906000018119812, - 0.0 + -1.505700, + -0.290600, + 0.000000 ] }, { "label": "N", "location": [ - -1.8177000284194947, - 1.1765999794006348, - 0.0 + -1.817700, + 1.176600, + 0.000000 ] }, { "label": "C", "location": [ - -0.7031000256538391, - 2.1803998947143556, - 0.0 + -0.703100, + 2.180400, + 0.000000 ] }, { "label": "N", "location": [ - 0.7235000133514404, - 1.7170000076293946, - 0.0 + 0.723500, + 1.717000, + 0.000000 ] }, { "label": "N", "location": [ - -2.3870999813079836, - -1.5033999681472779, - 0.0 + -2.387100, + -1.503400, + 0.000000 ] }, { "label": "C", "location": [ - -1.5053000450134278, - -2.7167999744415285, - 0.0 + -1.505300, + -2.716800, + 0.000000 ] }, { "label": "N", "location": [ - -0.0786999985575676, - -2.253200054168701, - 0.0 + -0.078700, + -2.253200, + 0.000000 ] }, { "label": "O", "location": [ - 2.176800012588501, - -0.120899997651577, - 0.0 + 2.176800, + -0.120900, + 0.000000 ] }, { "label": "N", "location": [ - -0.9527000188827515, - 3.3541998863220217, - 0.0 + -0.952700, + 3.354200, + 0.000000 ] }, { "label": "H", "location": [ - -3.587100028991699, - -1.5033999681472779, - 0.0 + -3.587100, + -1.503400, + 0.000000 ] } ], diff --git a/api/tests/integration/tests/formats/seq_to_ket.py b/api/tests/integration/tests/formats/seq_to_ket.py index fbb0992e84..6f8c0120f2 100644 --- a/api/tests/integration/tests/formats/seq_to_ket.py +++ b/api/tests/integration/tests/formats/seq_to_ket.py @@ -35,10 +35,14 @@ def find_diff(a, b): "seq_data": "ACD\nEFG\r\nHIKLMN OPQRSRUVWY", "ref": "spaces", }, + {"seq_type": "PEPTIDE", "seq_data": "BJZX", "ref": "aminoacids_variants"}, + {"seq_type": "RNA", "seq_data": "KN", "ref": "rna_variants"}, + {"seq_type": "DNA", "seq_data": "BN", "ref": "dna_variants"}, ] -# empty library - internal used for now -lib = indigo.loadMonomerLibrary('{"root":{}}') +lib = indigo.loadMonomerLibraryFromFile( + os.path.join(ref_path, "monomer_library.ket") +) for seq in seq_tests: mol = indigo.loadSequence(seq["seq_data"], seq["seq_type"], lib) diff --git a/api/wasm/indigo-ketcher/test/dna_ref.ket b/api/wasm/indigo-ketcher/test/dna_ref.ket index 8cf4556476..c292c79f5b 100644 --- a/api/wasm/indigo-ketcher/test/dna_ref.ket +++ b/api/wasm/indigo-ketcher/test/dna_ref.ket @@ -1 +1 @@ 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atoms\":[0,1]},{\"type\":2,\"atoms\":[0,2]},{\"type\":1,\"atoms\":[0,3]},{\"type\":1,\"atoms\":[0,4]}]},\"monomerTemplate-G___Guanine\":{\"type\":\"monomerTemplate\",\"id\":\"G___Guanine\",\"class\":\"Base\",\"classHELM\":\"RNA\",\"fullName\":\"Guanine\",\"alias\":\"G\",\"naturalAnalogShort\":\"G\",\"attachmentPoints\":[{\"attachmentAtom\":6,\"type\":\"left\",\"leavingGroup\":{\"atoms\":[11]}}],\"atoms\":[{\"label\":\"C\",\"location\":[1.035400,0.249800,0.000000]},{\"label\":\"C\",\"location\":[-0.079200,-0.754000,0.000000]},{\"label\":\"C\",\"location\":[-1.505700,-0.290600,0.000000]},{\"label\":\"N\",\"location\":[-1.817700,1.176600,0.000000]},{\"label\":\"C\",\"location\":[-0.703100,2.180400,0.000000]},{\"label\":\"N\",\"location\":[0.723500,1.717000,0.000000]},{\"label\":\"N\",\"location\":[-2.387100,-1.503400,0.000000]},{\"label\":\"C\",\"location\":[-1.505300,-2.716800,0.000000]},{\"label\":\"N\",\"location\":[-0.078700,-2.253200,0.000000]},{\"label\":\"O\",\"location\":[2.176800,-0.120900,0.000000]},{\"label\":\"N\",\"location\":[-0.952700,3.354200,0.000000]},{\"label\":\"H\",\"location\":[-3.587100,-1.503400,0.000000]}],\"bonds\":[{\"type\":2,\"atoms\":[0,9]},{\"type\":1,\"atoms\":[0,5]},{\"type\":1,\"atoms\":[0,1]},{\"type\":1,\"atoms\":[8,1]},{\"type\":2,\"atoms\":[1,2]},{\"type\":1,\"atoms\":[6,2]},{\"type\":1,\"atoms\":[2,3]},{\"type\":2,\"atoms\":[3,4]},{\"type\":1,\"atoms\":[4,5]},{\"type\":1,\"atoms\":[4,10]},{\"type\":1,\"atoms\":[6,7]},{\"type\":1,\"atoms\":[6,11]},{\"type\":2,\"atoms\":[7,8]}]},\"monomerTemplate-T___Thymine\":{\"type\":\"monomerTemplate\",\"id\":\"T___Thymine\",\"class\":\"Base\",\"classHELM\":\"RNA\",\"fullName\":\"Thymine\",\"alias\":\"T\",\"naturalAnalogShort\":\"T\",\"attachmentPoints\":[{\"attachmentAtom\":3,\"type\":\"left\",\"leavingGroup\":{\"atoms\":[8]}}],\"atoms\":[{\"label\":\"C\",\"location\":[1.861700,1.349900,0.000000]},{\"label\":\"C\",\"location\":[1.111700,0.050900,0.000000]},{\"label\":\"C\",\"location\":[-0.388300,0.050900,0.000000]},{\"label\":\"N\",\"location\":[-1.138200,1.350000,0.000000]},{\"label\":\"C\",\"location\":[-0.388200,2.649000,0.000000]},{\"label\":\"N\",\"location\":[1.111700,2.648900,0.000000]},{\"label\":\"O\",\"location\":[3.061800,1.349900,0.000000]},{\"label\":\"O\",\"location\":[-0.988200,3.688200,0.000000]},{\"label\":\"H\",\"location\":[-2.338300,1.350000,0.000000]},{\"label\":\"C\",\"location\":[1.711700,-0.988400,0.000000]}],\"bonds\":[{\"type\":2,\"atoms\":[0,6]},{\"type\":1,\"atoms\":[0,5]},{\"type\":1,\"atoms\":[0,1]},{\"type\":2,\"atoms\":[1,2]},{\"type\":1,\"atoms\":[2,3]},{\"type\":1,\"atoms\":[3,4]},{\"type\":1,\"atoms\":[3,8]},{\"type\":2,\"atoms\":[4,7]},{\"type\":1,\"atoms\":[4,5]},{\"type\":1,\"atoms\":[1,9]}]},\"monomerTemplate-U___Uracil\":{\"type\":\"monomerTemplate\",\"id\":\"U___Uracil\",\"class\":\"Base\",\"classHELM\":\"RNA\",\"fullName\":\"Uracil\",\"alias\":\"U\",\"naturalAnalogShort\":\"U\",\"attachmentPoints\":[{\"attachmentAtom\":3,\"type\":\"left\",\"leavingGroup\":{\"atoms\":[8]}}],\"atoms\":[{\"label\":\"C\",\"location\":[1.861700,1.349900,0.000000]},{\"label\":\"C\",\"location\":[1.111700,0.050900,0.000000]},{\"label\":\"C\",\"location\":[-0.388300,0.050900,0.000000]},{\"label\":\"N\",\"location\":[-1.138200,1.350000,0.000000]},{\"label\":\"C\",\"location\":[-0.388200,2.649000,0.000000]},{\"label\":\"N\",\"location\":[1.111700,2.648900,0.000000]},{\"label\":\"O\",\"location\":[3.061800,1.349900,0.000000]},{\"label\":\"O\",\"location\":[-0.988200,3.688200,0.000000]},{\"label\":\"H\",\"location\":[-2.338300,1.350000,0.000000]}],\"bonds\":[{\"type\":2,\"atoms\":[0,6]},{\"type\":1,\"atoms\":[0,5]},{\"type\":1,\"atoms\":[0,1]},{\"type\":2,\"atoms\":[1,2]},{\"type\":1,\"atoms\":[2,3]},{\"type\":1,\"atoms\":[3,4]},{\"type\":1,\"atoms\":[3,8]},{\"type\":2,\"atoms\":[4,7]},{\"type\":1,\"atoms\":[4,5]}]}}","format":"ket","original_format":"unknown"} \ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/monomer_library.ket