From 02ab8394183e0d7ca74fafcb7dc1aa54eb93774e Mon Sep 17 00:00:00 2001 From: Roman Rodionov Date: Tue, 1 Oct 2024 15:42:14 +0200 Subject: [PATCH 01/11] #5325 - Change natural analogue of monomers #5324 - Change symbols of monomers #5323 - Change names of monomers #5195 - Some content problems in monomer library #5111 - Change structure of monomers --- .../src/application/editor/data/monomers.ket | 12733 ++++++++-------- 1 file changed, 6401 insertions(+), 6332 deletions(-) diff --git a/packages/ketcher-core/src/application/editor/data/monomers.ket b/packages/ketcher-core/src/application/editor/data/monomers.ket index 5ef8d5cd00..afd97205bf 100644 --- a/packages/ketcher-core/src/application/editor/data/monomers.ket +++ b/packages/ketcher-core/src/application/editor/data/monomers.ket @@ -4,19 +4,19 @@ "connections": [], "templates": [ { - "$ref": "monomerTemplate-12ddR___1',2'-Di-Deoxy-Ribose" + "$ref": "monomerTemplate-12ddR___1',2'-dideoxyribose" }, { - "$ref": "monomerTemplate-25R___2,5-Ribose" + "$ref": "monomerTemplate-25R___Ribose (2,5 connectivity)" }, { "$ref": "monomerTemplate-3A6___6-amino-hexanol (3' end)" }, { - "$ref": "monomerTemplate-3FAM___3-FAM" + "$ref": "monomerTemplate-3FAM___6-FAM (3' end)" }, { - "$ref": "monomerTemplate-3SS6___3'-Thiol-Modifier 6 S-S from Glen Research" + "$ref": "monomerTemplate-3SS6___Thiol Modifier 6 S-S (3' end)" }, { "$ref": "monomerTemplate-4sR___4-Thio-Ribose" @@ -25,13 +25,13 @@ "$ref": "monomerTemplate-5A6___6-amino-hexanol (5' end)" }, { - "$ref": "monomerTemplate-5FAM___5'-6FAM (6-carboxyfluorescein)" + "$ref": "monomerTemplate-5FAM___6-FAM (5' end)" }, { "$ref": "monomerTemplate-5FBC6___4-Formylbenzamidehexanol (5' end)" }, { - "$ref": "monomerTemplate-5cGT___2-(methylamino)acetamide (GeneTools 5'-cap for PMO)" + "$ref": "monomerTemplate-5cGT___2-(methylamino)acetamidate (5' end)" }, { "$ref": "monomerTemplate-5eU___5-ethynyl-uracil" @@ -43,7 +43,7 @@ "$ref": "monomerTemplate-5iU___5-iodo-uracil" }, { - "$ref": "monomerTemplate-5meC___5-methyl-cytidine" + "$ref": "monomerTemplate-5meC___5-methylcytosine" }, { "$ref": "monomerTemplate-5tpU___5-tris-propynyl-uracil" @@ -112,7 +112,7 @@ "$ref": "monomerTemplate-bP___Boranophosphate" }, { - "$ref": "monomerTemplate-baA___N-benzyl-adenine" + "$ref": "monomerTemplate-baA___N6-benzyladenine" }, { "$ref": "monomerTemplate-cdaC___5-cyclopropyl-4-dimethylamino-cytosine" @@ -127,13 +127,13 @@ "$ref": "monomerTemplate-cpU___5-cyclopropyl-uracil" }, { - "$ref": "monomerTemplate-cpmA___N-cyclopropylmethyl-adenine" + "$ref": "monomerTemplate-cpmA___N6-cyclopropylmethyladenine" }, { "$ref": "monomerTemplate-dR___Deoxy-Ribose" }, { - "$ref": "monomerTemplate-daA___N,N-dimethyl-Adenine" + "$ref": "monomerTemplate-daA___N6,N6-dimethyladenine" }, { "$ref": "monomerTemplate-dabA___7-deaza-8-aza-7-bromo-2-amino-Adenine" @@ -148,7 +148,7 @@ "$ref": "monomerTemplate-eR___2'-O,4'-ethylene bridged Ribose" }, { - "$ref": "monomerTemplate-eaA___N-ethyl-adenine" + "$ref": "monomerTemplate-eaA___N6-ethyladenine" }, { "$ref": "monomerTemplate-fR___2'-Flu0ro-Ribose" @@ -163,16 +163,16 @@ "$ref": "monomerTemplate-mR___2'-O-Methyl-Ribose" }, { - "$ref": "monomerTemplate-meA___N-Methyl-Adenine" + "$ref": "monomerTemplate-meA___N6-methyladenine" }, { "$ref": "monomerTemplate-mph___morpholino" }, { - "$ref": "monomerTemplate-naP___Sodium Phosphate" + "$ref": "monomerTemplate-P-___Dihydrogen phosphate" }, { - "$ref": "monomerTemplate-nasP___Sodium Phosporothioate" + "$ref": "monomerTemplate-sP-___Dihydrogen phosphorothioate" }, { "$ref": "monomerTemplate-prpC___5-Propynyl-Cytosine" @@ -664,7 +664,7 @@ "$ref": "monomerTemplate-aThr___L-allo-Threonine" }, { - "$ref": "monomerTemplate-D-2Nal___D-3-(2-naphtyl)-alanine" + "$ref": "monomerTemplate-D-2Nal___D-3-(2-naphthyl)-alanine" }, { "$ref": "monomerTemplate-D-2Thi___3-(2-thienyl)-D-alanine" @@ -724,7 +724,7 @@ "$ref": "monomerTemplate-Pip___Pipecolic acid" }, { - "$ref": "monomerTemplate-3Pal___3-(2-pyridyl)-alanine" + "$ref": "monomerTemplate-3Pal___3-(3-pyridyl)-alanine" }, { "$ref": "monomerTemplate-4Pal___3-(4-Pyridyl)-alanine" @@ -814,7 +814,7 @@ "$ref": "monomerTemplate-DALeu___4-methylpentanoic acid" }, { - "$ref": "monomerTemplate-D-OAla___D-lactic acid" + "$ref": "monomerTemplate-D-OAla___D-Lactic acid" }, { "$ref": "monomerTemplate-L-OVal___2-hydroxyisovaleric acid" @@ -862,7 +862,7 @@ "$ref": "monomerTemplate-DPhgol___D-phenylglycinol" }, { - "$ref": "monomerTemplate-DThrol___L-threoninol" + "$ref": "monomerTemplate-Thr-ol___L-threoninol" }, { "$ref": "monomerTemplate-Gly-ol___aminomethanol" @@ -955,7 +955,7 @@ "$ref": "monomerTemplate-NMe2Ab___2-(methylamino)benzoic acid" }, { - "$ref": "monomerTemplate-NMebAl___3-(methylamino)propanoic acid" + "$ref": "monomerTemplate-NMebAl___N-methyl-beta-alanine" }, { "$ref": "monomerTemplate-aMePhe___alpha-methyl-L-phenylalanine" @@ -1069,7 +1069,7 @@ "$ref": "monomerTemplate-OBn-___N-Terminal benzyloxy" }, { - "$ref": "monomerTemplate-DALys___6-amino-2-hydroxyhexanoic acid" + "$ref": "monomerTemplate-DALys___(2S)-6-amino-2-hydroxyhexanoic acid" }, { "$ref": "monomerTemplate-NMe24A___4-(dimethylamino)benzoic acid" @@ -1090,7 +1090,7 @@ "$ref": "monomerTemplate-Phe-ol___L-phenylalaninol" }, { - "$ref": "monomerTemplate-Thr-ol___D-threoninol" + "$ref": "monomerTemplate-dThrol___D-threoninol" }, { "$ref": "monomerTemplate-Gly-al___2-aminoacetaldehyde" @@ -1156,7 +1156,7 @@ "$ref": "monomerTemplate-NMe4Ab___4-(methylamino)benzoic acid" }, { - "$ref": "monomerTemplate-aMeTyr___L-metyrosine" + "$ref": "monomerTemplate-aMeTyr___alpha-methyl-tyrosine" }, { "$ref": "monomerTemplate-Aoda___(2S)-2-amino-8-oxodecanoic acid" @@ -1243,19 +1243,19 @@ "$ref": "monomerTemplate-oC12o___1,12 Dodecanediol" }, { - "$ref": "monomerTemplate-m1Yra___1-Methyl-pseudouracil" + "$ref": "monomerTemplate-m1Yra___N1-methyl-pseudouracil" }, { - "$ref": "monomerTemplate-m1A___1-Methyladenine" + "$ref": "monomerTemplate-m1A___N1-methyladenine" }, { - "$ref": "monomerTemplate-m1G___1-Methylguanine" + "$ref": "monomerTemplate-m1G___N1-methylguanine" }, { "$ref": "monomerTemplate-nC62r___2-O-(6-aminohexyl)ribose" }, { - "$ref": "monomerTemplate-m22G___2,2-Dimethylguanine" + "$ref": "monomerTemplate-m22G___N2,N2-dimethylguanine" }, { "$ref": "monomerTemplate-ox23ar___2,3-Oxetanearabinose" @@ -1312,7 +1312,7 @@ "$ref": "monomerTemplate-m2A___2-Methyladenine" }, { - "$ref": "monomerTemplate-m2G___2-Methylguanine" + "$ref": "monomerTemplate-m2G___N2-methylguanine" }, { "$ref": "monomerTemplate-se2r___2-Methylseleno-2-deoxyribose" @@ -1495,13 +1495,13 @@ "$ref": "monomerTemplate-s2U___2-Thiouracil" }, { - "$ref": "monomerTemplate-Ae2d___2-alpha-C-Ethyl-2-deoxyribose" + "$ref": "monomerTemplate-Ae2d___2-ethyl-2-deoxyribose" }, { "$ref": "monomerTemplate-Am2d___2-alpha-C-Methyl-2-deoxyribose" }, { - "$ref": "monomerTemplate-m2nprn___3-(Dimethylamino)propylaminoadenine" + "$ref": "monomerTemplate-m2nprn___N3-(dimethylamino)propylaminoadenine" }, { "$ref": "monomerTemplate-clhna___3-Chloro HNA" @@ -1573,7 +1573,7 @@ "$ref": "monomerTemplate-25moe3___3-O-methoxyethyl ribose (2,5 connectivity)" }, { - "$ref": "monomerTemplate-afhna___3-ara FHNA" + "$ref": "monomerTemplate-afhna___Ara-FHNA" }, { "$ref": "monomerTemplate-Bcm3d___3-beta-C-Methyl-2-deoxyribose" @@ -1582,19 +1582,19 @@ "$ref": "monomerTemplate-Bcm3r___3-beta-C-Methylribose" }, { - "$ref": "monomerTemplate-h456U___4,5,6-Trihydrouracil" + "$ref": "monomerTemplate-h456U___tetrahydro-4-hydroxy-1H-pyrimidin-2-one" }, { - "$ref": "monomerTemplate-acn4d___4-Acetylamino-2-deoxyribose" + "$ref": "monomerTemplate-acn4d___N-acetyl-2-deoxyazaribose" }, { - "$ref": "monomerTemplate-ac4C___4-Acetylcytosine" + "$ref": "monomerTemplate-ac4C___N4-acetylcytosine" }, { - "$ref": "monomerTemplate-cnes4T___4-Cyanoethylthiothymidine" + "$ref": "monomerTemplate-cnes4T___4-Cyanoethylthiothymine" }, { - "$ref": "monomerTemplate-d4U___4-Deoxouracil" + "$ref": "monomerTemplate-d4U___2-hydroxypyrimidine" }, { "$ref": "monomerTemplate-oC64m5___4-Hexan-6-ol-5-methylcytosine" @@ -1603,7 +1603,7 @@ "$ref": "monomerTemplate-m4C___4-Methylcytosine" }, { - "$ref": "monomerTemplate-oh4C___4-N-Hydroxcytosine" + "$ref": "monomerTemplate-oh4C___4N-Hydroxycytosine" }, { "$ref": "monomerTemplate-s4d___4-Thio-2-deoxyribose" @@ -1621,10 +1621,10 @@ "$ref": "monomerTemplate-m6T___5,6-Dimethyluracil" }, { - "$ref": "monomerTemplate-pr56U___5,6-Propylene uracil" + "$ref": "monomerTemplate-pr56U___6,7-dihydro-1H-cyclopenta[d]pyrimidine-2,4(3H,5H)-dione" }, { - "$ref": "monomerTemplate-brviny___5-(2-Bromovinyl)uracil" + "$ref": "monomerTemplate-brviny___(E)-5-(2-bromovinyl)uracil" }, { "$ref": "monomerTemplate-npry5C___5-(Propargylamine)cytosine" @@ -1669,7 +1669,7 @@ "$ref": "monomerTemplate-CN5U___5-Cyanouracil" }, { - "$ref": "monomerTemplate-DBCOnC___5-DBCO-U (ethylene