diff --git a/api/tests/integration/tests/formats/ref/acgt_1412.ket b/api/tests/integration/tests/formats/ref/acgt_1412.ket index 55631e8c40..a5874e98d9 100644 --- a/api/tests/integration/tests/formats/ref/acgt_1412.ket +++ b/api/tests/integration/tests/formats/ref/acgt_1412.ket @@ -399,6 +399,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -498,6 +499,7 @@ "classHELM": "RNA", "alias": "R", "name": "Rib", + "fullName": "Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -726,6 +728,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ @@ -922,6 +925,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -1081,6 +1085,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -1292,6 +1297,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ @@ -1466,6 +1472,7 @@ "classHELM": "RNA", "alias": "U", "name": "Ura", + "fullName": "Uracil", "naturalAnalogShort": "U", "naturalAnalog": "Ura", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/all_aminoacids.ket b/api/tests/integration/tests/formats/ref/all_aminoacids.ket index 3b2e70151d..0d9b0545ae 100644 --- a/api/tests/integration/tests/formats/ref/all_aminoacids.ket +++ b/api/tests/integration/tests/formats/ref/all_aminoacids.ket @@ -616,6 +616,7 @@ "classHELM": "PEPTIDE", "alias": "A", "name": "Ala", + "fullName": "Alanine", "naturalAnalogShort": "A", "naturalAnalog": "Ala", "attachmentPoints": [ @@ -748,6 +749,7 @@ "classHELM": "PEPTIDE", "alias": "C", "name": "Cys", + "fullName": "Cysteine", "naturalAnalogShort": "C", "naturalAnalog": "Cys", "attachmentPoints": [ @@ -918,6 +920,7 @@ "classHELM": "PEPTIDE", "alias": "D", "name": "Asp", + "fullName": "Aspartic acid", "naturalAnalogShort": "D", "naturalAnalog": "Asp", "attachmentPoints": [ @@ -1118,6 +1121,7 @@ "classHELM": "PEPTIDE", "alias": "E", "name": "Glu", + "fullName": "Glutamic acid", "naturalAnalogShort": "E", "naturalAnalog": "Glu", "attachmentPoints": [ @@ -1333,6 +1337,7 @@ "classHELM": "PEPTIDE", "alias": "F", "name": "Phe", + "fullName": "Phenylalanine", "naturalAnalogShort": "F", "naturalAnalog": "Phe", "attachmentPoints": [ @@ -1562,6 +1567,7 @@ "classHELM": "PEPTIDE", "alias": "G", "name": "Gly", + "fullName": "Glycine", "naturalAnalogShort": "G", "naturalAnalog": "Gly", "attachmentPoints": [ @@ -1677,6 +1683,7 @@ "classHELM": "PEPTIDE", "alias": "H", "name": "His", + "fullName": "Histidine", "naturalAnalogShort": "H", "naturalAnalog": "His", "attachmentPoints": [ @@ -1914,6 +1921,7 @@ "classHELM": "PEPTIDE", "alias": "I", "name": "Ile", + "fullName": "Isoleucine", "naturalAnalogShort": "I", "naturalAnalog": "Ile", "attachmentPoints": [ @@ -2093,6 +2101,7 @@ "classHELM": "PEPTIDE", "alias": "K", "name": "Lys", + "fullName": "Lysine", "naturalAnalogShort": "K", "naturalAnalog": "Lys", "attachmentPoints": [ @@ -2308,6 +2317,7 @@ "classHELM": "PEPTIDE", "alias": "L", "name": "Leu", + "fullName": "Leucine", "naturalAnalogShort": "L", "naturalAnalog": "Leu", "attachmentPoints": [ @@ -2485,6 +2495,7 @@ "classHELM": "PEPTIDE", "alias": "M", "name": "Met", + "fullName": "Methionine", "naturalAnalogShort": "M", "naturalAnalog": "Met", "attachmentPoints": [ @@ -2662,6 +2673,7 @@ "classHELM": "PEPTIDE", "alias": "N", "name": "Asn", + "fullName": "Asparagine", "naturalAnalogShort": "N", "naturalAnalog": "Asn", "attachmentPoints": [ @@ -2862,6 +2874,7 @@ "classHELM": "PEPTIDE", "alias": "O", "name": "Pyl", + "fullName": "Pyrrolysine", "naturalAnalogShort": "O", "attachmentPoints": [ { @@ -3182,6 +3195,7 @@ "classHELM": "PEPTIDE", "alias": "P", "name": "Pro", + "fullName": "Proline", "naturalAnalogShort": "P", "naturalAnalog": "Pro", "attachmentPoints": [ @@ -3351,6 +3365,7 @@ "classHELM": "PEPTIDE", "alias": "Q", "name": "Gln", + "fullName": "Glutamine", "naturalAnalogShort": "Q", "naturalAnalog": "Gln", "attachmentPoints": [ @@ -3566,6 +3581,7 @@ "classHELM": "PEPTIDE", "alias": "R", "name": "Arg", + "fullName": "Arginine", "naturalAnalogShort": "R", "naturalAnalog": "Arg", "attachmentPoints": [ @@ -3811,6 +3827,7 @@ "classHELM": "PEPTIDE", "alias": "S", "name": "Ser", + "fullName": "Serine", "naturalAnalogShort": "S", "naturalAnalog": "Ser", "attachmentPoints": [ @@ -3981,6 +3998,7 @@ "classHELM": "PEPTIDE", "alias": "U", "name": "Sec", + "fullName": "Selenocysteine", "naturalAnalogShort": "C", "naturalAnalog": "Cys", "attachmentPoints": [ @@ -4128,6 +4146,7 @@ "classHELM": "PEPTIDE", "alias": "V", "name": "Val", + "fullName": "Valine", "naturalAnalogShort": "V", "naturalAnalog": "Val", "attachmentPoints": [ @@ -4290,6 +4309,7 @@ "classHELM": "PEPTIDE", "alias": "W", "name": "Trp", + "fullName": "Tryptophan", "naturalAnalogShort": "W", "naturalAnalog": "Trp", "attachmentPoints": [ @@ -4594,6 +4614,7 @@ "classHELM": "PEPTIDE", "alias": "Y", "name": "Tyr", + "fullName": "Tyrosine", "naturalAnalogShort": "Y", "naturalAnalog": "Tyr", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/conjugate.ket b/api/tests/integration/tests/formats/ref/conjugate.ket index 690d5dc78c..5b56dc5f98 100644 --- a/api/tests/integration/tests/formats/ref/conjugate.ket +++ b/api/tests/integration/tests/formats/ref/conjugate.ket @@ -4805,6 +4805,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -4904,6 +4905,7 @@ "classHELM": "RNA", "alias": "dR", "name": "dRib", + "fullName": "Deoxy-Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -5115,6 +5117,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ @@ -5289,6 +5292,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -5500,6 +5504,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -5659,6 +5664,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/dna_acgtu.ket b/api/tests/integration/tests/formats/ref/dna_acgtu.ket index 7a0f14ba4c..e42daa1072 100644 --- a/api/tests/integration/tests/formats/ref/dna_acgtu.ket +++ b/api/tests/integration/tests/formats/ref/dna_acgtu.ket @@ -374,6 +374,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ @@ -570,6 +571,7 @@ "classHELM": "RNA", "alias": "dR", "name": "dRib", + "fullName": "Deoxy-Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -781,6 +783,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -940,6 +943,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -1039,6 +1043,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -1250,6 +1255,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ @@ -1424,6 +1430,7 @@ "classHELM": "RNA", "alias": "U", "name": "Ura", + "fullName": "Uracil", "naturalAnalogShort": "U", "naturalAnalog": "Ura", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/dna_mod.ket b/api/tests/integration/tests/formats/ref/dna_mod.ket index 5a2db8636c..aa1a68f39d 100644 --- a/api/tests/integration/tests/formats/ref/dna_mod.ket +++ b/api/tests/integration/tests/formats/ref/dna_mod.ket @@ -3555,6 +3555,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -3654,6 +3655,7 @@ "classHELM": "RNA", "alias": "dR", "name": "dRib", + "fullName": "Deoxy-Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -3865,6 +3867,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ @@ -4039,6 +4042,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -4250,6 +4254,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -4409,6 +4414,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/dna_mod.seq b/api/tests/integration/tests/formats/ref/dna_mod.seq index 50e5e14b5a..dd7bda3369 100644 --- a/api/tests/integration/tests/formats/ref/dna_mod.seq +++ b/api/tests/integration/tests/formats/ref/dna_mod.seq @@ -1 +1 @@ -TGGCGAACTCACCAGTC*CCGC \ No newline at end of file +TGGCGAACTCACCAGTCTCCGC \ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/removed_phosphate.ket b/api/tests/integration/tests/formats/ref/removed_phosphate.ket index 2718ca3488..175c0815cf 100644 --- a/api/tests/integration/tests/formats/ref/removed_phosphate.ket +++ b/api/tests/integration/tests/formats/ref/removed_phosphate.ket @@ -619,6 +619,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -718,6 +719,7 @@ "classHELM": "RNA", "alias": "R", "name": "Rib", + "fullName": "Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -946,6 +948,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -1105,6 +1108,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -1316,6 +1320,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/rna_acgtu.ket b/api/tests/integration/tests/formats/ref/rna_acgtu.ket index 89ff259ce1..9f8479c133 100644 --- a/api/tests/integration/tests/formats/ref/rna_acgtu.ket +++ b/api/tests/integration/tests/formats/ref/rna_acgtu.ket @@ -374,6 +374,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ @@ -570,6 +571,7 @@ "classHELM": "RNA", "alias": "R", "name": "Rib", + "fullName": "Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -798,6 +800,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -957,6 +960,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -1056,6 +1060,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -1267,6 +1272,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ @@ -1441,6 +1447,7 @@ "classHELM": "RNA", "alias": "U", "name": "Ura", + "fullName": "Uracil", "naturalAnalogShort": "U", "naturalAnalog": "Ura", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/rna_mod.ket b/api/tests/integration/tests/formats/ref/rna_mod.ket index e23a58b43c..ca4d4bcddd 100644 --- a/api/tests/integration/tests/formats/ref/rna_mod.ket +++ b/api/tests/integration/tests/formats/ref/rna_mod.ket @@ -2606,6 +2606,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -2705,6 +2706,7 @@ "classHELM": "RNA", "alias": "R", "name": "Rib", + "fullName": "Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -2933,6 +2935,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -3092,6 +3095,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ @@ -3303,6 +3307,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/rna_mod.seq b/api/tests/integration/tests/formats/ref/rna_mod.seq index b66361ee86..9a87e6812b 100644 --- a/api/tests/integration/tests/formats/ref/rna_mod.seq +++ b/api/tests/integration/tests/formats/ref/rna_mod.seq @@ -1 +1 @@ -CCG*GCGGAA*CACCA \ No newline at end of file +CCGCGCGGAANCACCA \ No newline at end of file diff --git a/api/tests/integration/tests/formats/ref/test_dna.ket b/api/tests/integration/tests/formats/ref/test_dna.ket index 2b19d72cc5..7ddfb936ac 100644 --- a/api/tests/integration/tests/formats/ref/test_dna.ket +++ b/api/tests/integration/tests/formats/ref/test_dna.ket @@ -9521,6 +9521,7 @@ "classHELM": "RNA", "alias": "T", "name": "Thy", + "fullName": "Thymine", "naturalAnalogShort": "T", "naturalAnalog": "Thy", "attachmentPoints": [ @@ -9695,6 +9696,7 @@ "classHELM": "RNA", "alias": "dR", "name": "dRib", + "fullName": "Deoxy-Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -9906,6 +9908,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -10065,6 +10068,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -10164,6 +10168,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ @@ -10360,6 +10365,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/test_peptide.ket b/api/tests/integration/tests/formats/ref/test_peptide.ket index 8c79afabdf..931cc35f7f 100644 --- a/api/tests/integration/tests/formats/ref/test_peptide.ket +++ b/api/tests/integration/tests/formats/ref/test_peptide.ket @@ -12563,6 +12563,7 @@ "classHELM": "PEPTIDE", "alias": "M", "name": "Met", + "fullName": "Methionine", "naturalAnalogShort": "M", "naturalAnalog": "Met", "attachmentPoints": [ @@ -12740,6 +12741,7 @@ "classHELM": "PEPTIDE", "alias": "I", "name": "Ile", + "fullName": "Isoleucine", "naturalAnalogShort": "I", "naturalAnalog": "Ile", "attachmentPoints": [ @@ -12919,6 +12921,7 @@ "classHELM": "PEPTIDE", "alias": "G", "name": "Gly", + "fullName": "Glycine", "naturalAnalogShort": "G", "naturalAnalog": "Gly", "attachmentPoints": [ @@ -13034,6 +13037,7 @@ "classHELM": "PEPTIDE", "alias": "Y", "name": "Tyr", + "fullName": "Tyrosine", "naturalAnalogShort": "Y", "naturalAnalog": "Tyr", "attachmentPoints": [ @@ -13301,6 +13305,7 @@ "classHELM": "PEPTIDE", "alias": "V", "name": "Val", + "fullName": "Valine", "naturalAnalogShort": "V", "naturalAnalog": "Val", "attachmentPoints": [ @@ -13463,6 +13468,7 @@ "classHELM": "PEPTIDE", "alias": "Q", "name": "Gln", + "fullName": "Glutamine", "naturalAnalogShort": "Q", "naturalAnalog": "Gln", "attachmentPoints": [ @@ -13678,6 +13684,7 @@ "classHELM": "PEPTIDE", "alias": "A", "name": "Ala", + "fullName": "Alanine", "naturalAnalogShort": "A", "naturalAnalog": "Ala", "attachmentPoints": [ @@ -13810,6 +13817,7 @@ "classHELM": "PEPTIDE", "alias": "T", "name": "Thr", + "fullName": "Threonine", "naturalAnalogShort": "T", "naturalAnalog": "Thr", "attachmentPoints": [ @@ -13997,6 +14005,7 @@ "classHELM": "PEPTIDE", "alias": "E", "name": "Glu", + "fullName": "Glutamic acid", "naturalAnalogShort": "E", "naturalAnalog": "Glu", "attachmentPoints": [ @@ -14212,6 +14221,7 @@ "classHELM": "PEPTIDE", "alias": "L", "name": "Leu", + "fullName": "Leucine", "naturalAnalogShort": "L", "naturalAnalog": "Leu", "attachmentPoints": [ @@ -14389,6 +14399,7 @@ "classHELM": "PEPTIDE", "alias": "R", "name": "Arg", + "fullName": "Arginine", "naturalAnalogShort": "R", "naturalAnalog": "Arg", "attachmentPoints": [ @@ -14634,6 +14645,7 @@ "classHELM": "PEPTIDE", "alias": "P", "name": "Pro", + "fullName": "Proline", "naturalAnalogShort": "P", "naturalAnalog": "Pro", "attachmentPoints": [ @@ -14803,6 +14815,7 @@ "classHELM": "PEPTIDE", "alias": "D", "name": "Asp", + "fullName": "Aspartic acid", "naturalAnalogShort": "D", "naturalAnalog": "Asp", "attachmentPoints": [ @@ -15003,6 +15016,7 @@ "classHELM": "PEPTIDE", "alias": "N", "name": "Asn", + "fullName": "Asparagine", "naturalAnalogShort": "N", "naturalAnalog": "Asn", "attachmentPoints": [ @@ -15203,6 +15217,7 @@ "classHELM": "PEPTIDE", "alias": "K", "name": "Lys", + "fullName": "Lysine", "naturalAnalogShort": "K", "naturalAnalog": "Lys", "attachmentPoints": [ @@ -15418,6 +15433,7 @@ "classHELM": "PEPTIDE", "alias": "S", "name": "Ser", + "fullName": "Serine", "naturalAnalogShort": "S", "naturalAnalog": "Ser", "attachmentPoints": [ @@ -15588,6 +15604,7 @@ "classHELM": "PEPTIDE", "alias": "F", "name": "Phe", + "fullName": "Phenylalanine", "naturalAnalogShort": "F", "naturalAnalog": "Phe", "attachmentPoints": [ @@ -15817,6 +15834,7 @@ "classHELM": "PEPTIDE", "alias": "C", "name": "Cys", + "fullName": "Cysteine", "naturalAnalogShort": "C", "naturalAnalog": "Cys", "attachmentPoints": [ @@ -15987,6 +16005,7 @@ "classHELM": "PEPTIDE", "alias": "H", "name": "His", + "fullName": "Histidine", "naturalAnalogShort": "H", "naturalAnalog": "His", "attachmentPoints": [ @@ -16224,6 +16243,7 @@ "classHELM": "PEPTIDE", "alias": "W", "name": "Trp", + "fullName": "Tryptophan", "naturalAnalogShort": "W", "naturalAnalog": "Trp", "attachmentPoints": [ diff --git a/api/tests/integration/tests/formats/ref/test_rna.ket b/api/tests/integration/tests/formats/ref/test_rna.ket index c4ae80d939..83763dc43a 100644 --- a/api/tests/integration/tests/formats/ref/test_rna.ket +++ b/api/tests/integration/tests/formats/ref/test_rna.ket @@ -9521,6 +9521,7 @@ "classHELM": "RNA", "alias": "U", "name": "Ura", + "fullName": "Uracil", "naturalAnalogShort": "U", "naturalAnalog": "Ura", "attachmentPoints": [ @@ -9680,6 +9681,7 @@ "classHELM": "RNA", "alias": "R", "name": "Rib", + "fullName": "Ribose", "naturalAnalogShort": "R", "naturalAnalog": "Rib", "attachmentPoints": [ @@ -9908,6 +9910,7 @@ "classHELM": "RNA", "alias": "C", "name": "Cyt", + "fullName": "Cytosine", "naturalAnalogShort": "C", "naturalAnalog": "Cyt", "attachmentPoints": [ @@ -10067,6 +10070,7 @@ "classHELM": "RNA", "alias": "P", "name": "P", + "fullName": "Phosphate", "naturalAnalogShort": "P", "attachmentPoints": [ { @@ -10166,6 +10170,7 @@ "classHELM": "RNA", "alias": "A", "name": "Ade", + "fullName": "Adenine", "naturalAnalogShort": "A", "naturalAnalog": "Ade", "attachmentPoints": [ @@ -10362,6 +10367,7 @@ "classHELM": "RNA", "alias": "G", "name": "Gua", + "fullName": "Guanine", "naturalAnalogShort": "G", "naturalAnalog": "Gua", "attachmentPoints": [ diff --git a/api/wasm/indigo-ketcher/test/dna_ref.ket b/api/wasm/indigo-ketcher/test/dna_ref.ket index c48cf63350..8cf4556476 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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\ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/peptide_ref.ket b/api/wasm/indigo-ketcher/test/peptide_ref.ket index 6d26a033b0..87483bb629 100644 --- a/api/wasm/indigo-ketcher/test/peptide_ref.ket +++ b/api/wasm/indigo-ketcher/test/peptide_ref.ket @@ -1 +1 @@ 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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 0ff8960096..bcc1878163 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_dna_ref.ket b/api/wasm/indigo-ketcher/test/test_dna_ref.ket index 58228e7da4..d855ebd6f6 100644 --- a/api/wasm/indigo-ketcher/test/test_dna_ref.ket +++ b/api/wasm/indigo-ketcher/test/test_dna_ref.ket @@ -1 +1 @@ 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\ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/test_peptide_ref.ket b/api/wasm/indigo-ketcher/test/test_peptide_ref.ket index a9da633531..57f4032e39 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 ede3b4c6fb..51dbdb93fc 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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\ No newline at end of file diff --git a/core/indigo-core/molecule/molecule_json_saver.h b/core/indigo-core/molecule/molecule_json_saver.h index bf5c4594a3..a933e24ea7 100644 --- a/core/indigo-core/molecule/molecule_json_saver.h +++ b/core/indigo-core/molecule/molecule_json_saver.h @@ -190,7 +190,6 @@ namespace indigo static std::string monomerId(const TGroup& tg); static std::string monomerKETClass(const std::string& class_name); static std::string monomerHELMClass(const std::string& class_name); - static std::string naturalAnalog(const std::string& natreplace); bool add_stereo_desc; bool pretty_json; diff --git a/core/indigo-core/molecule/molecule_tgroups.h b/core/indigo-core/molecule/molecule_tgroups.h index cae93e7ceb..5dcad25aba 100644 --- a/core/indigo-core/molecule/molecule_tgroups.h +++ b/core/indigo-core/molecule/molecule_tgroups.h @@ -39,6 +39,7 @@ namespace indigo public: Array tgroup_class; Array tgroup_name; + Array tgroup_full_name; Array tgroup_alias; Array tgroup_comment; Array tgroup_natreplace; diff --git a/core/indigo-core/molecule/monomer_commons.h b/core/indigo-core/molecule/monomer_commons.h index 296f604858..0ec2ecc6dc 100644 --- a/core/indigo-core/molecule/monomer_commons.h +++ b/core/indigo-core/molecule/monomer_commons.h @@ -46,6 +46,8 @@ namespace indigo const auto kPrefix_d("d"); const auto kPrefix_r("r"); + std::string extractMonomerName(const std::string& str); + bool isNucleicClass(const std::string& monomer_class); bool isNucleotideClass(const std::string& monomer_class); diff --git a/core/indigo-core/molecule/monomers_basic_templates.h b/core/indigo-core/molecule/monomers_basic_templates.h index e9870c3d4c..8523972cce 100644 --- a/core/indigo-core/molecule/monomers_basic_templates.h +++ b/core/indigo-core/molecule/monomers_basic_templates.h @@ -103,6 +103,7 @@ namespace indigo " \"monomerTemplate-P\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"P\",\n" + " \"fullName\": \"Phosphate\",\n" " \"class\": \"Phosphate\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"P\",\n" @@ -202,6 +203,7 @@ namespace indigo " \"monomerTemplate-Rib\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Rib\",\n" + " \"fullName\": \"Ribose\",\n" " \"class\": \"Sugar\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"R\",\n" @@ -429,6 +431,7 @@ namespace indigo " \"monomerTemplate-Ade\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Ade\",\n" + " \"fullName\": \"Adenine\",\n" " \"class\": \"Base\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"A\",\n" @@ -624,6 +627,7 @@ namespace indigo " \"monomerTemplate-Cyt\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Cyt\",\n" + " \"fullName\": \"Cytosine\",\n" " \"class\": \"Base\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"C\",\n" @@ -782,6 +786,7 @@ namespace indigo " \"monomerTemplate-Gua\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Gua\",\n" + " \"fullName\": \"Guanine\",\n" " \"class\": \"Base\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"G\",\n" @@ -992,6 +997,7 @@ namespace indigo " \"monomerTemplate-Thy\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Thy\",\n" + " \"fullName\": \"Thymine\",\n" " \"class\": \"Base\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"T\",\n" @@ -1165,6 +1171,7 @@ namespace indigo " \"monomerTemplate-Ura\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Ura\",\n" + " \"fullName\": \"Uracil\",\n" " \"class\": \"Base\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"U\",\n" @@ -1323,6 +1330,7 @@ namespace indigo " \"monomerTemplate-dRib\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"dRib\",\n" + " \"fullName\": \"Deoxy-Ribose\",\n" " \"class\": \"Sugar\",\n" " \"classHELM\": \"RNA\",\n" " \"alias\": \"dR\",\n" @@ -1533,6 +1541,7 @@ namespace indigo " \"monomerTemplate-Ala\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Ala\",\n" + " \"fullName\": \"Alanine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"A\",\n" @@ -1665,6 +1674,7 @@ namespace indigo " \"monomerTemplate-Asp\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Asp\",\n" + " \"fullName\": \"Aspartic acid\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"D\",\n" @@ -1865,6 +1875,7 @@ namespace indigo " \"monomerTemplate-Glu\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Glu\",\n" + " \"fullName\": \"Glutamic acid\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"E\",\n" @@ -2080,6 +2091,7 @@ namespace indigo " \"monomerTemplate-Phe\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Phe\",\n" + " \"fullName\": \"Phenylalanine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"F\",\n" @@ -2309,6 +2321,7 @@ namespace indigo " \"monomerTemplate-Gly\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Gly\",\n" + " \"fullName\": \"Glycine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"G\",\n" @@ -2424,6 +2437,7 @@ namespace indigo " \"monomerTemplate-His\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"His\",\n" + " \"fullName\": \"Histidine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"H\",\n" @@ -2661,6 +2675,7 @@ namespace indigo " \"monomerTemplate-Ile\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Ile\",\n" + " \"fullName\": \"Isoleucine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"I\",\n" @@ -2840,6 +2855,7 @@ namespace indigo " \"monomerTemplate-Lys\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Lys\",\n" + " \"fullName\": \"Lysine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"K\",\n" @@ -3055,6 +3071,7 @@ namespace indigo " \"monomerTemplate-Leu\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Leu\",\n" + " \"fullName\": \"Leucine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"L\",\n" @@ -3232,6 +3249,7 @@ namespace indigo " \"monomerTemplate-Met\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Met\",\n" + " \"fullName\": \"Methionine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"M\",\n" @@ -3409,6 +3427,7 @@ namespace indigo " \"monomerTemplate-Asn\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Asn\",\n" + " \"fullName\": \"Asparagine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"N\",\n" @@ -3609,6 +3628,7 @@ namespace indigo " \"monomerTemplate-Pro\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Pro\",\n" + " \"fullName\": \"Proline\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"P\",\n" @@ -3778,6 +3798,7 @@ namespace indigo " \"monomerTemplate-Gln\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Gln\",\n" + " \"fullName\": \"Glutamine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"Q\",\n" @@ -3993,6 +4014,7 @@ namespace indigo " \"monomerTemplate-Arg\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Arg\",\n" + " \"fullName\": \"Arginine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"R\",\n" @@ -4238,6 +4260,7 @@ namespace indigo " \"monomerTemplate-Ser\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Ser\",\n" + " \"fullName\": \"Serine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"S\",\n" @@ -4408,6 +4431,7 @@ namespace indigo " \"monomerTemplate-Sec\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Sec\",\n" + " \"fullName\": \"Selenocysteine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"U\",\n" @@ -4555,6 +4579,7 @@ namespace indigo " \"monomerTemplate-Thr\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Thr\",\n" + " \"fullName\": \"Threonine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"T\",\n" @@ -4742,6 +4767,7 @@ namespace indigo " \"monomerTemplate-Val\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Val\",\n" + " \"fullName\": \"Valine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"V\",\n" @@ -4904,6 +4930,7 @@ namespace indigo " \"monomerTemplate-Trp\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Trp\",\n" + " \"fullName\": \"Tryptophan\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"W\",\n" @@ -5208,6 +5235,7 @@ namespace indigo " \"monomerTemplate-Tyr\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Tyr\",\n" + " \"fullName\": \"Tyrosine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"Y\",\n" @@ -5475,6 +5503,7 @@ namespace indigo " \"monomerTemplate-Cys\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Cys\",\n" + " \"fullName\": \"Cysteine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"C\",\n" @@ -5645,6 +5674,7 @@ namespace indigo " \"monomerTemplate-Pyl\": {\n" " \"type\": \"monomerTemplate\",\n" " \"id\": \"Pyl\",\n" + " \"fullName\": \"Pyrrolysine\",\n" " \"class\": \"AminoAcid\",\n" " \"classHELM\": \"PEPTIDE\",\n" " \"alias\": \"O\",\n" diff --git a/core/indigo-core/molecule/sequence_saver.h b/core/indigo-core/molecule/sequence_saver.h index f61ddcca76..bb0940edf5 100644 --- a/core/indigo-core/molecule/sequence_saver.h +++ b/core/indigo-core/molecule/sequence_saver.h @@ -21,6 +21,7 @@ #include "base_cpp/exception.h" #include "base_cpp/tlscont.h" +#include "molecule/monomers_lib.h" #ifdef _WIN32 #pragma warning(push) @@ -53,6 +54,8 @@ namespace indigo private: SequenceSaver(const SequenceSaver&); // no implicit copy Output& _output; + const MonomerTemplates& _mon_lib; + std::unordered_map, std::reference_wrapper, pair_hash> _templates; }; } // namespace indigo diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp index 4c950af13d..90fca4b28e 100644 --- a/core/indigo-core/molecule/src/base_molecule.cpp +++ b/core/indigo-core/molecule/src/base_molecule.cpp @@ -3244,6 +3244,7 @@ int BaseMolecule::_transformSGroupToTGroup(int sg_idx, int& tg_id) tg.tgroup_name.copy(su.subscript); tg.tgroup_alias.clear(); tg.tgroup_comment.clear(); + tg.tgroup_full_name.clear(); if (su.sa_natreplace.size() > 0) tg.tgroup_natreplace.copy(su.sa_natreplace); diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp index b8ff0127ee..24fe6cbd12 100644 --- a/core/indigo-core/molecule/src/molecule_json_loader.cpp +++ b/core/indigo-core/molecule/src/molecule_json_loader.cpp @@ -1193,6 +1193,12 @@ void MoleculeJsonLoader::parseMonomerTemplate(const rapidjson::Value& monomer_te } } + if (monomer_template.HasMember("fullName")) + { + std::string tg_full_name = monomer_template["fullName"].GetString(); + tg.tgroup_full_name.readString(tg_full_name.c_str(), true); + } + if (monomer_template.HasMember("attachmentPoints")) { auto& att_points = monomer_template["attachmentPoints"]; diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp index edb85959ce..e50b9b102b 100644 --- a/core/indigo-core/molecule/src/molecule_json_saver.cpp +++ b/core/indigo-core/molecule/src/molecule_json_saver.cpp @@ -1096,18 +1096,6 @@ std::string MoleculeJsonSaver::monomerKETClass(const std::string& class_name) return mclass; } -std::string MoleculeJsonSaver::naturalAnalog(const std::string& natreplace) -{ - std::string res = natreplace; - if (natreplace.size()) - { - auto nat_replace = split(std::string(natreplace.c_str()), '/'); - if (nat_replace.size() > 1) - res = normalizeMonomerName(nat_replace.front(), nat_replace[1]); - } - return res; -} - void MoleculeJsonSaver::saveMonomerTemplate(TGroup& tg, JsonWriter& writer) { std::string template_id("monomerTemplate-"); @@ -1138,6 +1126,12 @@ void MoleculeJsonSaver::saveMonomerTemplate(TGroup& tg, JsonWriter& writer) writer.String(tg.tgroup_name.ptr()); } + if (tg.tgroup_full_name.size()) + { + writer.Key("fullName"); + writer.String(tg.tgroup_full_name.ptr()); + } + std::string natreplace; if (tg.tgroup_natreplace.size() == 0) { @@ -1150,7 +1144,7 @@ void MoleculeJsonSaver::saveMonomerTemplate(TGroup& tg, JsonWriter& writer) if (natreplace.size()) { - auto analog = naturalAnalog(natreplace); + auto analog = extractMonomerName(natreplace); auto nat_alias = monomerAliasByName(tg.tgroup_class.ptr(), analog); writer.Key("naturalAnalogShort"); writer.String(nat_alias.c_str()); diff --git a/core/indigo-core/molecule/src/molecule_tgroups.cpp b/core/indigo-core/molecule/src/molecule_tgroups.cpp index 63abe860a9..3289925230 100644 --- a/core/indigo-core/molecule/src/molecule_tgroups.cpp +++ b/core/indigo-core/molecule/src/molecule_tgroups.cpp @@ -105,6 +105,7 @@ void TGroup::copy(TGroup& other) { tgroup_class.copy(other.tgroup_class); tgroup_name.copy(other.tgroup_name); + tgroup_full_name.copy(other.tgroup_full_name); tgroup_alias.copy(other.tgroup_alias); tgroup_text_id.copy(other.tgroup_text_id); tgroup_comment.copy(other.tgroup_comment); diff --git a/core/indigo-core/molecule/src/monomer_commons.cpp b/core/indigo-core/molecule/src/monomer_commons.cpp index 229511d192..e3dbd5f141 100644 --- a/core/indigo-core/molecule/src/monomer_commons.cpp +++ b/core/indigo-core/molecule/src/monomer_commons.cpp @@ -27,6 +27,18 @@ namespace indigo { + std::string extractMonomerName(const std::string& str) + { + std::string res = str; + if (str.size()) + { + auto nat_replace = split(std::string(str.c_str()), '/'); + if (nat_replace.size() > 1) + res = normalizeMonomerName(nat_replace.front(), nat_replace[1]); + } + return res; + } + std::string classToPrefix(const std::string& monomer_class) { if (monomer_class == kMonomerClassdAA || monomer_class == kMonomerClassDNA) diff --git a/core/indigo-core/molecule/src/monomers_lib.cpp b/core/indigo-core/molecule/src/monomers_lib.cpp index 3cc9d3b5b4..74b619ffa0 100644 --- a/core/indigo-core/molecule/src/monomers_lib.cpp +++ b/core/indigo-core/molecule/src/monomers_lib.cpp @@ -114,7 +114,7 @@ namespace indigo { auto ct_it = getStrToMonomerType().find(mon_type); if (ct_it != _instance().getStrToMonomerType().end()) - return getMonomerTemplate(ct_it->first, alias, tgroup); + return getMonomerTemplate(ct_it->second, alias, tgroup); return false; } diff --git a/core/indigo-core/molecule/src/sequence_loader.cpp b/core/indigo-core/molecule/src/sequence_loader.cpp index b79cd4ef94..6dc618250f 100644 --- a/core/indigo-core/molecule/src/sequence_loader.cpp +++ b/core/indigo-core/molecule/src/sequence_loader.cpp @@ -151,6 +151,8 @@ void SequenceLoader::loadSequence(BaseMolecule& mol, SeqType seq_type) while (!_scanner.isEOF()) { auto ch = _scanner.readChar(); + if (ch == '\n' || ch == '\r') + continue; if (!addMonomer(mol, ch, seq_type)) { if (invalid_symbols.size()) diff --git a/core/indigo-core/molecule/src/sequence_saver.cpp b/core/indigo-core/molecule/src/sequence_saver.cpp index 44f32c7107..4271251e4d 100644 --- a/core/indigo-core/molecule/src/sequence_saver.cpp +++ b/core/indigo-core/molecule/src/sequence_saver.cpp @@ -29,7 +29,7 @@ IMPL_ERROR(SequenceSaver, "Sequence saver"); CP_DEF(SequenceSaver); -SequenceSaver::SequenceSaver(Output& output) : _output(output) +SequenceSaver::SequenceSaver(Output& output) : _output(output), _mon_lib(MonomerTemplates::_instance()) { } @@ -39,12 +39,14 @@ SequenceSaver::~SequenceSaver() void SequenceSaver::saveMolecule(BaseMolecule& mol, SeqFormat sf) { + if (!mol.isQueryMolecule()) + mol.getTemplatesMap(_templates); + for (int idx = 0; idx < mol.countComponents(); ++idx) { Filter filt(mol.getDecomposition().ptr(), Filter::EQ, idx); std::unique_ptr component(mol.neu()); component->makeSubmolecule(mol, filt, NULL, NULL); - if (sf == SeqFormat::FASTA) { std::string fasta_header = ">"; @@ -83,27 +85,60 @@ void SequenceSaver::saveMolecule(BaseMolecule& mol, SeqFormat