b/api/wasm/indigo-ketcher/test/monomer_library.ket index 4a594c4632..5dab2bcfc5 100644 --- a/api/wasm/indigo-ketcher/test/monomer_library.ket +++ b/api/wasm/indigo-ketcher/test/monomer_library.ket @@ -561,6 +561,9 @@ { "$ref": "monomerTemplate-pnT___PNA Thymine" }, + { + "$ref": "monomerTemplate-U___Selenocysteine" + }, { "$ref": "monomerTemplate-seC___SelenoCysteine" }, @@ -609,6 +612,9 @@ { "$ref": "monomerTemplate-NMe___C-Terminal NMe" }, + { + "$ref": "monomerTemplate-O___Pyrrolysine" + }, { "$ref": "monomerTemplate-OMe___C-Terminal OMe" }, @@ -2234,6 +2240,9 @@ }, { "$ref": "monomerGroupTemplate-dR(U)P" + }, + { + "$ref": "monomerTemplate-UNSPLIT" } ] }, @@ -42534,6 +42543,178 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-U___Selenocysteine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "N", + "location": [ + 14.558974596215561, + -10.200000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -9.700000000000001, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 16.291025403784438, + -10.200000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 17.15705080756888, + -9.700000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 16.291025403784438, + -11.200000000000003, + 0 + ] + }, + { + "label": "H", + "location": [ + 13.692949192431122, + -9.700000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -8.700000000000001, + 0 + ] + }, + { + "label": "Se", + "location": [ + 14.558974596215563, + -8.2, + 0 + ] + }, + { + "label": "H", + "location": [ + 14.558974596215563, + -7.2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "U___Selenocysteine", + "fullName": "Selenocysteine", + "alias": "U", + "attachmentPoints": [ + { + "attachmentAtom": 0, + "leavingGroup": { + "atoms": [ + 5 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 2, + "leavingGroup": { + "atoms": [ + 3 + ] + }, + "type": "right" + }, + { + "attachmentAtom": 7, + "leavingGroup": { + "atoms": [ + 8 + ] + }, + "type": "side" + } + ], + "naturalAnalogShort": "U" + }, "monomerTemplate-seC___SelenoCysteine": { "type": "monomerTemplate", "atoms": [ @@ -46245,6 +46426,328 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-O___Pyrrolysine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "H", + "location": [ + -2.0487, + -3.86, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.0256, + -4.4508, + 0 + ] + }, + { + "label": "C", + "location": [ 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\ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/rna_ref.ket b/api/wasm/indigo-ketcher/test/rna_ref.ket index bcc1878163..ed4089bb5e 100644 --- a/api/wasm/indigo-ketcher/test/rna_ref.ket +++ b/api/wasm/indigo-ketcher/test/rna_ref.ket @@ -1 +1 @@ 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\ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/test.js b/api/wasm/indigo-ketcher/test/test.js index ae6f212f8c..43d0bec95d 100644 --- a/api/wasm/indigo-ketcher/test/test.js +++ b/api/wasm/indigo-ketcher/test/test.js @@ -819,12 +819,14 @@ M END // RNA/DNA/PEPTIDE { test("PEPTIDE", "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"); const peptide_seq_ref = "ACDEFGHIKLMNOPQRSRUVWY"; const peptide_ket = indigo.convert(peptide_seq_ref, "ket", options); - var fs = require('fs'); // fs.writeFileSync("peptide_ref.ket", peptide_ket); const peptide_ket_ref = fs.readFileSync("peptide_ref.ket"); assert.equal(peptide_ket, peptide_ket_ref.toString()); @@ -839,12 +841,14 @@ M END { test("RNA", "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-rna-sequence"); const rna_seq_ref = "ACGTU"; const rna_ket = indigo.convert(rna_seq_ref, "ket", options); - var fs = require('fs'); // fs.writeFileSync("rna_ref.ket", rna_ket); const rna_ket_ref = fs.readFileSync("rna_ref.ket"); assert.equal(rna_ket, rna_ket_ref.toString()); @@ -860,12 +864,14 @@ M END { test("DNA", "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-dna-sequence"); const dna_seq_ref = "ACGTU"; const dna_ket = indigo.convert(dna_seq_ref, "ket", options); - var fs = require('fs'); // fs.writeFileSync("dna_ref.ket", dna_ket); const dna_ket_ref = fs.readFileSync("dna_ref.ket"); assert.equal(dna_ket, dna_ket_ref.toString()); @@ -883,6 +889,8 @@ M END test("PEPTIDE-FASTA", "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-fasta"); const fasta = fs.readFileSync("test_peptide.fasta"); @@ -906,6 +914,8 @@ M END test("RNA-FASTA", "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-rna-fasta"); const fasta = fs.readFileSync("test_rna.fasta"); @@ -929,13 +939,15 @@ M END test("DNA-FASTA", "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-dna-fasta"); const fasta = fs.readFileSync("test_dna.fasta"); const dna_ket = indigo.convert(fasta, "ket", options); const dna_fasta = indigo.convert(fasta, "fasta", options); - // fs.writeFileSync("test_dna_ref.ket", dna_ket); + fs.writeFileSync("test_dna_ref.ket", dna_ket); // fs.writeFileSync("test_dna_ref.fasta", dna_fasta); const dna_ket_ref = fs.readFileSync("test_dna_ref.ket"); diff --git a/api/wasm/indigo-ketcher/test/test_peptide_ref.ket b/api/wasm/indigo-ketcher/test/test_peptide_ref.ket index 57f4032e39..888cee2be3 100644 --- a/api/wasm/indigo-ketcher/test/test_peptide_ref.ket +++ b/api/wasm/indigo-ketcher/test/test_peptide_ref.ket @@ -1 +1 @@ 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\ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/test_rna_ref.ket b/api/wasm/indigo-ketcher/test/test_rna_ref.ket index eb4e9ad990..0de6eee2f1 100644 --- a/api/wasm/indigo-ketcher/test/test_rna_ref.ket +++ b/api/wasm/indigo-ketcher/test/test_rna_ref.ket @@ -1 +1 @@ 