carbamoyl hexylamino linker)" + "$ref": "monomerTemplate-DBCOnC___5-DBCO-U" }, { "$ref": "monomerTemplate-d5m___5-Deoxy-2-O-methylribose" @@ -1741,7 +1741,7 @@ "$ref": "monomerTemplate-thiz5C___5-Thiazolecytidine" }, { - "$ref": "monomerTemplate-thiz5U___5-Thiazoleuridine" + "$ref": "monomerTemplate-thiz5U___5-Thiazoleuracil" }, { "$ref": "monomerTemplate-thien5___5-Thienyl-6-azauracil" @@ -1753,7 +1753,7 @@ "$ref": "monomerTemplate-vinyl5___5-Vinyluracil" }, { - "$ref": "monomerTemplate-mnm5U___5-[(Methylamino)methyl]uridine" + "$ref": "monomerTemplate-mnm5U___5-[(methylamino)methyl]uracil" }, { "$ref": "monomerTemplate-nobn6p___6-(p-Nitrobenzylthio)purine" @@ -1783,10 +1783,10 @@ "$ref": "monomerTemplate-cl6pur___6-Chloropurine" }, { - "$ref": "monomerTemplate-cyh6A___6-Cyclohexyladenine" + "$ref": "monomerTemplate-cyh6A___N6-cyclohexyladenine" }, { - "$ref": "monomerTemplate-cyp6A___6-Cyclopentyladenine" + "$ref": "monomerTemplate-cyp6A___N6-cyclopentyladenine" }, { "$ref": "monomerTemplate-e6A___6-Ethyladenine" @@ -1795,7 +1795,7 @@ "$ref": "monomerTemplate-mo6pur___6-Methoxypurine" }, { - "$ref": "monomerTemplate-m6G___6-Methylguanine" + "$ref": "monomerTemplate-m6G___6-O-methylguanine" }, { "$ref": "monomerTemplate-m6pur___6-Methylpurine" @@ -1813,7 +1813,7 @@ "$ref": "monomerTemplate-s6G___6-Thioguanine" }, { - "$ref": "monomerTemplate-s6puri___6-Thiopurine" + "$ref": "monomerTemplate-s6puri___6-Mercaptopurine" }, { "$ref": "monomerTemplate-Bcoh4d___6-beta-Hydroxycarbo-2-deoxyribose" @@ -1846,10 +1846,10 @@ "$ref": "monomerTemplate-c7G___7-Deazaguanine" }, { - "$ref": "monomerTemplate-m7h8G___7-Methyl 8-dihydroguanine" + "$ref": "monomerTemplate-m7h8G___N7-methyl-8-dihydroguanine" }, { - "$ref": "monomerTemplate-m7G___7-Methylguanine" + "$ref": "monomerTemplate-m7G___N7-methylguanine" }, { "$ref": "monomerTemplate-tCnitr___7-Nitro-1,3-diaza-2-oxophenothiazin" @@ -1888,7 +1888,7 @@ "$ref": "monomerTemplate-s8G___8-Thioguanine" }, { - "$ref": "monomerTemplate-allyl9___9-Allylguanine" + "$ref": "monomerTemplate-allyl9___N9-allyl-8-oxoguanine" }, { "$ref": "monomerTemplate-Smclna___(2S)-methyl-cLNA" @@ -1924,19 +1924,19 @@ "$ref": "monomerTemplate-Sm6ALl___(6S)-6-methyl-alpha-L-LNA" }, { - "$ref": "monomerTemplate-nen___(Aminoethyl)amino" + "$ref": "monomerTemplate-nen___Ethylenediamine" }, { "$ref": "monomerTemplate-Diprgl___(D)-2-O-(2,3-Isopropylidene glycer-1-yl)ribose" }, { - "$ref": "monomerTemplate-m2nen___(Dimethylaminoethyl)amino" + "$ref": "monomerTemplate-m2nen___N1,N1-dimethylethane-1,2-diamine" }, { "$ref": "monomerTemplate-Liprgl___(L)-2-O-(2,3-Isopropylidene glycer-1-yl)ribose" }, { - "$ref": "monomerTemplate-h456UR___(R)-4,5,6-Trihydrouracil" + "$ref": "monomerTemplate-h456UR___(R)-tetrahydro-4-hydroxy-1H-pyrimidin-2-one" }, { "$ref": "monomerTemplate-Rm5fl2___(R)-2-Fluoro-5-methylribose" @@ -2011,7 +2011,7 @@ "$ref": "monomerTemplate-nC6n5C___Amino-Modier C6 dC" }, { - "$ref": "monomerTemplate-az8A___Azidoadenine" + "$ref": "monomerTemplate-az8A___8-azidoadenine" }, { "$ref": "monomerTemplate-bnn___Benzylamino" @@ -2047,10 +2047,10 @@ "$ref": "monomerTemplate-fcena___Fluoro-CeNA" }, { - "$ref": "monomerTemplate-gclamp___G-clamp (9-(aminoethoxy)phenoxazine)" + "$ref": "monomerTemplate-gclamp___G-clamp" }, { - "$ref": "monomerTemplate-ggclam___G-clamp (9-(guanylethoxy)phenoxazine)" + "$ref": "monomerTemplate-ggclam___guanidino-G-clamp" }, { "$ref": "monomerTemplate-Oro___Orotic Acid" @@ -2074,13 +2074,13 @@ "$ref": "monomerTemplate-meclna___Methylene cLNA" }, { - "$ref": "monomerTemplate-mepo2___Methylenephosphonate" + "$ref": "monomerTemplate-mepo2___Hydroxymethylphosphonic acid" }, { "$ref": "monomerTemplate-mp___Methylphosphonate" }, { - "$ref": "monomerTemplate-msp___Methylthiophosphonate" + "$ref": "monomerTemplate-msp___Methylphosphonothioic acid" }, { "$ref": "monomerTemplate-nen2G___N2-(2-Amino)ethyl guanine" @@ -2113,7 +2113,7 @@ "$ref": "monomerTemplate-4ime6A___N6-[2-(4-Imidazoyl)ethyl]adenine" }, { - "$ref": "monomerTemplate-imprn2___N-(Aminopropyl)imidazoleadenine" + "$ref": "monomerTemplate-imprn2___2-(1-(3-aminopropyl)imidazole)adenine" }, { "$ref": "monomerTemplate-mnobna___N-(Methyl)aminooxy BNA" @@ -2137,7 +2137,7 @@ "$ref": "monomerTemplate-Nmc___North-methanocarbocycle" }, { - "$ref": "monomerTemplate-oxy___Oxy (ether)" + "$ref": "monomerTemplate-oxy___Oxy" }, { "$ref": "monomerTemplate-Sp18___PEG/HEG 18 atom spacer" @@ -2233,7 +2233,7 @@ "$ref": "monomerTemplate-AmdA___2, 6-Diaminopurine" }, { - "$ref": "monomerTemplate-5HydMe-dC___5-Hydroxymethyl dC" + "$ref": "monomerTemplate-5hMedC___5-Hydroxymethyl dC" }, { "$ref": "monomerTemplate-Super-dG___Super G" @@ -2242,7 +2242,7 @@ "$ref": "monomerTemplate-Super-dT___Super T" }, { - "$ref": "monomerTemplate-5Br-dU___5-Bromo dU" + "$ref": "monomerTemplate-5Br-dU___5-Bromo-deoxyuridine" }, { "$ref": "monomerTemplate-5NitInd___5-Nitroindole" @@ -2345,7 +2345,7 @@ } ] }, - "monomerTemplate-12ddR___1',2'-Di-Deoxy-Ribose": { + "monomerTemplate-12ddR___1',2'-dideoxyribose": { "type": "monomerTemplate", "atoms": [ { @@ -2507,8 +2507,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "12ddR___1',2'-Di-Deoxy-Ribose", - "fullName": "1',2'-Di-Deoxy-Ribose", + "id": "12ddR___1',2'-dideoxyribose", + "fullName": "1',2'-dideoxyribose", "alias": "12ddR", "attachmentPoints": [ { @@ -2532,7 +2532,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-25R___2,5-Ribose": { + "monomerTemplate-25R___Ribose (2,5 connectivity)": { "type": "monomerTemplate", "atoms": [ { @@ -2728,8 +2728,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "25R___2,5-Ribose", - "fullName": "2,5-Ribose", + "id": "25R___Ribose (2,5 connectivity)", + "fullName": "Ribose (2,5 connectivity)", "alias": "25R", "attachmentPoints": [ { @@ -2962,7 +2962,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-3FAM___3-FAM": { + "monomerTemplate-3FAM___6-FAM (3' end)": { "type": "monomerTemplate", "atoms": [ { @@ -3568,8 +3568,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "3FAM___3-FAM", - "fullName": "3-FAM", + "id": "3FAM___6-FAM (3' end)", + "fullName": "6-FAM (3' end)", "alias": "3FAM", "attachmentPoints": [ { @@ -3593,7 +3593,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-3SS6___3'-Thiol-Modifier 6 S-S from Glen Research": { + "monomerTemplate-3SS6___Thiol Modifier 6 S-S (3' end)": { "type": "monomerTemplate", "atoms": [ { @@ -3864,8 +3864,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "3SS6___3'-Thiol-Modifier 6 S-S from Glen Research", - "fullName": "3'-Thiol-Modifier 6 S-S from Glen Research", + "id": "3SS6___Thiol Modifier 6 S-S (3' end)", + "fullName": "Thiol Modifier 6 S-S (3' end)", "alias": "3SS6", "attachmentPoints": [ { @@ -4319,7 +4319,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-5FAM___5'-6FAM (6-carboxyfluorescein)": { + "monomerTemplate-5FAM___6-FAM (5' end)": { "type": "monomerTemplate", "atoms": [ { @@ -4888,8 +4888,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "5FAM___5'-6FAM (6-carboxyfluorescein)", - "fullName": "5'-6FAM (6-carboxyfluorescein)", + "id": "5FAM___6-FAM (5' end)", + "fullName": "6-FAM (5' end)", "alias": "5FAM", "attachmentPoints": [ { @@ -5228,7 +5228,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-5cGT___2-(methylamino)acetamide (GeneTools 5'-cap for PMO)": { + "monomerTemplate-5cGT___2-(methylamino)acetamidate (5' end)": { "type": "monomerTemplate", "atoms": [ { @@ -5334,8 +5334,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "5cGT___2-(methylamino)acetamide (GeneTools 5'-cap for PMO)", - "fullName": "2-(methylamino)acetamide (GeneTools 5'-cap for PMO)", + "id": "5cGT___2-(methylamino)acetamidate (5' end)", + "fullName": "2-(methylamino)acetamidate (5' end)", "alias": "5cGT", "attachmentPoints": [ { @@ -5887,7 +5887,7 @@ ], "naturalAnalogShort": "U" }, - "monomerTemplate-5meC___5-methyl-cytidine": { + "monomerTemplate-5meC___5-methylcytosine": { "type": "monomerTemplate", "atoms": [ { @@ -6045,8 +6045,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "5meC___5-methyl-cytidine", - "fullName": "5-methyl-cytidine", + "id": "5meC___5-methylcytosine", + "fullName": "5-methylcytosine", "alias": "5meC", "attachmentPoints": [ { @@ -10764,7 +10764,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-baA___N-benzyl-adenine": { + "monomerTemplate-baA___N6-benzyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -11056,8 +11056,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "baA___N-benzyl-adenine", - "fullName": "N-benzyl-adenine", + "id": "baA___N6-benzyladenine", + "fullName": "N6-benzyladenine", "alias": "baA", "attachmentPoints": [ { @@ -12080,7 +12080,7 @@ ], "naturalAnalogShort": "U" }, - "monomerTemplate-cpmA___N-cyclopropylmethyl-adenine": { + "monomerTemplate-cpmA___N6-cyclopropylmethyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -12327,8 +12327,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "cpmA___N-cyclopropylmethyl-adenine", - "fullName": "N-cyclopropylmethyl-adenine", + "id": "cpmA___N6-cyclopropylmethyladenine", + "fullName": "N6-cyclopropylmethyladenine", "alias": "cpmA", "attachmentPoints": [ { @@ -12556,7 +12556,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-daA___N,N-dimethyl-Adenine": { + "monomerTemplate-daA___N6,N6-dimethyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -12766,8 +12766,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "daA___N,N-dimethyl-Adenine", - "fullName": "N,N-dimethyl-Adenine", + "id": "daA___N6,N6-dimethyladenine", + "fullName": "N6,N6-dimethyladenine", "alias": "daA", "attachmentPoints": [ { @@ -14217,7 +14217,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-eaA___N-ethyl-adenine": { + "monomerTemplate-eaA___N6-ethyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -14427,8 +14427,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "eaA___N-ethyl-adenine", - "fullName": "N-ethyl-adenine", + "id": "eaA___N6-ethyladenine", + "fullName": "N6-ethyladenine", "alias": "eaA", "attachmentPoints": [ { @@ -15398,7 +15398,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-meA___N-Methyl-Adenine": { + "monomerTemplate-meA___N6-methyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -15593,8 +15593,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "meA___N-Methyl-Adenine", - "fullName": "N-Methyl-Adenine", + "id": "meA___N6-methyladenine", + "fullName": "N6-methyladenine", "alias": "meA", "attachmentPoints": [ { @@ -15820,7 +15820,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-naP___Sodium Phosphate": { + "monomerTemplate-P-___Dihydrogen phosphate": { "type": "monomerTemplate", "atoms": [ { @@ -15897,9 +15897,9 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "naP___Sodium Phosphate", - "fullName": "Sodium Phosphate", - "alias": "naP", + "id": "P-___Dihydrogen phosphate", + "fullName": "Dihydrogen phosphate", + "alias": "P-", "attachmentPoints": [ { "attachmentAtom": 0, @@ -15922,7 +15922,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-nasP___Sodium Phosporothioate": { + "monomerTemplate-sP-___Dihydrogen phosphorothioate": { "type": "monomerTemplate", "atoms": [ { @@ -15999,9 +15999,9 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "nasP___Sodium Phosporothioate", - "fullName": "Sodium Phosporothioate", - "alias": "nasP", + "id": "sP-___Dihydrogen phosphorothioate", + "fullName": "Dihydrogen phosphorothioate", + "alias": "sP-", "attachmentPoints": [ { "attachmentAtom": 0, @@ -16739,78 +16739,78 @@ }, "monomerTemplate-sP___Phosporothioate": { "type": "monomerTemplate", - "atoms": [ - { - "label": "P", - "location": [ - -0.2399, - 0, - 0 - ] - }, - { - "label": "O", - "location": [ - -1.4399, - 0, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.3598, - -1.0394, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.9601, - 0, - 0 - ] - }, - { - "label": "S", - "location": [ - 0.3598, - 1.0394, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 2 - ] - }, - { - "type": 1, "atoms": [ - 0, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 4 - ] - } - ], + { + "label": "O", + "location": [ + 6, + -6.025, + 0 + ] + }, + { + "label": "P", + "location": [ + 7, + -6.025, + 0 + ] + }, + { + "label": "O", + "location": [ + 7.5, + -6.891025403784439, + 0 + ] + }, + { + "label": "S", + "location": [ + 7.499999999999999, + -5.158974596215561, + 0 + ] + }, + { + "label": "O", + "location": [ + 8, + -6.025, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 2, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 4 + ] + } + ], "class": "Phosphate", "classHELM": "RNA", "id": "sP___Phosporothioate", @@ -16818,19 +16818,19 @@ "alias": "sP", "attachmentPoints": [ { - "attachmentAtom": 0, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 1 + 0 ] }, "type": "left" }, { - "attachmentAtom": 0, + "attachmentAtom": 1, "leavingGroup": { "atoms": [ - 3 + 4 ] }, "type": "right" @@ -47732,151 +47732,166 @@ "type": "right" } ], - "naturalAnalogShort": "E" + "naturalAnalogShort": "G" }, "monomerTemplate-D-Pyr___D-Pyroglutamic acid": { "type": "monomerTemplate", - "atoms": [ - { - "label": "O", - "location": [ - 3.1202, - -2.0921, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.6281, - -2.2462, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.0161, - -3.6157, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.75, - -1.0323, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "C", - "location": [ - 1.2135, - 0.3943, - 0 - ] - }, - { - "label": "C", - "location": [ - 0, - 1.276, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.2135, - 0.3943, - 0 - ] - }, - { - "label": "O", - "location": [ - -2.6401, - 0.8578, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.75, - -1.0323, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 1 + { + "label": "N", + "location": [ + 7.776375054004451, + -8.268482852301501, + 0 + ] + }, + { + "label": "C", + "location": [ + 7.1470827045986045, + -7.491336688298125, + 0 + ] + }, + { + "label": "C", + "location": [ + 7.691709820041229, + -6.6526301279767015, + 0 + ] + }, + { + "label": "C", + "location": [ + 8.657623659596354, + -6.911445961243541, + 0 + ] + }, + { + "label": "C", + "location": [ + 8.709931296998795, + -7.910100706523872, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + 6.148453370780793, + -7.543676478502077, + 0 + ] + }, + { + "label": "C", + "location": [ + 9.548599773947375, + -8.454742961378148, + 0 + ] + }, + { + "label": "O", + "location": [ + 9.496259983743423, + -9.45337229519596, + 0 + ] + }, + { + "label": "O", + "location": [ + 10.439608041099905, + -8.000755882414612, + 0 + ] + }, + { + "label": "H", + "location": [ + 7.5175560089019315, + -9.234408678590569, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 2, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 0 + ] + }, + { + "type": 2, + "atoms": [ + 1, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 6 + ], + "stereo": 6 + }, + { + "type": 2, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 8 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 9 + ] + } ], - "stereo": 6 - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 2, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 8 - ] - } - ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "D-Pyr___D-Pyroglutamic acid", @@ -47884,16 +47899,25 @@ "alias": "D-Pyr", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 0 + 9 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 6, + "leavingGroup": { + "atoms": [ + 8 ] }, "type": "right" } ], - "naturalAnalogShort": "E" + "naturalAnalogShort": "G" }, "monomerTemplate-Phe3Cl___3-Chloro-L-phenylalanine": { "type": "monomerTemplate", @@ -49955,7 +49979,7 @@ ], "naturalAnalogShort": "T" }, - "monomerTemplate-D-2Nal___D-3-(2-naphtyl)-alanine": { + "monomerTemplate-D-2Nal___D-3-(2-naphthyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -50227,8 +50251,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-2Nal___D-3-(2-naphtyl)-alanine", - "fullName": "D-3-(2-naphtyl)-alanine", + "id": "D-2Nal___D-3-(2-naphthyl)-alanine", + "fullName": "D-3-(2-naphthyl)-alanine", "alias": "D-2Nal", "attachmentPoints": [ { @@ -54416,7 +54440,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-3Pal___3-(2-pyridyl)-alanine": { + "monomerTemplate-3Pal___3-(3-pyridyl)-alanine": { "type": "monomerTemplate", "atoms": [ { @@ -54621,8 +54645,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "3Pal___3-(2-pyridyl)-alanine", - "fullName": "3-(2-pyridyl)-alanine", + "id": "3Pal___3-(3-pyridyl)-alanine", + "fullName": "3-(3-pyridyl)-alanine", "alias": "3Pal", "attachmentPoints": [ { @@ -58372,184 +58396,193 @@ "naturalAnalogShort": "G" }, "monomerTemplate-DAGlyO___2-hydroxyacetic acid": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "C", + "location": [ + 6.792508195019402, + -8.825260398785275, + 0 + ] + }, + { + "label": "C", + "location": [ + 7.658533598803841, + -8.325260398785275, + 0 + ] + }, + { + "label": "O", + "location": [ + 8.52455900258828, + -8.825260398785275, + 0 + ] + }, + { + "label": "O", + "location": [ + 7.658533598803841, + -7.325260398785275, + 0 + ] + }, + { + "label": "O", + "location": [ + 5.926482791234964, + 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1.2997, + 1.0157, + -3.6164, 0 ] }, { "label": "O", "location": [ - 9.7021, - 2.5983, + 0.2661, + -2.3171, 0 ] }, { "label": "C", "location": [ - 7.4505, - 1.2997, + 0.2657, + -4.9164, 0 ] }, { - "label": "O", + "label": "C", "location": [ - 6.6992, - 0.0004, + 1.0144, + -6.2142, 0 ] }, { - "label": "H", + "label": "C", "location": [ - 5.1992, - 0.0004, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - } - ], - "class": "AminoAcid", - "classHELM": "PEPTIDE", - "id": "DAGlyO___2-hydroxyacetic acid", - "fullName": "2-hydroxyacetic acid", - "alias": "DAGlyO", - "attachmentPoints": [ - { - "attachmentAtom": 