sf) int nei_atom_idx = v.neiVertex(nei_idx); if (component->isTemplateAtom(nei_atom_idx) && std::string(component->getTemplateAtomClass(nei_atom_idx)) == kMonomerClassBASE) { - label = monomerAliasByName(kMonomerClassBASE, component->getTemplateAtom(nei_atom_idx)); + mon_class = kMonomerClassBASE; + label = monomerAliasByName(mon_class, component->getTemplateAtom(nei_atom_idx)); break; } } } else if (isAminoAcidClass(mon_class)) + { + mon_class = kMonomerClassAA; label = monomerAliasByName(kMonomerClassAA, component->getTemplateAtom(atom_idx)); + } else if (isNucleotideClass(mon_class)) + { + mon_class = kMonomerClassBASE; // treat nucleotide symbol as a base label = monomerAliasByName(kMonomerClassBASE, component->getTemplateAtom(atom_idx)); + } + if (label.size()) - { // unknown symbol - switch (sf) + { + TGroup temp; + if (!_mon_lib.getMonomerTemplate(mon_class, label, temp)) { - case SeqFormat::FASTA: - if (label.size() > 1) - throw Error("Can't save '%s' to FASTA", label.c_str()); - seq_string += label; - break; - default: - seq_string += label.size() > 1 ? "*" : label; + // if symbol is not standard, check its natural analog + const char* natrep = nullptr; + int temp_idx = component->getTemplateAtomTemplateIndex(atom_idx); + if (temp_idx > -1) + { + auto& tg = component->tgroups.getTGroup(temp_idx); + natrep = tg.tgroup_natreplace.ptr(); + } + else + { + auto tg_ref = findTemplateInMap(label, mon_class, _templates); + if (tg_ref.has_value()) + { + auto& tg = tg_ref.value().get(); + natrep = tg.tgroup_natreplace.ptr(); + } + } + std::string natural_analog; + if (natrep) + natural_analog = monomerAliasByName(mon_class, extractMonomerName(natrep)); + + if (_mon_lib.getMonomerTemplate(mon_class, natural_analog, temp)) + label = natural_analog; + else if (mon_class == kMonomerClassBASE) + label = "N"; + else if (mon_class == kMonomerClassAA) + label = "X"; } + + if (label.size() > 1) + throw Error("Can't save '%s' to sequence format", label.c_str()); + seq_string += label; } } } 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 0360d0c366..3dd4a64407 100644 --- a/utils/indigo-service/backend/service/tests/api/indigo_test.py +++ b/utils/indigo-service/backend/service/tests/api/indigo_test.py @@ -3279,14 +3279,14 @@ def test_convert_fasta(self): ) # write references - with open( - os.path.join(ref_path, "peptide_fasta_ref") + ".fasta", "w" - ) as file: - file.write(json.loads(result_peptide_fasta.text)["struct"]) - with open( - os.path.join(ref_path, "peptide_fasta_ref") + ".ket", "w" - ) as file: - file.write(json.loads(result_peptide_ket.text)["struct"]) + # with open( + # os.path.join(ref_path, "peptide_fasta_ref") + ".fasta", "w" + # ) as file: + # file.write(json.loads(result_peptide_fasta.text)["struct"]) + # with open( + # os.path.join(ref_path, "peptide_fasta_ref") + ".ket", "w" + # ) as file: + # file.write(json.loads(result_peptide_ket.text)["struct"]) # check with open( @@ -3334,14 +3334,14 @@ def test_convert_fasta(self): ) # write references - with open( - os.path.join(ref_path, "rna_fasta_ref") + ".fasta", "w" - ) as file: - file.write(json.loads(result_rna_fasta.text)["struct"]) - with open( - os.path.join(ref_path, "rna_fasta_ref") + ".ket", "w" - ) as file: - file.write(json.loads(result_rna_ket.text)["struct"]) + # with open( + # os.path.join(ref_path, "rna_fasta_ref") + ".fasta", "w" + # ) as file: + # file.write(json.loads(result_rna_fasta.text)["struct"]) + # with open( + # os.path.join(ref_path, "rna_fasta_ref") + ".ket", "w" + # ) as file: + # file.write(json.loads(result_rna_ket.text)["struct"]) # check with open( @@ -3389,14 +3389,14 @@ def test_convert_fasta(self): ) # write references - with open( - os.path.join(ref_path, "dna_fasta_ref") + ".fasta", "w" - ) as file: - file.write(json.loads(result_dna_fasta.text)["struct"]) - with open( - os.path.join(ref_path, "dna_fasta_ref") + ".ket", "w" - ) as file: - file.write(json.loads(result_dna_ket.text)["struct"]) + # with open( + # os.path.join(ref_path, "dna_fasta_ref") + ".fasta", "w" + # ) as file: + # file.write(json.loads(result_dna_fasta.text)["struct"]) + # with open( + # os.path.join(ref_path, "dna_fasta_ref") + ".ket", "w" + # ) as file: + # file.write(json.loads(result_dna_ket.text)["struct"]) # check with open( 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 db78b59a78..58071f6883 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 edb48e7218..ece3516dbe 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 d78ee3f1d5..add7e652c4 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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