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type\":2,\"atoms\":[1,2]},{\"type\":1,\"atoms\":[6,2]},{\"type\":1,\"atoms\":[2,3]},{\"type\":2,\"atoms\":[3,4]},{\"type\":1,\"atoms\":[4,5]},{\"type\":1,\"atoms\":[6,7]},{\"type\":1,\"atoms\":[6,10]},{\"type\":2,\"atoms\":[7,8]}]},\"monomerTemplate-G___Guanine\":{\"type\":\"monomerTemplate\",\"id\":\"G___Guanine\",\"class\":\"Base\",\"classHELM\":\"RNA\",\"fullName\":\"Guanine\",\"alias\":\"G\",\"naturalAnalogShort\":\"G\",\"attachmentPoints\":[{\"attachmentAtom\":6,\"type\":\"left\",\"leavingGroup\":{\"atoms\":[11]}}],\"atoms\":[{\"label\":\"C\",\"location\":[1.035400,0.249800,0.000000]},{\"label\":\"C\",\"location\":[-0.079200,-0.754000,0.000000]},{\"label\":\"C\",\"location\":[-1.505700,-0.290600,0.000000]},{\"label\":\"N\",\"location\":[-1.817700,1.176600,0.000000]},{\"label\":\"C\",\"location\":[-0.703100,2.180400,0.000000]},{\"label\":\"N\",\"location\":[0.723500,1.717000,0.000000]},{\"label\":\"N\",\"location\":[-2.387100,-1.503400,0.000000]},{\"label\":\"C\",\"location\":[-1.505300,-2.716800,0.000000]},{\"label\":\"N\",\"location\":[-0.078700,-2.253200,0.000000]},{\"label\":\"O\",\"location\":[2.176800,-0.120900,0.000000]},{\"label\":\"N\",\"location\":[-0.952700,3.354200,0.000000]},{\"label\":\"H\",\"location\":[-3.587100,-1.503400,0.000000]}],\"bonds\":[{\"type\":2,\"atoms\":[0,9]},{\"type\":1,\"atoms\":[0,5]},{\"type\":1,\"atoms\":[0,1]},{\"type\":1,\"atoms\":[8,1]},{\"type\":2,\"atoms\":[1,2]},{\"type\":1,\"atoms\":[6,2]},{\"type\":1,\"atoms\":[2,3]},{\"type\":2,\"atoms\":[3,4]},{\"type\":1,\"atoms\":[4,5]},{\"type\":1,\"atoms\":[4,10]},{\"type\":1,\"atoms\":[6,7]},{\"type\":1,\"atoms\":[6,11]},{\"type\":2,\"atoms\":[7,8]}]}}","format":"ket","original_format":"unknown"} \ No newline at end of file diff --git a/core/indigo-core/molecule/ket_document.h b/core/indigo-core/molecule/ket_document.h index a36ac62071..c10702f571 100644 --- a/core/indigo-core/molecule/ket_document.h +++ b/core/indigo-core/molecule/ket_document.h @@ -133,7 +133,7 @@ namespace indigo void processVariantMonomerTemplates(); - void parseSimplePolymers(std::vector>& sequences, bool for_sequence = false); + void parseSimplePolymers(std::vector>& sequences, bool for_idt = false); MonomerClass getMonomerClass(const KetBaseMonomer& monomer) const; @@ -162,6 +162,16 @@ namespace indigo return _json_molecules; }; + void setFastaProps(std::vector fasta_properties) + { + _fasta_properties = fasta_properties; + }; + + const std::vector& fastaProps() + { + return _fasta_properties; + }; + protected: void collect_sequence_side(const std::string& monomer_id, bool left_side, std::set& monomers, std::set& used_monomers, std::deque& sequence, std::map, const KetConnection&>& ap_to_connection); @@ -183,6 +193,7 @@ namespace indigo rapidjson::Value _r_groups; rapidjson::Value _json_molecules; rapidjson::Document _json_document; + std::vector _fasta_properties; }; } diff --git a/core/indigo-core/molecule/monomer_commons.h b/core/indigo-core/molecule/monomer_commons.h index ccdee79e39..d763122213 100644 --- a/core/indigo-core/molecule/monomer_commons.h +++ b/core/indigo-core/molecule/monomer_commons.h @@ -113,6 +113,19 @@ namespace indigo HELMType getHELMTypeFromString(const std::string& helm_type); const std::string& getStringFromHELMType(HELMType helm_type); + static const std::unordered_set STANDARD_PEPTIDES = {"A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", + "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "Y"}; + static const std::unordered_set STANDARD_NUCLEOTIDES = {"A", "C", "G", "T", "U"}; + + static const std::unordered_set IDT_STANDARD_BASES = {"A", "T", "C", "G", "U", "I", "In"}; static const std::map IDT_BASE_TO_RATIO_IDX = {{"A", 0}, {"C", 1}, {"G", 2}, {"T", 3}, {"U", 3}}; + static const std::map IDT_STANDARD_SUGARS{{"R", "r"}, {"LR", "+"}, {"mR", "m"}, {"dR", ""}}; + + static const std::map> STANDARD_MIXED_PEPTIDES = { + {"B", {"D", "N"}}, {"J", {"L", "I"}}, {"Z", {"E", "Q"}}, {"X", {"A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", + "N", "O", "P", "G", "R", "S", "T", "U", "V", "W", "Y"}}}; + static const std::map> STANDARD_MIXED_BASES = { + {"R", {"A", "G"}}, {"Y", {"C", "T"}}, {"M", {"A", "C"}}, {"K", {"G", "T"}}, {"S", {"G", "C"}}, {"W", {"A", "T"}}, + {"H", {"A", "C", "T"}}, {"B", {"C", "G", "T"}}, {"V", {"A", "C", "G"}}, {"D", {"A", "G", "T"}}, {"N", {"A", "C", "G", "T"}}}; } #endif \ No newline at end of file diff --git a/core/indigo-core/molecule/sequence_loader.h b/core/indigo-core/molecule/sequence_loader.h index afc027f187..5f23e8ee02 100644 --- a/core/indigo-core/molecule/sequence_loader.h +++ b/core/indigo-core/molecule/sequence_loader.h @@ -66,9 +66,14 @@ namespace indigo void loadFasta(BaseMolecule& mol, const std::string& seq_type_str); void loadFasta(BaseMolecule& mol, SeqType seq_type); void loadIdt(BaseMolecule& mol); - void loadIdt(KetDocument& document); void loadHELM(BaseMolecule& mol); + void loadSequence(KetDocument& document, const std::string& seq_type_str); + void loadSequence(KetDocument& document, SeqType seq_type); + void loadFasta(KetDocument& document, const std::string& seq_type_str); + void loadFasta(KetDocument& document, SeqType seq_type); + void loadIdt(KetDocument& document); + private: Vec3f getBackboneMonomerPosition(); bool addMonomer(BaseMolecule& mol, char ch, SeqType seq_type); @@ -82,7 +87,12 @@ namespace indigo void addAminoAcid(BaseMolecule& mol, char ch); void addNucleotide(BaseMolecule& mol, std::string base, const std::string& sugar_alias, const std::string& phosphate_alias, bool phosphate_at_left = true); - void addNucleotide(KetDocument& document, std::string base_alias, const std::string& sugar_alias, const std::string& phosphate_alias, + + void addMonomer(KetDocument& mol, const std::string& monomer, SeqType seq_type, bool mixed = false); + void addAminoAcid(KetDocument& document, const std::string& monomer, bool mixed = false); + void addNucleotideTemplates(KetDocument& document, const std::string& base_alias, const std::string& sugar_alias, const std::string& phosphate_alias, + bool variant = false); + void addNucleotide(KetDocument& document, const std::string& base_alias, const std::string& sugar_alias, const std::string& phosphate_alias, bool phosphate_at_left = true, bool variant = false); int addTemplateAtom(BaseMolecule& mol, const char* alias, const char* monomer_class, int seq_id); diff --git a/core/indigo-core/molecule/sequence_saver.h b/core/indigo-core/molecule/sequence_saver.h index 0e0760806a..2b2115bc93 100644 --- a/core/indigo-core/molecule/sequence_saver.h +++ b/core/indigo-core/molecule/sequence_saver.h @@ -60,6 +60,7 @@ namespace indigo protected: TGroup& getTGroup(); std::string saveIdt(BaseMolecule& mol, std::deque& sequence); + void saveIdt(KetDocument& doc, std::vector> sequences, std::string& seq_text); std::string saveHELM(BaseMolecule& mol, std::vector>& sequence); void _validateSequence(BaseMolecule& bmol); diff --git a/core/indigo-core/molecule/src/ket_document.cpp b/core/indigo-core/molecule/src/ket_document.cpp index 034c8433c3..e85bcfa897 100644 --- a/core/indigo-core/molecule/src/ket_document.cpp +++ b/core/indigo-core/molecule/src/ket_document.cpp @@ -246,7 +246,7 @@ static bool isSimplePolymerConnection(MonomerClass cl1, const std::string& ap1, return false; } -static bool isSequenceConnection(MonomerClass cl1, const std::string& ap1, MonomerClass cl2, const std::string& ap2) +static bool isIdtConnection(MonomerClass cl1, const std::string& ap1, MonomerClass cl2, const std::string& ap2) { bool is_simple_pol_connection = isSimplePolymerConnection(cl1, ap1, cl2, ap2); if (is_simple_pol_connection) @@ -366,7 +366,7 @@ bool is_backbone_class(MonomerClass monomer_class) return false; } -void KetDocument::parseSimplePolymers(std::vector>& sequences, bool for_sequence) +void KetDocument::parseSimplePolymers(std::vector>& sequences, bool for_idt) { std::map id_to_class; std::set monomers; @@ -413,8 +413,8 @@ void KetDocument::parseSimplePolymers(std::vector>& sequ ap_to_connection.emplace(std::make_pair(mon_id_2, ap_id_2), connection); bool sequence_connection = false; - if (for_sequence) - sequence_connection = isSequenceConnection(mon1_class, ap_id_1, mon2_class, ap_id_2); + if (for_idt) + sequence_connection = isIdtConnection(mon1_class, ap_id_1, mon2_class, ap_id_2); else sequence_connection = isSimplePolymerConnection(mon1_class, ap_id_1, mon2_class, ap_id_2); if (!sequence_connection) diff --git a/core/indigo-core/molecule/src/ket_objects.cpp b/core/indigo-core/molecule/src/ket_objects.cpp index 05b6aae350..8853142e74 100644 --- a/core/indigo-core/molecule/src/ket_objects.cpp +++ b/core/indigo-core/molecule/src/ket_objects.cpp @@ -583,7 +583,7 @@ IMPL_ERROR(KetBaseMonomer, "Ket Base Monomer") void KetBaseMonomer::connectAttachmentPointTo(const std::string& ap_id, const std::string& monomer_ref, const std::string& other_ap_id) { if (_attachment_points.find(ap_id) == _attachment_points.end()) - throw Error("Unknown attachment point '%S'", ap_id.c_str()); + throw Error("Unknown attachment point '%s'", ap_id.c_str()); auto it = _connections.find(ap_id); if (it != _connections.end()) throw Error("Monomer '%s' attachment point '%s' already connected to monomer'%s' attachment point '%s'", _id.c_str(), ap_id.c_str(), diff --git a/core/indigo-core/molecule/src/sequence_loader.cpp b/core/indigo-core/molecule/src/sequence_loader.cpp index 7ab6954448..c2defc5d24 100644 --- a/core/indigo-core/molecule/src/sequence_loader.cpp +++ b/core/indigo-core/molecule/src/sequence_loader.cpp @@ -364,7 +364,93 @@ void SequenceLoader::addNucleotide(BaseMolecule& mol, std::string base, const st _last_monomer_idx = sugar_idx; } -void SequenceLoader::addNucleotide(KetDocument& document, std::string base_alias, const std::string& sugar_alias, const std::string& phosphate_alias, +void SequenceLoader::addMonomer(KetDocument& document, const std::string& monomer, SeqType seq_type, bool mixed) +{ + MonomerClass monomer_class = seq_type == SeqType::PEPTIDESeq ? MonomerClass::AminoAcid : MonomerClass::Base; + if (!mixed) + _alias_to_id.emplace(monomer, checkAddTemplate(document, monomer_class, monomer)); + else if (!document.hasVariantMonomerTemplate(monomer)) + { + std::optional>> mixture; + if (seq_type == SeqType::PEPTIDESeq) + { + const auto& it = STANDARD_MIXED_PEPTIDES.find(monomer); + if (it == STANDARD_MIXED_PEPTIDES.end()) + throw Error("Unknown mixed peptide '%s'", monomer.c_str()); + mixture.emplace(std::cref(it->second)); + } + else + { + const auto& it = STANDARD_MIXED_BASES.find(monomer); + if (it == STANDARD_MIXED_BASES.end()) + throw Error("Unknown mixed base '%s'", monomer.c_str()); + mixture.emplace(std::cref(it->second)); + } + + std::vector options; + for (auto template_alias : mixture.value().get()) + { + auto& template_id = _library.getMonomerTemplateIdByAlias(monomer_class, template_alias); + if (template_id.size() == 0) + throw Error("Monomer base template '%s' not found", template_alias.c_str()); + auto& option = options.emplace_back(template_id); + auto& monomer_template = _library.getMonomerTemplateById(template_id); + checkAddTemplate(document, monomer_template); + _alias_to_id.emplace(template_alias, template_id); + } + document.addVariantMonomerTemplate("mixture", monomer, monomer, IdtAlias(), options); + _alias_to_id.emplace(monomer, monomer); + } + + std::string sugar_alias = seq_type == SeqType::RNASeq ? "R" : "dR"; + std::string phosphate_alias = "P"; + if (seq_type != SeqType::PEPTIDESeq) + { + // add sugar template + if (_seq_id == 0) + { + _alias_to_id.emplace(sugar_alias, checkAddTemplate(document, MonomerClass::Sugar, sugar_alias)); + phosphate_alias = ""; + } + + // add phosphate template + if (_seq_id == 1) + _alias_to_id.emplace(phosphate_alias, checkAddTemplate(document, MonomerClass::Phosphate, phosphate_alias)); + } + + _seq_id++; + switch (seq_type) + { + case SeqType::PEPTIDESeq: + addAminoAcid(document, monomer, mixed); + break; + case SeqType::RNASeq: + addNucleotide(document, monomer, sugar_alias, phosphate_alias, true, mixed); + break; + case