4, - "leavingGroup": { - "atoms": [ - 5 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "G" - }, - "monomerTemplate-DAGlyT___2-thiopheneacetic acid": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "O", - "location": [ - 2.5157, - -3.6164, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.0157, - -3.6164, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.2661, - -2.3171, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.2657, - -4.9164, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.0144, - -6.2142, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.4067, - -7.5856, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.5232, - -8.5873, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.8209, - -7.835, - 0 - ] - }, - { - "label": "S", - "location": [ - 2.5065, - -6.3683, + 0.4067, + -7.5856, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.5232, + -8.5873, + 0 + ] + }, + { + "label": "C", + "location": [ + 2.8209, + -7.835, + 0 + ] + }, + { + "label": "S", + "location": [ + 2.5065, + -6.3683, 0 ] } @@ -59043,190 +59076,190 @@ }, "monomerTemplate-PhLA___3-phenyllactic acid": { "type": "monomerTemplate", - "atoms": [ - { - "label": "O", - "location": [ - 0.3451, - -1.7039, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.8451, - -1.7039, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.5947, - -0.4046, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.5951, - -3.0039, - 0 - ] - }, - { - "label": "O", - "location": [ - 4.0951, - -3.0039, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.8451, - -4.3039, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.5951, - -5.6039, - 0 - ] - }, - { - "label": "C", - "location": [ - 1.8474, - -6.9042, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.5997, - -8.202, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.0997, - -8.1994, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.8474, - -6.899, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.0951, - -5.6013, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, "atoms": [ - 0, - 1 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 3 - ] - }, - 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"type": 1, + "atoms": [ + 8, + 9 + ] + }, + { + "type": 2, + "atoms": [ + 8, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 11 + ] + } + ], "class": "AminoAcid", "classHELM": "PEPTIDE", "id": "PhLA___3-phenyllactic acid", @@ -59234,10 +59267,10 @@ "alias": "PhLA", "attachmentPoints": [ { - "attachmentAtom": 3, + "attachmentAtom": 8, "leavingGroup": { "atoms": [ - 4 + 9 ] }, "type": "right" @@ -59586,7 +59619,7 @@ ], "naturalAnalogShort": "L" }, - "monomerTemplate-D-OAla___D-lactic acid": { + "monomerTemplate-D-OAla___D-Lactic acid": { "type": "monomerTemplate", "atoms": [ { @@ -59679,8 +59712,8 @@ ], "class": "AminoAcid", "classHELM": "PEPTIDE", - "id": "D-OAla___D-lactic acid", - "fullName": "D-lactic acid", + "id": "D-OAla___D-Lactic acid", + "fullName": "D-Lactic acid", "alias": "D-OAla", "attachmentPoints": [ { @@ -62227,7 +62260,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-DThrol___L-threoninol": { + "monomerTemplate-Thr-ol___L-threoninol": { "type": 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"classHELM": "RNA", - "id": "m22G___2,2-Dimethylguanine", - "fullName": "2,2-Dimethylguanine", + "id": "m22G___N2,N2-dimethylguanine", + "fullName": "N2,N2-dimethylguanine", "alias": "m22G", "attachmentPoints": [ { @@ -95226,7 +95325,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-m2G___2-Methylguanine": { + "monomerTemplate-m2G___N2-methylguanine": { "type": "monomerTemplate", "atoms": [ { @@ -95436,8 +95535,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "m2G___2-Methylguanine", - "fullName": "2-Methylguanine", + "id": "m2G___N2-methylguanine", + "fullName": "N2-methylguanine", "alias": "m2G", "attachmentPoints": [ { @@ -115265,7 +115364,7 @@ ], "naturalAnalogShort": "U" }, - "monomerTemplate-Ae2d___2-alpha-C-Ethyl-2-deoxyribose": { + "monomerTemplate-Ae2d___2-ethyl-2-deoxyribose": { "type": "monomerTemplate", "atoms": [ { @@ -115476,8 +115575,8 @@ ], "class": "Sugar", "classHELM": "RNA", - "id": "Ae2d___2-alpha-C-Ethyl-2-deoxyribose", - "fullName": 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"fullName": "5-Aminopropyluracil", + "alias": "npr5U", "attachmentPoints": [ { - "attachmentAtom": 12, + "attachmentAtom": 2, "leavingGroup": { "atoms": [ - 14 + 7 ] }, "type": "left" - }, - { - "attachmentAtom": 7, - "leavingGroup": { - "atoms": [ - 11 - ] - }, - "type": "right" - }, - { - "attachmentAtom": 5, - "leavingGroup": { - "atoms": [ - 9 - ] - }, - "type": "side" } ], - "naturalAnalogShort": "R" + "naturalAnalogShort": "U" }, - "monomerTemplate-allyl5___5-Allyluracil": { + "monomerTemplate-br5C___5-Bromocytosine": { "type": "monomerTemplate", "atoms": [ - { - "label": "C", - "location": [ - 4.8481, - 2.7991, - 0 - ] - }, { "label": "N", "location": [ - 4.0981, - 1.5, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.8481, - 0.201, + 3.75, + 4.299, 0 ] }, { "label": "C", "location": [ - 6.3481, - 2.7991, + 2.25, + 4.299, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 7.0981, 1.5, + 3, 0 ] }, { - "label": "N", + "label": "C", "location": [ - 6.3481, - 0.201, + 2.25, + 1.701, 0 ] }, { - "label": "H", + "label": "C", "location": [ - 2.5981, - 1.5, + 3.75, + 1.701, 0 ] }, { "label": "C", "location": [ - 7.0958, - 4.1004, + 4.5, + 3, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 6.3436, - 5.399, + 6, + 3, 0 ] }, { - "label": "C", + "label": "H", "location": [ - 7.0909, - 6.6996, + 0, + 3, 0 ] }, { "label": "O", "location": [ - 8.5981, 1.5, + 5.5981, 0 ] }, { - "label": "O", + "label": "Br", "location": [ - 4.0981, - -1.0981, + 4.5, + 0.4019, 0 ] } @@ -126701,14 +127744,14 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ - 0, + 2, 3 ] }, { - "type": 1, + "type": 2, "atoms": [ 3, 4 @@ -126722,74 +127765,60 @@ ] }, { - "type": 1, + "type": 2, "atoms": [ - 5, - 2 + 0, + 5 ] }, { "type": 1, "atoms": [ - 1, + 5, 6 ] }, { "type": 1, "atoms": [ - 3, + 2, 7 ] }, - { - "type": 1, - "atoms": [ - 7, - 8 - ] - }, { "type": 2, "atoms": [ - 8, - 9 + 1, + 8 ] }, { - "type": 2, + "type": 1, "atoms": [ 4, - 10 - ] - }, - { - "type": 2, - "atoms": [ - 2, - 11 + 9 ] } ], "class": "Base", "classHELM": "RNA", - "id": "allyl5___5-Allyluracil", - "fullName": "5-Allyluracil", - "alias": "allyl5", + "id": "br5C___5-Bromocytosine", + "fullName": "5-Bromocytosine", + "alias": "br5C", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 2, "leavingGroup": { "atoms": [ - 6 + 7 ] }, "type": "left" } ], - "naturalAnalogShort": "U" + "naturalAnalogShort": "C" }, - "monomerTemplate-nC65C___5-Aminohexylcytosine": { + "monomerTemplate-br5U___5-Bromouracil": { "type": "monomerTemplate", "atoms": [ { @@ -126841,7 +127870,7 @@ ] }, { - "label": "N", + "label": "O", "location": [ 6, 3, @@ -126865,58 +127894,10 @@ ] }, { - "label": "C", - "location": [ - 4.4977, - 0.3997, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.7455, - -0.899, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.4932, - -2.2003, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.7409, - -3.499, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.4887, - -4.8003, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.7364, - -6.099, - 0 - ] - }, - { - "label": "N", + "label": "Br", "location": [ - 4.4837, - -7.3996, + 4.5, + 0.4019, 0 ] } @@ -126958,14 +127939,14 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ 0, 5 ] }, { - "type": 1, + "type": 2, "atoms": [ 5, 6 @@ -126991,55 +127972,13 @@ 4, 9 ] - }, - { - "type": 1, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 12 - ] - }, - { - "type": 1, - "atoms": [ - 12, - 13 - ] - }, - { - "type": 1, - "atoms": [ - 13, - 14 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 15 - ] } ], "class": "Base", "classHELM": "RNA", - "id": "nC65C___5-Aminohexylcytosine", - "fullName": "5-Aminohexylcytosine", - "alias": "nC65C", + "id": "br5U___5-Bromouracil", + "fullName": "5-Bromouracil", + "alias": "br5U", "attachmentPoints": [ { "attachmentAtom": 2, @@ -127051,151 +127990,95 @@ "type": "left" } ], - "naturalAnalogShort": "C" + "naturalAnalogShort": "U" }, - "monomerTemplate-nC65U___5-Aminohexyluracil": { + "monomerTemplate-cl5C___5-Chlorocytosine": { "type": "monomerTemplate", "atoms": [ - { - "label": "N", - "location": [ - -4.2493, - 1.5455, - 0 - ] - }, - { - "label": "C", - "location": [ - -4.663, - 0.1037, - 0 - ] - }, - { - "label": "N", - "location": [ - -3.6212, - -0.9755, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.1657, - -0.6129, - 0 - ] - }, { "label": "C", "location": [ - -1.752, - 0.8289, + 2.25, + -4.299, 0 ] }, { "label": "C", "location": [ - -2.7938, - 1.9081, - 0 - ] - }, - { - "label": "O", - "location": [ - -2.3801, - 3.3499, - 0 - ] - }, - { - "label": "H", - "location": [ - -4.0349, - -2.4173, - 