SeqType::DNASeq: + addNucleotide(document, monomer, sugar_alias, phosphate_alias, true, mixed); + break; + } + _col++; +} + +void SequenceLoader::addAminoAcid(KetDocument& document, const std::string& monomer, bool variant) +{ + Vec3f pos(_col * MoleculeLayout::DEFAULT_BOND_LENGTH, -MoleculeLayout::DEFAULT_BOND_LENGTH * _row, 0); + auto amino_idx = document.monomers().size(); + auto& amino_acid = document.addMonomer(monomer, _alias_to_id.at(monomer)); + if (variant) + amino_acid->setAttachmentPoints(document.variantTemplates().at(_alias_to_id.at(monomer)).attachmentPoints()); + else + amino_acid->setAttachmentPoints(document.templates().at(_alias_to_id.at(monomer)).attachmentPoints()); + amino_acid->setIntProp("seqid", _seq_id); + amino_acid->setPosition(pos); + + if (_seq_id > 1) + addTemplateConnection(document, amino_idx - 1, amino_idx); +} + +void SequenceLoader::addNucleotide(KetDocument& document, const std::string& base_alias, const std::string& sugar_alias, const std::string& phosphate_alias, bool phosphate_at_left, bool variant) { Vec3f pos = getBackboneMonomerPosition(); @@ -372,6 +458,7 @@ void SequenceLoader::addNucleotide(KetDocument& document, std::string base_alias // add sugar auto sugar_idx = document.monomers().size(); auto& sugar = document.addMonomer(sugar_alias, _alias_to_id.at(sugar_alias)); + sugar->setAttachmentPoints(document.templates().at(_alias_to_id.at(sugar_alias)).attachmentPoints()); sugar->setIntProp("seqid", _seq_id); sugar->setPosition(pos); @@ -381,6 +468,10 @@ void SequenceLoader::addNucleotide(KetDocument& document, std::string base_alias auto nuc_base_idx = document.monomers().size(); auto& base = variant ? document.addVariantMonomer(base_alias, _alias_to_id.at(base_alias)) : document.addMonomer(base_alias, _alias_to_id.at(base_alias)); + if (variant) + base->setAttachmentPoints(document.variantTemplates().at(_alias_to_id.at(base_alias)).attachmentPoints()); + else + base->setAttachmentPoints(document.templates().at(_alias_to_id.at(base_alias)).attachmentPoints()); base->setIntProp("seqid", _seq_id); Vec3f base_coord(pos.x, pos.y - MoleculeLayout::DEFAULT_BOND_LENGTH, 0); base->setPosition(base_coord); @@ -398,6 +489,7 @@ void SequenceLoader::addNucleotide(KetDocument& document, std::string base_alias // add phosphate auto phosphate_idx = document.monomers().size(); auto& phosphate = document.addMonomer(phosphate_alias, _alias_to_id.at(phosphate_alias)); + phosphate->setAttachmentPoints(document.templates().at(_alias_to_id.at(phosphate_alias)).attachmentPoints()); phosphate->setIntProp("seqid", _seq_id - 1); Vec3f phosphate_coord(pos.x - MoleculeLayout::DEFAULT_BOND_LENGTH, pos.y, 0); phosphate->setPosition(phosphate_coord); @@ -411,6 +503,7 @@ void SequenceLoader::addNucleotide(KetDocument& document, std::string base_alias // add phosphate auto phosphate_idx = document.monomers().size(); auto& phosphate = document.addMonomer(phosphate_alias, _alias_to_id.at(phosphate_alias)); + phosphate->setAttachmentPoints(document.templates().at(_alias_to_id.at(phosphate_alias)).attachmentPoints()); phosphate->setIntProp("seqid", _seq_id); Vec3f phosphate_coord(pos.x + MoleculeLayout::DEFAULT_BOND_LENGTH, pos.y, 0); phosphate->setPosition(phosphate_coord); @@ -508,7 +601,6 @@ void SequenceLoader::loadIdt(BaseMolecule& mol) const auto IDT_DEF_SUGAR = "dR"; const auto IDT_DEF_PHOSPHATE = "P"; const auto IDT_MODIFIED_PHOSPHATE = "sP"; - static const std::unordered_set IDT_STANDARD_BASES = {'A', 'T', 'C', 'G', 'U', 'I'}; constexpr int MAX_STD_TOKEN_SIZE = 2; _row = 0; mol.clear(); @@ -645,7 +737,7 @@ void SequenceLoader::loadIdt(BaseMolecule& mol) if (idt_alias.size() == 1) { - if (IDT_STANDARD_BASES.count(idt_alias[0]) == 0) + if (IDT_STANDARD_BASES.count(idt_alias) == 0) { if (invalid_symbols.size()) invalid_symbols += ','; @@ -791,10 +883,6 @@ void SequenceLoader::loadIdt(KetDocument& document) const auto IDT_DEF_SUGAR = "dR"; const auto IDT_DEF_PHOSPHATE = "P"; const auto IDT_MODIFIED_PHOSPHATE = "sP"; - static const std::unordered_set IDT_STANDARD_BASES = {'A', 'T', 'C', 'G', 'U', 'I'}; - static const std::map> IDT_STANDARD_MIXED_BASES = { - {"R", {"A", "G"}}, {"Y", {"C", "T"}}, {"M", {"A", "C"}}, {"K", {"G", "T"}}, {"S", {"G", "C"}}, {"W", {"A", "T"}}, - {"H", {"A", "C", "T"}}, {"B", {"G", "C", "T"}}, {"V", {"A", "C", "G"}}, {"D", {"A", "G", "T"}}, {"N", {"A", "C", "G", "T"}}}; constexpr int MAX_STD_TOKEN_SIZE = 2; _row = 0; std::string invalid_symbols; @@ -970,12 +1058,12 @@ void SequenceLoader::loadIdt(KetDocument& document) } } - if (IDT_STANDARD_MIXED_BASES.count(idt_alias) != 0 || idt_alias.back() == ')') + if (STANDARD_MIXED_BASES.count(idt_alias) != 0 || idt_alias.back() == ')') variant_monomer = true; if (idt_alias.size() == 1 || variant_monomer) { - if (IDT_STANDARD_BASES.count(idt_alias[0]) == 0 && !variant_monomer) + if (IDT_STANDARD_BASES.count(idt_alias) == 0 && !variant_monomer) { if (invalid_symbols.size()) invalid_symbols += ','; @@ -1006,8 +1094,8 @@ void SequenceLoader::loadIdt(KetDocument& document) idt_alias = 'r' + idt_alias; if (!document.hasVariantMonomerTemplate(idt_alias)) { - auto it = IDT_STANDARD_MIXED_BASES.find(mixed_base); - if (it == IDT_STANDARD_MIXED_BASES.end()) + auto it = STANDARD_MIXED_BASES.find(mixed_base); + if (it == STANDARD_MIXED_BASES.end()) throw Error("Unknown mixed base '%s'", mixed_base.c_str()); std::vector options; @@ -1624,3 +1712,171 @@ void SequenceLoader::loadHELM(BaseMolecule& mol) if (helm_part != helm_parts::End) throw Error(unexpected_eod); } + +void SequenceLoader::loadSequence(KetDocument& document, const std::string& seq_type_str) +{ + if (seq_type_str == kMonomerClassDNA) + loadSequence(document, SeqType::DNASeq); + else if (seq_type_str == kMonomerClassRNA) + loadSequence(document, SeqType::RNASeq); + else if (seq_type_str == kMonomerClassPEPTIDE) + loadSequence(document, SeqType::PEPTIDESeq); + else + throw Error("Bad sequence type: %s", seq_type_str.c_str()); +} + +void SequenceLoader::loadSequence(KetDocument& document, SeqType seq_type) +{ + _seq_id = 0; + _last_monomer_idx = -1; + _row = 0; + _col = 0; + const int row_size = seq_type == SeqType::PEPTIDESeq ? 