0 - ] - }, - { - "label": "O", - "location": [ - -6.1185, - -0.259, + 3.75, + -4.299, 0 ] }, { "label": "C", "location": [ - -0.2949, - 1.1888, + 4.5, + -3, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 0.7459, - 0.1075, + 1.5, + -3, 0 ] }, { "label": "C", "location": [ - 2.203, - 0.4673, + 2.25, + -1.701, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 3.2438, - -0.6139, + 3.75, + -1.701, 0 ] }, { - "label": "C", + "label": "O", "location": [ - 4.7009, - -0.2541, + 1.5, + -0.4019, 0 ] }, { - "label": "C", + "label": "N", "location": [ - 5.7417, - -1.3354, + 6, + -3, 0 ] }, { - "label": "N", + "label": "H", "location": [ - 7.1988, - -0.9755, + 0, + -3, 0 ] }, { - "label": "H", + "label": "Cl", "location": [ - 8.239, - -2.0562, + 4.5, + -5.5981, 0 ] } ], "bonds": [ { - "type": 1, + "type": 2, "atoms": [ 0, 1 @@ -127211,12 +128094,12 @@ { "type": 1, "atoms": [ - 2, + 0, 3 ] }, { - "type": 2, + "type": 1, "atoms": [ 3, 4 @@ -127230,16 +128113,16 @@ ] }, { - "type": 1, + "type": 2, "atoms": [ - 0, - 5 + 5, + 2 ] }, { "type": 2, "atoms": [ - 5, + 4, 6 ] }, @@ -127251,846 +128134,47 @@ ] }, { - "type": 2, + "type": 1, "atoms": [ - 1, + 3, 8 ] }, { "type": 1, "atoms": [ - 4, + 1, 9 ] - }, + } + ], + "class": "Base", + "classHELM": "RNA", + "id": "cl5C___5-Chlorocytosine", + "fullName": "5-Chlorocytosine", + "alias": "cl5C", + "attachmentPoints": [ { - "type": 1, - "atoms": [ - 9, - 10 - ] - }, + "attachmentAtom": 3, + "leavingGroup": { + "atoms": [ + 8 + ] + }, + "type": "left" + } + ], + "naturalAnalogShort": "C" + }, + "monomerTemplate-cl5U___5-Chlorouracil": { + "type": "monomerTemplate", + "atoms": [ { - "type": 1, - "atoms": [ - 10, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 12 - ] - }, - { - "type": 1, - "atoms": [ - 12, - 13 - ] - }, - { - "type": 1, - "atoms": [ - 13, - 14 - ] - }, - { - "type": 1, - "atoms": [ - 14, - 15 - ] - }, - { - "type": 1, - "atoms": [ - 15, - 16 - ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "nC65U___5-Aminohexyluracil", - "fullName": "5-Aminohexyluracil", - "alias": "nC65U", - "attachmentPoints": [ - { - "attachmentAtom": 2, - "leavingGroup": { - "atoms": [ - 7 - ] - }, - "type": "left" - }, - { - "attachmentAtom": 15, - "leavingGroup": { - "atoms": [ - 16 - ] - }, - "type": "right" - } - ], - "naturalAnalogShort": "U" - }, - "monomerTemplate-npr5U___5-Aminopropyluracil": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - 3.75, - 4.299, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - 4.299, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.5, - 3, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - 1.701, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.75, - 1.701, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.5, - 3, - 0 - ] - }, - { - "label": "O", - "location": [ - 6, - 3, - 0 - ] - }, - { - "label": "H", - "location": [ - 0, - 3, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.5, - 5.5981, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.4977, - 0.3997, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.7455, - -0.899, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.4932, - -2.2003, - 0 - ] - }, - { - "label": "N", - "location": [ - 3.7413, - -3.4983, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 7 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 9 - ] - }, - { - "type": 1, - "atoms": [ - 9, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 10, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 11, - 12 - ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "npr5U___5-Aminopropyluracil", - "fullName": "5-Aminopropyluracil", - "alias": "npr5U", - "attachmentPoints": [ - { - "attachmentAtom": 2, - "leavingGroup": { - "atoms": [ - 7 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "U" - }, - "monomerTemplate-br5C___5-Bromocytosine": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - 3.75, - 4.299, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - 4.299, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.5, - 3, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - 1.701, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.75, - 1.701, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.5, - 3, - 0 - ] - }, - { - "label": "N", - "location": [ - 6, - 3, - 0 - ] - }, - { - "label": "H", - "location": [ - 0, - 3, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.5, - 5.5981, - 0 - ] - }, - { - "label": "Br", - "location": [ - 4.5, - 0.4019, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 7 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 9 - ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "br5C___5-Bromocytosine", - "fullName": "5-Bromocytosine", - "alias": "br5C", - "attachmentPoints": [ - { - "attachmentAtom": 2, - "leavingGroup": { - "atoms": [ - 7 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "C" - }, - "monomerTemplate-br5U___5-Bromouracil": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - 3.75, - 4.299, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - 4.299, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.5, - 3, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - 1.701, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.75, - 1.701, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.5, - 3, - 0 - ] - }, - { - "label": "O", - "location": [ - 6, - 3, - 0 - ] - }, - { - "label": "H", - "location": [ - 0, - 3, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.5, - 5.5981, - 0 - ] - }, - { - "label": "Br", - "location": [ - 4.5, - 0.4019, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 2, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 7 - ] - }, - { - "type": 2, - "atoms": [ - 1, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 9 - ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "br5U___5-Bromouracil", - "fullName": "5-Bromouracil", - "alias": "br5U", - "attachmentPoints": [ - { - "attachmentAtom": 2, - "leavingGroup": { - "atoms": [ - 7 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "U" - }, - "monomerTemplate-cl5C___5-Chlorocytosine": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 2.25, - -4.299, - 0 - ] - }, - { - "label": "C", - "location": [ - 3.75, - -4.299, - 0 - ] - }, - { - "label": "C", - "location": [ - 4.5, - -3, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.5, - -3, - 0 - ] - }, - { - "label": "C", - "location": [ - 2.25, - -1.701, - 0 - ] - }, - { - "label": "N", - "location": [ - 3.75, - -1.701, - 0 - ] - }, - { - "label": "O", - "location": [ - 1.5, - -0.4019, - 0 - ] - }, - { - "label": "N", - "location": [ - 6, - -3, - 0 - ] - }, - { - "label": "H", - "location": [ - 0, - -3, - 0 - ] - }, - { - "label": "Cl", - "location": [ - 4.5, - -5.5981, - 0 - ] - } - ], - "bonds": [ - { - "type": 2, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 2, - "atoms": [ - 5, - 2 - ] - }, - { - "type": 2, - "atoms": [ - 4, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 7 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 9 - ] - } - ], - "class": "Base", - "classHELM": "RNA", - "id": "cl5C___5-Chlorocytosine", - "fullName": "5-Chlorocytosine", - "alias": "cl5C", - "attachmentPoints": [ - { - "attachmentAtom": 3, - "leavingGroup": { - "atoms": [ - 8 - ] - }, - "type": "left" - } - ], - "naturalAnalogShort": "C" - }, - "monomerTemplate-cl5U___5-Chlorouracil": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 2.25, - -4.299, - 0 + "label": "C", + "location": [ + 2.25, + -4.299, + 0 ] }, { @@ -128445,7 +128529,7 @@ ], "naturalAnalogShort": "U" }, - "monomerTemplate-DBCOnC___5-DBCO-U (ethylene carbamoyl hexylamino linker)": { + "monomerTemplate-DBCOnC___5-DBCO-U": { "type": "monomerTemplate", "atoms": [ { @@ -129149,8 +129233,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "DBCOnC___5-DBCO-U (ethylene carbamoyl hexylamino linker)", - "fullName": "5-DBCO-U (ethylene carbamoyl hexylamino linker)", + "id": "DBCOnC___5-DBCO-U", + "fullName": "5-DBCO-U", "alias": "DBCOnC", "attachmentPoints": [ { @@ -133981,7 +134065,7 @@ ], "naturalAnalogShort": "C" }, - "monomerTemplate-thiz5U___5-Thiazoleuridine": { + "monomerTemplate-thiz5U___5-Thiazoleuracil": { "type": "monomerTemplate", "atoms": [ { @@ -134206,8 +134290,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "thiz5U___5-Thiazoleuridine", - "fullName": "5-Thiazoleuridine", + "id": "thiz5U___5-Thiazoleuracil", + "fullName": "5-Thiazoleuracil", "alias": "thiz5U", "attachmentPoints": [ { @@ -134871,7 +134955,7 @@ ], "naturalAnalogShort": "U" }, - "monomerTemplate-mnm5U___5-[(Methylamino)methyl]uridine": { + "monomerTemplate-mnm5U___5-[(methylamino)methyl]uracil": { "type": "monomerTemplate", "atoms": [ { @@ -135059,8 +135143,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "mnm5U___5-[(Methylamino)methyl]uridine", - "fullName": "5-[(Methylamino)methyl]uridine", + "id": "mnm5U___5-[(methylamino)methyl]uracil", + "fullName": "5-[(methylamino)methyl]uracil", "alias": "mnm5U", "attachmentPoints": [ { @@ -137261,7 +137345,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-cyh6A___6-Cyclohexyladenine": { + "monomerTemplate-cyh6A___N6-cyclohexyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -137538,8 +137622,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "cyh6A___6-Cyclohexyladenine", - "fullName": "6-Cyclohexyladenine", + "id": "cyh6A___N6-cyclohexyladenine", + "fullName": "N6-cyclohexyladenine", "alias": "cyh6A", "attachmentPoints": [ { @@ -137554,7 +137638,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-cyp6A___6-Cyclopentyladenine": { + "monomerTemplate-cyp6A___N6-cyclopentyladenine": { "type": "monomerTemplate", "atoms": [ { @@ -137816,8 +137900,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "cyp6A___6-Cyclopentyladenine", - "fullName": "6-Cyclopentyladenine", + "id": "cyp6A___N6-cyclopentyladenine", + "fullName": "N6-cyclopentyladenine", "alias": "cyp6A", "attachmentPoints": [ { @@ -138284,7 +138368,7 @@ ], "naturalAnalogShort": "X" }, - "monomerTemplate-m6G___6-Methylguanine": { + "monomerTemplate-m6G___6-O-methylguanine": { "type": "monomerTemplate", "atoms": [ { @@ -138494,8 +138578,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "m6G___6-Methylguanine", - "fullName": "6-Methylguanine", + "id": "m6G___6-O-methylguanine", + "fullName": "6-O-methylguanine", "alias": "m6G", "attachmentPoints": [ { @@ -139528,7 +139612,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-s6puri___6-Thiopurine": { + "monomerTemplate-s6puri___6-Mercaptopurine": { "type": "monomerTemplate", "atoms": [ { @@ -139708,8 +139792,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "s6puri___6-Thiopurine", - "fullName": "6-Thiopurine", + "id": "s6puri___6-Mercaptopurine", + "fullName": "6-Mercaptopurine", "alias": "s6puri", "attachmentPoints": [ { @@ -141958,7 +142042,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-m7h8G___7-Methyl 8-dihydroguanine": { + "monomerTemplate-m7h8G___N7-methyl-8-dihydroguanine": { "type": "monomerTemplate", "atoms": [ { @@ -142168,8 +142252,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "m7h8G___7-Methyl 8-dihydroguanine", - "fullName": "7-Methyl 8-dihydroguanine", + "id": "m7h8G___N7-methyl-8-dihydroguanine", + "fullName": "N7-methyl-8-dihydroguanine", "alias": "m7h8G", "attachmentPoints": [ { @@ -142184,226 +142268,227 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-m7G___7-Methylguanine": { - "type": "monomerTemplate", - "atoms": [ - { - "label": "C", - "location": [ - 1.299, - -0.75, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.299, - 0.75, - 0 - ] - }, - { - "label": "C", - "location": [ - 0, - 1.5, - 0 - ] - }, - { - "label": "N", - "location": [ - -1.299, - 0.75, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.299, - -0.75, - 0 - ] - }, - { - "label": "C", - "location": [ - 0, - -1.5, - 0 - ] - }, - { - "label": "N", - "location": [ - -0.3114, - -2.9665, - 0 - ] - }, - { - "label": "C", - "location": [ - -1.8032, - -3.1233, - 0 - ] - }, - { - "label": "N", - "location": [ - -2.4133, - -1.753, - 0 + "monomerTemplate-m7G___N7-methylguanine": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "C", + "location": [ + 11.28097469362997, + -9.983627197902761, + 0 + ] + }, + { + "label": "C", + "location": [ + 10.414936587813589, + -9.483619864381199, + 0 + ] + }, + { + "label": "N", + "location": [ + 10.414923885735071, + -8.483627197983433, + 0 + ] + }, + { + "label": "C", + "location": [ + 11.280949289472934, + -7.983641865107227, + 0 + ] + }, + { + "label": "N", + "location": [ + 12.146987395289315, + -8.483649198628788, + 0 + ] + }, + { + "label": "C", + "location": [ + 12.147000097367833, + -9.483641865026556, + 0 + ] + }, + { + "label": "N", + "location": [ + 9.671810198831132, + -10.152792864657853, + 0 + ] + }, + { + "label": "C", + "location": [ + 10.078562544037318, + -11.066392469092866, + 0 + ] + }, + { + "label": "N", + "location": [ + 11.073101786805452, + -10.961840141061288, + 0 + ], + "charge": 1 + }, + { + "label": "O", + "location": [ + 13.013025501152272, + -9.983641865026557, + 0 + ], + "charge": -1 + }, + { + "label": "N", + "location": [ + 11.280955640558771, + -6.983641865127395, + 0 + ] + }, + { + "label": "C", + "location": [ + 11.742259680748496, + -11.704960395780338, + 0 + ] + }, + { + "label": "H", + "location": [ + 8.693658838989839, + -9.944898859836579, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 5, + 0 + ] + }, + { + "type": 2, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 2 + ] + }, + { + "type": 2, + "atoms": [ + 2, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 2, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 8 + ] + }, + { + "type": 2, + "atoms": [ + 8, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 6 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 5, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 10 + ] + }, + { + "type": 1, + "atoms": [ + 8, + 11 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 12 + ] + } ], - "charge": 1 - }, - { - "label": "N", - "location": [ - 0, - 3, - 0 - ] - }, - { - "label": "O", - "location": [ - 2.5981, - -1.5, - 0 - ] - }, - { - "label": "H", - "location": [ - -3.8805, - -1.441, - 0 - ] - }, - { - "label": "C", - "location": [ - 0.6924, - -4.0811, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 2, - "atoms": [ - 2, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 3, - 4 - ] - }, - { - "type": 2, - "atoms": [ - 4, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 0 - ] - }, - { - "type": 1, - "atoms": [ - 5, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 7 - ] - }, - { - "type": 2, - "atoms": [ - 7, - 8 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 2, - 9 - ] - }, - { - "type": 2, - "atoms": [ - 0, - 10 - ] - }, - { - "type": 1, - "atoms": [ - 8, - 11 - ] - }, - { - "type": 1, - "atoms": [ - 6, - 12 - ] - } - ], "class": "Base", "classHELM": "RNA", - "id": "m7G___7-Methylguanine", - "fullName": "7-Methylguanine", + "id": "m7G___N7-methylguanine", + "fullName": "N7-methylguanine", "alias": "m7G", "attachmentPoints": [ { - "attachmentAtom": 8, + "attachmentAtom": 6, "leavingGroup": { "atoms": [ - 11 + 12 ] }, "type": "left" @@ -145117,7 +145202,7 @@ ], "naturalAnalogShort": "G" }, - "monomerTemplate-allyl9___9-Allylguanine": { + "monomerTemplate-allyl9___N9-allyl-8-oxoguanine": { "type": "monomerTemplate", "atoms": [ { @@ -145372,8 +145457,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "allyl9___9-Allylguanine", - "fullName": "9-Allylguanine", + "id": "allyl9___N9-allyl-8-oxoguanine", + "fullName": "N9-allyl-8-oxoguanine", "alias": "allyl9", "attachmentPoints": [ { @@ -148409,7 +148494,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-nen___(Aminoethyl)amino": { + "monomerTemplate-nen___Ethylenediamine": { "type": "monomerTemplate", "atoms": [ { @@ -148500,8 +148585,8 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "nen___(Aminoethyl)amino", - "fullName": "(Aminoethyl)amino", + "id": "nen___Ethylenediamine", + "fullName": "Ethylenediamine", "alias": "nen", "attachmentPoints": [ { @@ -148884,7 +148969,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-m2nen___(Dimethylaminoethyl)amino": { + "monomerTemplate-m2nen___N1,N1-dimethylethane-1,2-diamine": { "type": "monomerTemplate", "atoms": [ { @@ -149005,8 +149090,8 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "m2nen___(Dimethylaminoethyl)amino", - "fullName": "(Dimethylaminoethyl)amino", + "id": "m2nen___N1,N1-dimethylethane-1,2-diamine", + "fullName": "N1,N1-dimethylethane-1,2-diamine", "alias": "m2nen", "attachmentPoints": [ { @@ -149389,7 +149474,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-h456UR___(R)-4,5,6-Trihydrouracil": { + "monomerTemplate-h456UR___(R)-tetrahydro-4-hydroxy-1H-pyrimidin-2-one": { "type": "monomerTemplate", "atoms": [ { @@ -149534,8 +149619,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "h456UR___(R)-4,5,6-Trihydrouracil", - "fullName": "(R)-4,5,6-Trihydrouracil", + "id": "h456UR___(R)-tetrahydro-4-hydroxy-1H-pyrimidin-2-one", + "fullName": "(R)-tetrahydro-4-hydroxy-1H-pyrimidin-2-one", "alias": "h456UR", "attachmentPoints": [ { @@ -155401,7 +155486,7 @@ ], "naturalAnalogShort": "C" }, - "monomerTemplate-az8A___Azidoadenine": { + "monomerTemplate-az8A___8-azidoadenine": { "type": "monomerTemplate", "atoms": [ { @@ -155628,8 +155713,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "az8A___Azidoadenine", - "fullName": "Azidoadenine", + "id": "az8A___8-azidoadenine", + "fullName": "8-azidoadenine", "alias": "az8A", "attachmentPoints": [ { @@ -157459,7 +157544,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-gclamp___G-clamp (9-(aminoethoxy)phenoxazine)": { + "monomerTemplate-gclamp___G-clamp": { "type": "monomerTemplate", "atoms": [ { @@ -157781,8 +157866,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "gclamp___G-clamp (9-(aminoethoxy)phenoxazine)", - "fullName": "G-clamp (9-(aminoethoxy)phenoxazine)", + "id": "gclamp___G-clamp", + "fullName": "G-clamp", "alias": "gclamp", "attachmentPoints": [ { @@ -157797,7 +157882,7 @@ ], "naturalAnalogShort": "C" }, - "monomerTemplate-ggclam___G-clamp (9-(guanylethoxy)phenoxazine)": { + "monomerTemplate-ggclam___guanidino-G-clamp": { "type": "monomerTemplate", "atoms": [ { @@ -158164,8 +158249,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "ggclam___G-clamp (9-(guanylethoxy)phenoxazine)", - "fullName": "G-clamp (9-(guanylethoxy)phenoxazine)", + "id": "ggclam___guanidino-G-clamp", + "fullName": "guanidino-G-clamp", "alias": "ggclam", "attachmentPoints": [ { @@ -158382,7 +158467,7 @@ "type": "left" } ], - "naturalAnalogShort": "X" + "naturalAnalogShort": "U" }, "monomerTemplate-ibun___Isobutylamino": { "type": "monomerTemplate", @@ -159363,7 +159448,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-mepo2___Methylenephosphonate": { + "monomerTemplate-mepo2___Hydroxymethylphosphonic acid": { "type": "monomerTemplate", "atoms": [ { @@ -159454,8 +159539,8 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "mepo2___Methylenephosphonate", - "fullName": "Methylenephosphonate", + "id": "mepo2___Hydroxymethylphosphonic acid", + "fullName": "Hydroxymethylphosphonic acid", "alias": "mepo2", "attachmentPoints": [ { @@ -159580,7 +159665,7 @@ ], "naturalAnalogShort": "P" }, - "monomerTemplate-msp___Methylthiophosphonate": { + "monomerTemplate-msp___Methylphosphonothioic acid": { "type": "monomerTemplate", "atoms": [ { @@ -159656,8 +159741,8 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "msp___Methylthiophosphonate", - "fullName": "Methylthiophosphonate", + "id": "msp___Methylphosphonothioic acid", + "fullName": "Methylphosphonothioic acid", "alias": "msp", "attachmentPoints": [ { @@ -162614,7 +162699,7 @@ ], "naturalAnalogShort": "A" }, - "monomerTemplate-imprn2___N-(Aminopropyl)imidazoleadenine": { + "monomerTemplate-imprn2___2-(1-(3-aminopropyl)imidazole)adenine": { "type": "monomerTemplate", "atoms": [ { @@ -162936,8 +163021,8 @@ ], "class": "Base", "classHELM": "RNA", - "id": "imprn2___N-(Aminopropyl)imidazoleadenine", - "fullName": "N-(Aminopropyl)imidazoleadenine", + "id": "imprn2___2-(1-(3-aminopropyl)imidazole)adenine", + "fullName": "2-(1-(3-aminopropyl)imidazole)adenine", "alias": "imprn2", "attachmentPoints": [ { @@ -164792,7 +164877,7 @@ ], "naturalAnalogShort": "R" }, - "monomerTemplate-oxy___Oxy (ether)": { + "monomerTemplate-oxy___Oxy": { "type": "monomerTemplate", "atoms": [ { @@ -164838,8 +164923,8 @@ ], "class": "Phosphate", "classHELM": "RNA", - "id": "oxy___Oxy (ether)", - "fullName": "Oxy (ether)", + "id": "oxy___Oxy", + "fullName": "Oxy", "alias": "oxy", "attachmentPoints": [ { @@ -166196,123 +166281,108 @@ }, "monomerTemplate-m2np___Phosphorodiamidate": { "type": "monomerTemplate", - "atoms": [ - { - "label": "N", - "location": [ - -0.8449, - 1.1367, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0936, - -0.1625, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.8432, - -1.4618, - 0 - ] - }, - { - "label": "O", - "location": [ - 0.6566, - -1.4615, - 0 - ] - }, - { - "label": "N", - "location": [ - 1.4072, - -0.1625, - 0 - ] - }, - { - "label": "C", - "location": [ - -2.3449, - 1.1367, - 0 - ] - }, - { - "label": "C", - "location": [ - -0.0953, - 2.436, - 0 - ] - }, - { - "label": "H", - "location": [ - 2.158, - -1.4611, - 0 - ] - } - ], - "bonds": [ - { - "type": 1, - "atoms": [ - 0, - 1 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 2 - ] - }, - { - "type": 1, "atoms": [ - 1, - 3 - ] - }, - { - "type": 1, - "atoms": [ - 1, - 4 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 5 - ] - }, - { - "type": 1, - "atoms": [ - 0, - 6 - ] - }, - { - "type": 1, - "atoms": [ - 4, - 7 - ] - } - ], + { + "label": "P", + "location": [ + 13.225000000000003, + -14.3, + 0 + ] + }, + { + "label": "O", + "location": [ + 12.358974596215564, + -14.8, + 0 + ] + }, + { + "label": "N", + "location": [ + 14.09102540378444, + -14.8, + 0 + ] + }, + { + "label": "O", + "location": [ + 13.225000000000003, + -13.3, + 0 + ] + }, + { + "label": "N", + "location": [ + 13.225000000000003, + -15.3, + 0 + ] + }, + { + "label": "C", + "location": [ + 12.358974596215564, + -15.8, + 0 + ] + }, + { + "label": "C", + "location": [ + 14.091025403784442, + -15.8, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 2, + "atoms": [ + 0, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 5 + ] + }, + { + "type": 1, + "atoms": [ + 4, + 6 + ] + } + ], "class": "Phosphate", "classHELM": "RNA", "id": "m2np___Phosphorodiamidate", @@ -166320,19 +166390,19 @@ "alias": "m2np", "attachmentPoints": [ { - "attachmentAtom": 1, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 3 + 1 ] }, "type": "left" }, { - "attachmentAtom": 4, + "attachmentAtom": 0, "leavingGroup": { "atoms": [ - 7 + 2 ] }, "type": "right" @@ -169793,7 +169863,7 @@ "$ref": "monomerTemplate-MOE___2'-O-Methoxyethyl ribose" }, { - "$ref": "monomerTemplate-5meC___5-methyl-cytidine" + "$ref": "monomerTemplate-5meC___5-methylcytosine" }, { "$ref": "monomerTemplate-P___Phosphate" @@ -169864,7 +169934,7 @@ "type": "monomerTemplate", "id": "AmdA___2, 6-Diaminopurine", "fullName": "2,6-Diaminopurine", - "alias": "2-Amino-dA", + "alias": "2-damdA", "naturalAnalogShort": "A", "class": "RNA", "classHELM": "RNA", @@ -169876,2037 +169946,2037 @@ "endpoint3": "3AmdA" } }, - "atoms": [ - { - "label": "N", - "location": [ - 23.577641145999202, - -9.269672229377672, - 0 - ] - }, - { - "label": "C", - "location": [ - 22.352896532868577, - -8.044927794030507, - 0 - ] - }, - { - "label": "C", - "location": [ - 23.318822123396952, - -8.303746487060764, - 0 - ] - }, - { - "label": "C", - "location": [ - 21.64578925545723, - -8.752033922692299, - 0 - ] - }, - { - "label": "C", - "location": [ - 22.87053413339016, - -9.976779058426786, - 0 - ] - }, - { - "label": "N", - "location": [ - 21.904608572405124, - -9.717960187785433, - 0 - ] - }, - { - "label": "N", - "location": [ - 21.898906894436173, - -7.153920918587078, - 0 - ] - }, - { - "label": "N", - "location": [ - 20.754783018438236, - -8.298042858689463, - 0 - ] - }, - { - "label": "C", - "location": [ - 20.911218132557558, - -7.310354820802242, - 0 - ] - }, - { - "label": "C", - "location": [ - 19.863776263170696, - -8.75203265775606, - 0 - ], - "stereoLabel": "abs" - }, - { - "label": "O", - "location": [ - 18.97276980060869, - -8.298041615620248, - 0 - ] - }, - { - "label": "C", - "location": [ - 18.26566290748329, 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"attachmentAtom": 32, "leavingGroup": { "atoms": [ - 34 + 33 ] }, "type": "side" From 2763c830488f11b06a5c5f8e8f451fb211cb750f Mon Sep 17 00:00:00 2001 From: Alexey Girin Date: Tue, 1 Oct 2024 22:43:20 +0300 Subject: [PATCH 02/11] Locators update --- ...nd-save-in-idt-format-1-chromium-linux.png | Bin 0 -> 4567 bytes .../import-saving-ket.spec.ts | 3 +- .../macro-micro-switcher.spec.ts | 29 +++--- .../macro-micro-switcher2.spec.ts | 6 +- .../RNA-Builder/add-custom-preset.spec.ts | 12 ++- .../RNA-Builder/rna-library.spec.ts | 36 ++++--- .../sequence-mode-edit-in-rna-builder.spec.ts | 20 ++-- .../sequence-mode-replacement.spec.ts | 6 +- .../test-data/IDT/unresolved-monomers.idt | 1 + .../tests/test-data/KET/25R-expected.ket | 8 +- .../Automation of Bond tests (203-211).ket | 32 +++---- .../tests/test-data/KET/D-2Nal-expected.ket | 8 +- .../BondPreviewToolTipPositions.ket | 12 +-- .../Horizontal - Part1.ket | 18 ++-- .../Horizontal - Part2.ket | 18 ++-- .../Horizontal - Part3.ket | 18 ++-- .../tests/test-data/KET/all-entities.ket | 40 ++++---- .../test-data/KET/all-kind-of-monomers.ket | 24 ++--- .../KET/all-types-of-modifications.ket | 88 +++++++++--------- .../all-types-of-possible-modifications.ket | 50 +++++----- .../KET/chain-with-unsplit-nucleotides.ket | 16 ++-- .../tests/test-data/KET/five-monomers.ket | 16 ++-- .../tests/test-data/KET/mod-base-sequence.ket | 8 +- .../KET/mod-sugar-base-phosphate-sequence.ket | 16 ++-- .../test-data/KET/mod-sugar-sequence.ket | 8 +- .../tests/test-data/KET/modified-agtcup.ket | 14 +-- .../KET/modified-and-unmodified-sequence.ket | 26 +++--- .../KET/modified-nucleotide-chain.ket | 8 +- .../tests/test-data/KET/monomers-chains.ket | 8 +- .../KET/phosphates-not-part-of-nucleoside.ket | 8 +- .../test-data/KET/r3-r2-sugar-phosphate.ket | 8 +- .../test-data/KET/rna-nucleotide-chem.ket | 8 +- .../KET/sequence-with-side-connection.ket | 8 +- ...