1 : 2; + std::string invalid_symbols; + + bool isGenBankPept = false; + bool start_char = true; + + while (!_scanner.isEOF()) + { + auto ch = _scanner.readChar(); + if (ch == '\n' || ch == '\r') + continue; + + if (start_char) + { + if (isdigit(ch)) + isGenBankPept = true; + start_char = false; + } + + if (isGenBankPept) + { + if (ch == ' ' || isdigit(ch)) + continue; + if (islower(ch)) + ch -= CHAR_SHIFT_CONVERT; + } + + if (!isGenBankPept && ch == ' ') + { + _seq_id = 0; + _col = 0; + _row += row_size; + continue; + } + std::string monomer(1, ch); + if ((seq_type == SeqType::PEPTIDESeq && STANDARD_PEPTIDES.count(monomer) > 0) || + (seq_type != SeqType::PEPTIDESeq && STANDARD_NUCLEOTIDES.count(monomer) > 0)) + { + addMonomer(document, monomer, seq_type); + } + else if ((seq_type == SeqType::PEPTIDESeq && STANDARD_MIXED_PEPTIDES.count(monomer) > 0) || + (seq_type != SeqType::PEPTIDESeq && STANDARD_MIXED_BASES.count(monomer) > 0)) + { + addMonomer(document, monomer, seq_type, true); + } + else + { + if (invalid_symbols.size()) + invalid_symbols += ','; + invalid_symbols += ch; + } + } + + if (invalid_symbols.size()) + throw Error("Invalid symbols in the sequence: %s", invalid_symbols.c_str()); +} + +void SequenceLoader::loadFasta(KetDocument& document, const std::string& seq_type_str) +{ + if (seq_type_str == kMonomerClassDNA) + loadFasta(document, SeqType::DNASeq); + else if (seq_type_str == kMonomerClassRNA) + loadFasta(document, SeqType::RNASeq); + else if (seq_type_str == kMonomerClassPEPTIDE) + loadFasta(document, SeqType::PEPTIDESeq); + else + throw Error("Bad sequence type: %s", seq_type_str.c_str()); +} + +void SequenceLoader::loadFasta(KetDocument& document, SeqType seq_type) +{ + _seq_id = 0; + _last_monomer_idx = -1; + _row = 0; + _col = 0; + const int row_size = seq_type == SeqType::PEPTIDESeq ? 1 : 2; + std::string invalid_symbols; + Array mapping; + std::vector properties; + + while (!_scanner.isEOF()) + { + Array str; + _scanner.readLine(str, true); + if (str.size()) + { + std::string fasta_str = str.ptr(); + switch (fasta_str.front()) + { + case ';': + // handle comment + continue; + break; + case '>': + // handle header + if (_seq_id) + { + _seq_id = 0; + _col = 0; + _row += row_size; + } + _last_monomer_idx = -1; + properties.emplace_back(fasta_str); + continue; + break; + default: + break; + } + + for (auto ch : fasta_str) + { + auto monomer = std::string(1, ch); + if (ch == '-') + continue; + else if (ch == '*' && seq_type == SeqType::PEPTIDESeq) + { + _seq_id = 0; + _col = 0; + _row += row_size; + continue; + } + if ((seq_type == SeqType::PEPTIDESeq && STANDARD_PEPTIDES.count(monomer) > 0) || + (seq_type != SeqType::PEPTIDESeq && STANDARD_NUCLEOTIDES.count(monomer) > 0)) + { + addMonomer(document, monomer, seq_type); + } + else if ((seq_type == SeqType::PEPTIDESeq && STANDARD_MIXED_PEPTIDES.count(monomer) > 0) || + (seq_type != SeqType::PEPTIDESeq && STANDARD_MIXED_BASES.count(monomer) > 0)) + { + addMonomer(document, monomer, seq_type, true); + } + else + { + if (invalid_symbols.size()) + invalid_symbols += ','; + invalid_symbols += ch; + } + } + + if (invalid_symbols.size()) + throw Error("Invalid symbols in the sequence: %s", invalid_symbols.c_str()); + } + } + + if (!properties.size()) + throw Error("Invalid FASTA: no '>' headers"); + else + document.setFastaProps(properties); +} diff --git a/core/indigo-core/molecule/src/sequence_saver.cpp b/core/indigo-core/molecule/src/sequence_saver.cpp index 330444f452..e10a4940c3 100644 --- a/core/indigo-core/molecule/src/sequence_saver.cpp +++ b/core/indigo-core/molecule/src/sequence_saver.cpp @@ -738,11 +738,88 @@ void SequenceSaver::saveMolecule(BaseMolecule& mol, SeqFormat sf) void SequenceSaver::saveKetDocument(KetDocument& doc, SeqFormat sf) { - if (sf == SeqFormat::FASTA || sf == SeqFormat::Sequence || sf == SeqFormat::HELM) + if (sf == SeqFormat::HELM) throw Error("Not supported yet"); std::vector> sequences; - doc.parseSimplePolymers(sequences, true); + int seq_idx = 0; std::string seq_text; + if (sf == SeqFormat::IDT) + { + doc.parseSimplePolymers(sequences, true); + saveIdt(doc, sequences, seq_text); + } + else if (sf == SeqFormat::FASTA || sf == SeqFormat::Sequence) + { + auto& monomers = doc.monomers(); + doc.parseSimplePolymers(sequences, false); + auto prop_it = doc.fastaProps().begin(); + for (auto& sequence : sequences) + { + std::string seq_string; + for (auto monomer_id : sequence) + { + MonomerClass monomer_class = doc.getMonomerClass(monomer_id); + const auto& monomer = monomers.at(monomer_id); + auto monomer_alias = monomer->alias(); + if (monomer_class == MonomerClass::CHEM) + throw Error("Can't save chem '%s' to sequence format", monomer_alias.c_str()); + if (monomer_class == MonomerClass::Sugar || monomer_class == MonomerClass::Phosphate) + continue; + + if (monomer_alias.size() > 1 || + (monomer_class == MonomerClass::AminoAcid && STANDARD_NUCLEOTIDES.count(monomer_alias) == 0 && + STANDARD_MIXED_PEPTIDES.count(monomer_alias) == 0) || + (monomer_class == MonomerClass::Base && STANDARD_NUCLEOTIDES.count(monomer_alias) == 0 && STANDARD_MIXED_BASES.count(monomer_alias) == 0)) + { + const auto& monomer_template = doc.templates().at(monomer->templateId()); + if (monomer_template.hasStringProp("naturalAnalogShort")) + monomer_alias = monomer_template.getStringProp("naturalAnalogShort"); + else + throw Error("Can't save '%s' to sequence format", monomer_alias.c_str()); + } + seq_string += monomer_alias; + } + + if (seq_string.size()) + { + // sequences separators are different for FASTA, IDT and Sequence + if (sf == SeqFormat::FASTA) + { + if (seq_idx) + seq_text += "\n"; + std::string fasta_header; + if (prop_it != doc.fastaProps().end()) + { + fasta_header = *prop_it; + prop_it++; + } + else + { + fasta_header = ">Sequence"; + fasta_header += std::to_string(seq_idx + 1); + } + fasta_header += "\n"; + seq_text += fasta_header; + } + else if (seq_text.size()) + seq_text += sf == SeqFormat::Sequence ? " " : "\n"; + + seq_text += seq_string.substr(0, SEQ_LINE_LENGTH); + for (size_t format_ind = SEQ_LINE_LENGTH; format_ind < seq_string.size(); format_ind += SEQ_LINE_LENGTH) + { + seq_text += "\n"; + seq_text += seq_string.substr(format_ind, SEQ_LINE_LENGTH); + } + seq_idx++; + } + } + } + if (seq_text.size()) + _output.writeString(seq_text.c_str()); +} + +void SequenceSaver::saveIdt(KetDocument& doc, std::vector> sequences, std::string& seq_text) +{ auto& monomer_templates = doc.templates(); auto& variant_monomer_templates = doc.variantTemplates(); auto& monomers = doc.monomers(); @@ -846,7 +923,7 @@ void SequenceSaver::saveKetDocument(KetDocument& doc, SeqFormat sf) { base = monomers.at(base_id)->alias(); sequence.pop_front(); - if (IDT_STANDARD_BASES.count(base) == 0 && IDT_STANDARD_MIXED_BASES.count(base) == 0) + if (IDT_STANDARD_BASES.count(base) == 0 && STANDARD_MIXED_BASES.count(base) == 0) standard_base = false; if (base.back() == ')') { @@ -970,6 +1047,4 @@ void SequenceSaver::saveKetDocument(KetDocument& doc, SeqFormat sf) seq_text += "\n"; seq_text += seq_string; } - if (seq_text.size()) - _output.writeString(seq_text.c_str()); } diff --git a/data/molecules/basic/monomer_library.ket b/data/molecules/basic/monomer_library.ket index c4c3b1d280..5dab2bcfc5 100644 --- a/data/molecules/basic/monomer_library.ket +++ b/data/molecules/basic/monomer_library.ket @@ -561,6 +561,9 @@ { "$ref": "monomerTemplate-pnT___PNA Thymine" }, + { + "$ref": "monomerTemplate-U___Selenocysteine" + }, { "$ref": "monomerTemplate-seC___SelenoCysteine" }, @@ -609,6 +612,9 @@ { "$ref": "monomerTemplate-NMe___C-Terminal NMe" }, + { + "$ref": "monomerTemplate-O___Pyrrolysine" + }, { "$ref": "monomerTemplate-OMe___C-Terminal OMe" }, @@ -42537,6 +42543,178 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-U___Selenocysteine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "N", + "location": [ + 14.558974596215561, + -10.200000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -9.700000000000001, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 16.291025403784438, + -10.200000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 17.15705080756888, + -9.700000000000003, + 0 + ] + }, + { + "label": "O", + "location": [ + 16.291025403784438, + -11.200000000000003, + 0 + ] + }, + { + "label": "H", + "location": [ + 13.692949192431122, + -9.700000000000001, + 0 + ] + }, + { + "label": "C", + "location": [ + 15.425, + -8.700000000000001, + 0 + ] + }, + { + "label": "Se", + "location": [ + 14.558974596215563, + -8.2, + 0 + ] + }, + { + "label": "H", + "location": [ + 14.558974596215563, + -7.2, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "U___Selenocysteine", + "fullName": "Selenocysteine", + "alias": "U", + "attachmentPoints": [ + { + "attachmentAtom": 0, + "leavingGroup": { + "atoms": [ + 5 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 2, + "leavingGroup": { + "atoms": [ + 3 + ] + }, + "type": "right" + }, + { + "attachmentAtom": 7, + "leavingGroup": { + "atoms": [ + 8 + ] + }, + "type": "side" + } + ], + "naturalAnalogShort": "U" + }, "monomerTemplate-seC___SelenoCysteine": { "type": "monomerTemplate", "atoms": [ @@ -46248,6 +46426,328 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-O___Pyrrolysine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "H", + "location": [ + -2.0487, + -3.86, + 0 + ] + }, + { + "label": "N", + "location": [ + -1.0256, + -4.4508, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.0024, + -3.86, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.0208, + -4.4508, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.0439, + -3.86, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.0208, + -5.6322, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.0024, + -2.6786, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.5883, + -1.6554, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.0024, + -0.6322, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.5883, + 0.3909, + 0 + ] + }, + { + "label": "N", + "location": [ + -0.0024, + 1.4141, + 0 + ] + }, + { + "label": "C", + "location": [ + 0.5883, + 2.4373, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.0024, + 3.4604, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + 1.7698, + 2.4373, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.1768, + 3.5839, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.4223, + 4.739, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.3997, + 5.3294, + 0 + ] + }, + { + "label": "N", + "location": [ + 0.4779, + 4.5392, + 0 + ] + }, + { + "label": "C", + "location": [ + -2.0122, + 2.7484, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 3, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 9, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 10, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 11, + 12 + ] + }, + { + "type": 2, + "atoms": [ + 11, + 13 + ] + }, + { + "type": 2, + "atoms": [ + 16, + 17 + ] + }, + { + "type": 1, + "atoms": [ + 15, + 16 + ] + }, + { + "type": 1, + "atoms": [ + 14, + 15 + ] + }, + { + "type": 1, + "atoms": [ + 12, + 14 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 17, + 12 + ] + }, + { + "type": 1, + "atoms": [ + 14, + 18 + ] + } + ], + "class": "AminoAcid", + "classHELM": "PEPTIDE", + "id": "O___Pyrrolysine", + "fullName": "Pyrrolysine", + "alias": "O", + "attachmentPoints": [ + { + "attachmentAtom": 1, + "leavingGroup": { + "atoms": [ + 0 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 3, + "leavingGroup": { + "atoms": [ + 4 + ] + }, + "type": "right" + } + ], + "naturalAnalogShort": "O" + }, "monomerTemplate-OMe___C-Terminal OMe": { "type": "monomerTemplate", "atoms": [ diff --git a/utils/indigo-service/backend/service/tests/api/indigo_test.py b/utils/indigo-service/backend/service/tests/api/indigo_test.py