-with-unresolved-idt-monomers-expected.ket | 10 +- ...olved-idt-monomers-micro-mode-expected.ket | 14 +-- .../KET/sugar-base-chem-not-connected.ket | 16 ++-- .../KET/sugar-on-the-end-of-sequence.ket | 8 +- .../test-data/KET/sugar-phosphate-baA.ket | 8 +- .../KET/two-nucleotides-connected.ket | 8 +- .../utils/selectors/macromoleculeEditor.ts | 3 +- .../tests/utils/selectors/templateModal.ts | 8 +- 41 files changed, 334 insertions(+), 322 deletions(-) create mode 100644 ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-idt.spec.ts-snapshots/Import-Saving-idt-Files-Check-import-of-ket--6d250--unresolved-monomers-and-save-in-idt-format-1-chromium-linux.png create mode 100644 ketcher-autotests/tests/test-data/IDT/unresolved-monomers.idt diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-idt.spec.ts-snapshots/Import-Saving-idt-Files-Check-import-of-ket--6d250--unresolved-monomers-and-save-in-idt-format-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-idt.spec.ts-snapshots/Import-Saving-idt-Files-Check-import-of-ket--6d250--unresolved-monomers-and-save-in-idt-format-1-chromium-linux.png new file mode 100644 index 0000000000000000000000000000000000000000..694ee5bda83b00f8fda20d7c8ad229c0dfeb6744 GIT binary patch literal 4567 zcmeAS@N?(olHy`uVBq!ia0y~yVBW#Nz%+}44Jaa__4N{vVk{1FcVbv~PUa;8gWyC@ z7srr_Id5<6U)|3yfBfTi>vQ5ueT<|eL{7F$k#9bcWPB>&qx=u{HB)?bg3`DB*jV_F zVXov&jnv@wM;6a_-z~jv`=ZSHx!w8SA7`vzef_tw-S3#&VPRp{*nu`}+fkqMjSLjy}AHv@x1(*afn1_j3lObiSYMwO3-%xEGQ z%^ssA!DtydS{;BY%G>6@85nMOO`A6D+11tIpWoizZohA9_Vsm^!U zaNE?WQ@@_IV`A9Wv~=mx${!yd>ged?+<5l={r%^MTDgng-rCB0o26mxDfLqfAG+t+ z*Y8_cXl=ZC!v+KW_WYkIQ3{`|l}YutH#5I}{kpUM|Gz(9 zug8D>@$s=`#fJxH&cy60$;`X6!|?n(+u1W`F880`70vL2_uoO*hWjOde|^2VzyALm z`}(@Ne}63B-`_uwyj;WW=;M#L0}^Nu)Agv&uB{y7!spx+|lOz oXd)Qx(~Xt{qtyXP)xi(xt7|tcieazW0@TLf>FVdQ&MBb@0D(@*hX4Qo literal 0 HcmV?d00001 diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts index 67b0aab6f0..1cfbfc8fdb 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-ket.spec.ts @@ -20,6 +20,7 @@ import { selectClearCanvasTool, clickUndo, dragMouseTo, + Sugars, } from '@utils'; import { pageReload } from '@utils/common/helpers'; import { turnOnMacromoleculesEditor } from '@utils/macromolecules'; @@ -196,7 +197,7 @@ test.describe('Import-Saving .ket Files', () => { test.slow(); await page.getByTestId('RNA-TAB').click(); await page.getByTestId('summary-Sugars').click(); - await page.getByTestId('25R___2,5-Ribose').click(); + await page.getByTestId(Sugars.TwentyFiveR).click(); await clickInTheMiddleOfTheScreen(page); const expectedFile = await getKet(page); await saveToFile('KET/25R-expected.ket', expectedFile); diff --git a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts index 6f69a25a19..f6ab266063 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher.spec.ts @@ -59,6 +59,9 @@ import { selectClearCanvasTool, waitForIndigoToLoad, waitForKetcherInit, + Sugars, + Bases, + Phosphates, } from '@utils'; import { addSuperatomAttachmentPoint, @@ -113,9 +116,9 @@ async function addToFavoritesMonomers(page: Page) { await page.getByTestId('meM___N-Methyl-Methionine').getByText('★').click(); await page.getByTestId('RNA-TAB').click(); await page.getByTestId('summary-Sugars').click(); - await page.getByTestId('25R___2,5-Ribose').getByText('★').click(); + await page.getByTestId(Sugars.TwentyFiveR).getByText('★').click(); await page.getByTestId('summary-Bases').click(); - await page.getByTestId('baA___N-benzyl-adenine').getByText('★').click(); + await page.getByTestId(Bases.baA).getByText('★').click(); await page.getByTestId('summary-Phosphates').click(); await page.getByTestId('bP___Boranophosphate').getByText('★').click(); await page.getByTestId('CHEM-TAB').click(); @@ -1099,21 +1102,21 @@ test.describe('Macro-Micro-Switcher', () => { { description: 'Sugar', monomer: '25R', - monomerTestId: '25R___2,5-Ribose', + monomerTestId: Sugars.TwentyFiveR, summaryTestId: 'summary-Sugars', bondEndpoints: { first: 'R1', second: 'R2' }, }, { description: 'Base', monomer: 'meA', - monomerTestId: 'meA___N-Methyl-Adenine', + monomerTestId: Bases.meA, summaryTestId: 'summary-Bases', bondEndpoints: { first: 'R1', second: 'R1' }, }, { description: 'Phosphate', monomer: 'nasP', - monomerTestId: 'nasP___Sodium Phosporothioate', + monomerTestId: Phosphates.nasP, summaryTestId: 'summary-Phosphates', bondEndpoints: { first: 'R1', second: 'R2' }, }, @@ -1190,14 +1193,14 @@ test.describe('Macro-Micro-Switcher', () => { { description: 'Sugar', monomer: '25R', - monomerTestId: '25R___2,5-Ribose', + monomerTestId: Sugars.TwentyFiveR, summaryTestId: 'summary-Sugars', bondEndpoints: { first: 'R1', second: 'R2' }, }, { description: 'Base', monomer: 'meA', - monomerTestId: 'meA___N-Methyl-Adenine', + monomerTestId: Bases.meA, summaryTestId: 'summary-Bases', bondEndpoints: { first: 'R1', second: 'R1' }, }, @@ -1283,21 +1286,21 @@ test.describe('Macro-Micro-Switcher', () => { { description: 'Sugar', monomer: '25R', - monomerTestId: '25R___2,5-Ribose', + monomerTestId: Sugars.TwentyFiveR, summaryTestId: 'summary-Sugars', bondEndpoints: { first: 'R1', second: 'R2' }, }, { description: 'Base', monomer: 'meA', - monomerTestId: 'meA___N-Methyl-Adenine', + monomerTestId: Bases.meA, summaryTestId: 'summary-Bases', bondEndpoints: { first: 'R1', second: 'R1' }, }, { description: 'Phosphate', monomer: 'nasP', - monomerTestId: 'nasP___Sodium Phosporothioate', + monomerTestId: Phosphates.nasP, summaryTestId: 'summary-Phosphates', bondEndpoints: { first: 'R1', second: 'R2' }, }, @@ -1380,21 +1383,21 @@ test.describe('Macro-Micro-Switcher', () => { { description: 'Sugar', monomer: '25R', - monomerTestId: '25R___2,5-Ribose', + monomerTestId: Sugars.TwentyFiveR, summaryTestId: 'summary-Sugars', bondEndpoints: { first: 'R1', second: 'R2' }, }, { description: 'Base', monomer: 'meA', - monomerTestId: 'meA___N-Methyl-Adenine', + monomerTestId: Bases.meA, summaryTestId: 'summary-Bases', bondEndpoints: { first: 'R1', second: 'R1' }, }, { description: 'Phosphate', monomer: 'nasP', - monomerTestId: 'nasP___Sodium Phosporothioate', + monomerTestId: Phosphates.nasP, summaryTestId: 'summary-Phosphates', bondEndpoints: { first: 'R1', second: 'R2' }, }, diff --git a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher2.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher2.spec.ts index ca72fe19c5..3808a2e069 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher2.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/Macro-Micro-Switcher/macro-micro-switcher2.spec.ts @@ -26,6 +26,8 @@ import { selectDropdownTool, clickInTheMiddleOfTheScreen, selectClearCanvasTool, + Sugars, + Bases, } from '@utils'; import { Peptides } from '@utils/selectors/macromoleculeEditor'; @@ -38,9 +40,9 @@ async function addToFavoritesMonomers(page: Page) { await page.getByTestId('meM___N-Methyl-Methionine').getByText('★').click(); await page.getByTestId('RNA-TAB').click(); await page.getByTestId('summary-Sugars').click(); - await page.getByTestId('25R___2,5-Ribose').getByText('★').click(); + await page.getByTestId(Sugars.TwentyFiveR).getByText('★').click(); await page.getByTestId('summary-Bases').click(); - await page.getByTestId('baA___N-benzyl-adenine').getByText('★').click(); + await page.getByTestId(Bases.baA).getByText('★').click(); await page.getByTestId('summary-Phosphates').click(); await page.getByTestId('bP___Boranophosphate').getByText('★').click(); await page.getByTestId('CHEM-TAB').click(); diff --git a/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/add-custom-preset.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/add-custom-preset.spec.ts index 09d5d85a27..059e34d3a6 100644 --- a/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/add-custom-preset.spec.ts +++ b/ketcher-autotests/tests/Macromolecule-editor/RNA-Builder/add-custom-preset.spec.ts @@ -8,7 +8,9 @@ import { } from '@constants/testIdConstants'; import { waitForPageInit } from '@utils/common'; import { + Bases, moveMouseToTheMiddleOfTheScreen, + Sugars, takeEditorScreenshot, takeMonomerLibraryScreenshot, } from '@utils'; @@ -63,8 +65,8 @@ test.describe('Macromolecules custom presets', () => { test('Add new preset and duplicate it', async ({ page }) => { await selectRNAComponents(page, { - sugar: '25R___2,5-Ribose', - base: 'baA___N-benzyl-adenine', + sugar: Sugars.TwentyFiveR, + base: Bases.baA, phosphate: 'bP___Boranophosphate', }); await moveMouseToTheMiddleOfTheScreen(page); @@ -75,7 +77,7 @@ test.describe('Macromolecules custom presets', () => { await page.getByTestId('duplicate-btn').click(); await selectRNAComponents(page, { - sugar: "12ddR___1',2'-Di-Deoxy-Ribose", + sugar: "12ddR___1',2'-dideoxyribose", base: 'A___Adenine', phosphate: 'P___Phosphate', }); @@ -111,13 +113,13 @@ test.describe('Macromolecules custom presets', () => { await page.getByTestId(SUGAR).click(); // Click on
"25R ★" - await page.click('[data-testid="25R___2,5-Ribose"]'); + await page.click(`[data-testid="${Sugars.TwentyFiveR}"]`); // Click on
"Base Not selected" await page.getByTestId(BASE).click(); // Click on
"baA ★" - await page.click('[data-testid="baA___N-benzyl-adenine"]'); + await page.click(`[data-testid="${Bases.baA}"]`); // Click on