index 7f7373ab6c..855c5511f0 100644 --- a/utils/indigo-service/backend/service/tests/api/indigo_test.py +++ b/utils/indigo-service/backend/service/tests/api/indigo_test.py @@ -3153,9 +3153,15 @@ def test_convert_explicit_hydrogens_reaction(self): self.assertEqual("CC>>C", result_data["struct"]) def test_convert_sequences(self): + lib_file = "monomer_library.ket" + lib_path = os.path.join(joinPathPy("structures/", __file__), lib_file) + with open(lib_path, "r") as file: + monomer_library = file.read() + headers, data = self.get_headers( { "struct": "ACGTU", + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-rna-sequence", "output_format": "chemical/x-indigo-ket", } @@ -3167,6 +3173,7 @@ def test_convert_sequences(self): headers, data = self.get_headers( { "struct": "ACGTU", + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-rna-sequence", "output_format": "chemical/x-sequence", } @@ -3181,6 +3188,7 @@ def test_convert_sequences(self): headers, data = self.get_headers( { "struct": "ACGTU", + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-dna-sequence", "output_format": "chemical/x-indigo-ket", } @@ -3192,6 +3200,7 @@ def test_convert_sequences(self): headers, data = self.get_headers( { "struct": "ACGTU", + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-dna-sequence", "output_format": "chemical/x-sequence", } @@ -3205,6 +3214,7 @@ def test_convert_sequences(self): headers, data = self.get_headers( { "struct": "ACGTU", + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-peptide-sequence", "output_format": "chemical/x-indigo-ket", } @@ -3216,6 +3226,7 @@ def test_convert_sequences(self): headers, data = self.get_headers( { "struct": "ACDEFGHIKLMNOPQRSRUVWY", + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-peptide-sequence", "output_format": "chemical/x-sequence", } @@ -3260,9 +3271,15 @@ def test_convert_fasta(self): ) as file: peptide_fasta = file.read() + lib_file = "monomer_library.ket" + lib_path = os.path.join(joinPathPy("structures/", __file__), lib_file) + with open(lib_path, "r") as file: + monomer_library = file.read() + headers, data = self.get_headers( { "struct": peptide_fasta, + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-peptide-fasta", "output_format": "chemical/x-indigo-ket", } @@ -3275,6 +3292,7 @@ def test_convert_fasta(self): headers, data = self.get_headers( { "struct": peptide_fasta, + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-peptide-fasta", "output_format": "chemical/x-fasta", } @@ -3318,6 +3336,7 @@ def test_convert_fasta(self): headers, data = self.get_headers( { "struct": rna_fasta, + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-rna-fasta", "output_format": "chemical/x-indigo-ket", } @@ -3330,6 +3349,7 @@ def test_convert_fasta(self): headers, data = self.get_headers( { "struct": rna_fasta, + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-rna-fasta", "output_format": "chemical/x-fasta", } @@ -3345,7 +3365,7 @@ def test_convert_fasta(self): # ) as file: # file.write(json.loads(result_rna_fasta.text)["struct"]) # with open( - # os.path.join(ref_path, "rna_fasta_ref") + ".ket", "w" + # os.path.join(ref_path, "rna_fasta_ref") + ".ket", "w" # ) as file: # file.write(json.loads(result_rna_ket.text)["struct"]) @@ -3373,6 +3393,7 @@ def test_convert_fasta(self): headers, data = self.get_headers( { "struct": dna_fasta, + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-dna-fasta", "output_format": "chemical/x-indigo-ket", } @@ -3385,6 +3406,7 @@ def test_convert_fasta(self): headers, data = self.get_headers( { "struct": dna_fasta, + "options": {"monomerLibrary": monomer_library}, "input_format": "chemical/x-dna-fasta", "output_format": "chemical/x-fasta", } diff --git a/utils/indigo-service/backend/service/tests/api/ref/dna_fasta_ref.ket b/utils/indigo-service/backend/service/tests/api/ref/dna_fasta_ref.ket index 76d963ce94..8d46cd86bf 100644 --- a/utils/indigo-service/backend/service/tests/api/ref/dna_fasta_ref.ket +++ b/utils/indigo-service/backend/service/tests/api/ref/dna_fasta_ref.ket @@ -1 +1 @@ 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diff --git a/utils/indigo-service/backend/service/tests/api/ref/peptide_fasta_ref.ket b/utils/indigo-service/backend/service/tests/api/ref/peptide_fasta_ref.ket index ece3516dbe..c8e561644f 100644 --- a/utils/indigo-service/backend/service/tests/api/ref/peptide_fasta_ref.ket +++ b/utils/indigo-service/backend/service/tests/api/ref/peptide_fasta_ref.ket @@ -1 +1 @@ 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diff --git a/utils/indigo-service/backend/service/tests/api/ref/rna_fasta_ref.ket b/utils/indigo-service/backend/service/tests/api/ref/rna_fasta_ref.ket index c10c25ec98..b9e675d158 100644 --- a/utils/indigo-service/backend/service/tests/api/ref/rna_fasta_ref.ket +++ b/utils/indigo-service/backend/service/tests/api/ref/rna_fasta_ref.ket @@ -1 +1 @@ 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diff --git a/utils/indigo-service/backend/service/tests/api/structures/monomer_library.ket b/utils/indigo-service/backend/service/tests/api/structures/monomer_library.ket index 4a594c4632..5dab2bcfc5 100644 --- a/utils/indigo-service/backend/service/tests/api/structures/monomer_library.ket +++ b/utils/indigo-service/backend/service/tests/api/structures/monomer_library.ket @@ -561,6 +561,9 @@ { "$ref": "monomerTemplate-pnT___PNA Thymine" }, + { + "$ref": "monomerTemplate-U___Selenocysteine" + }, { "$ref": "monomerTemplate-seC___SelenoCysteine" }, @@ -609,6 +612,9 @@ { "$ref": "monomerTemplate-NMe___C-Terminal NMe" }, + { + "$ref": "monomerTemplate-O___Pyrrolysine" + }, { "$ref": "monomerTemplate-OMe___C-Terminal OMe" }, @@ -2234,6 +2240,9 @@ }, { "$ref": "monomerGroupTemplate-dR(U)P" + }, + { + "$ref": "monomerTemplate-UNSPLIT" } ] }, @@ -42534,6 +42543,178 @@ ], "naturalAnalogShort": "X" }, + "monomerTemplate-U___Selenocysteine": { + "type": "monomerTemplate", + "atoms": [ + { + 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