diff --git a/api/wasm/indigo-ketcher/indigo-ketcher.cpp b/api/wasm/indigo-ketcher/indigo-ketcher.cpp index e5260976a6..5414a47b2f 100644 --- a/api/wasm/indigo-ketcher/indigo-ketcher.cpp +++ b/api/wasm/indigo-ketcher/indigo-ketcher.cpp @@ -440,18 +440,38 @@ namespace indigo std::string convert(const std::string& data, const std::string& outputFormat, const std::map& options) { const IndigoSession session; - indigoSetOptions(options); - std::map options_copy = options; - if (outputFormat.find("smarts") != std::string::npos) + std::map options_copy; + for (const auto& option : options) { - options_copy["query"] = "true"; + if (option.first != "monomerLibrary") + { + options_copy[option.first] = option.second; + } } + auto monomerLibrary = options.find("monomerLibrary"); if (monomerLibrary != options.end() && monomerLibrary->second.size()) { - options_copy["monomerLibrary"] = ""; - IndigoKetcherObject iko = loadMoleculeOrReaction(monomerLibrary->second, options_copy); + const char* ignore_stereo_option = "ignore-stereochemistry-errors"; + std::map options_lib = options_copy; + options_lib["input-format"] = "chemical/x-indigo-ket"; + options_lib[ignore_stereo_option] = "true"; + indigoSetOptions(options_lib); + IndigoKetcherObject iko = loadMoleculeOrReaction(monomerLibrary->second, options_lib); + auto ignore_stereo = options.find(ignore_stereo_option); + if (ignore_stereo == options.end()) + { + // no ignore stereo erros option set - should reset to default "false" + options_lib[ignore_stereo_option] = "false"; + indigoSetOptions(options_lib); + } + } + + if (outputFormat.find("smarts") != std::string::npos) + { + options_copy["query"] = "true"; } + indigoSetOptions(options); IndigoKetcherObject iko = loadMoleculeOrReaction(data, options_copy); return iko.toString(options, outputFormat.size() ? outputFormat : "ket"); } diff --git a/api/wasm/indigo-ketcher/test/idt_maxmgc.ket b/api/wasm/indigo-ketcher/test/idt_maxmgc.ket index d8b2b1472b..cfb6ac49fa 100644 --- a/api/wasm/indigo-ketcher/test/idt_maxmgc.ket +++ b/api/wasm/indigo-ketcher/test/idt_maxmgc.ket @@ -1 +1 @@ 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"monomerTemplate-cpmA___N-cyclopropylmethyl-adenine" + }, + { + "$ref": "monomerTemplate-dR___Deoxy-Ribose" + }, + { + "$ref": "monomerTemplate-daA___N,N-dimethyl-Adenine" + }, + { + "$ref": "monomerTemplate-dabA___7-deaza-8-aza-7-bromo-2-amino-Adenine" + }, + { + "$ref": "monomerTemplate-dfB___2,4-Difluoro-Benzene" + }, + { + "$ref": "monomerTemplate-dier___5- 1,2-Dierucyl-rac-glycerol (Genzyme)" + }, + { + "$ref": "monomerTemplate-eR___2'-O,4'-ethylene bridged Ribose" + }, + { + "$ref": "monomerTemplate-eaA___N-ethyl-adenine" + }, + { + "$ref": "monomerTemplate-fR___2'-Flu0ro-Ribose" + }, + { + "$ref": "monomerTemplate-hx___hexitol" + }, + { + "$ref": "monomerTemplate-lLR___2,'4'-locked-Ribose (alpha-L-LNA)" + }, + { + "$ref": "monomerTemplate-mR___2'-O-Methyl-Ribose" + }, + { + "$ref": "monomerTemplate-meA___N-Methyl-Adenine" + }, + { + "$ref": "monomerTemplate-mph___morpholino" + }, + { + "$ref": "monomerTemplate-naP___Sodium Phosphate" + }, + { + "$ref": "monomerTemplate-nasP___Sodium Phosporothioate" + }, + { + "$ref": "monomerTemplate-prpC___5-Propynyl-Cytosine" + }, + { + "$ref": "monomerTemplate-prpU___5-propynyl Uracil" + }, + { + "$ref": "monomerTemplate-qR___2-O-beta-hydroxy-ethoxy-methyl Ribose (Qiagen)" + }, + { + "$ref": "monomerTemplate-sP___Phosporothioate" + }, + { + "$ref": "monomerTemplate-tR___Ribose" + }, + { + "$ref": "monomerTemplate-tfU___5-trifluoromethyl-uracil" + }, + { + "$ref": "monomerTemplate-A___Alanine" + }, + { + "$ref": "monomerTemplate-Test-6-P___Test-6-AP-Peptide" + }, + { + "$ref": "monomerTemplate-Aad___2-aminoadipic acid" + }, + { + "$ref": "monomerTemplate-Abu___2-aminobutanoic acid" + }, + { + "$ref": "monomerTemplate-Aca___2-aminocapric acid" + }, + { + "$ref": "monomerTemplate-Aib___alpha-aminoisobutyric acid (2-aminoalanine)" + }, + { + "$ref": "monomerTemplate-Apm___2-aminopimelic acid" + }, + { + "$ref": "monomerTemplate-App___gamma-amino-beta-hydroxybenzenepentanoic acid" + }, + { + "$ref": "monomerTemplate-Asu___2-aminosuberic acid" + }, + { + "$ref": "monomerTemplate-Aze___2-carboxyazetidine" + }, + { + "$ref": "monomerTemplate-Bal___beta-Alanine" + }, + { + "$ref": "monomerTemplate-Bua___butanoic acid" + }, + { + "$ref": "monomerTemplate-Bux___4-amino-3-hydroxybutanoic acid" + }, + { + "$ref": "monomerTemplate-C___Cysteine" + }, + { + "$ref": "monomerTemplate-Cap___gamma-amino-beta-hydroxycyclohexanepentanoic acid" + }, + { + "$ref": "monomerTemplate-Cha___3-cyclohexylalanine" + }, + { + "$ref": "monomerTemplate-Cit___citrullin" + }, + { + "$ref": "monomerTemplate-Cya___3-sulfoalanine" + }, + { + "$ref": "monomerTemplate-D___Aspartic acid" + }, + { + "$ref": "monomerTemplate-AspOH___Aspartic acid (OH)" + }, + { + "$ref": "monomerTemplate-Pyrro___Pyrrolidine" + }, + { + "$ref": "monomerTemplate-Dab___2,4-diaminobutanoic acid" + }, + { + "$ref": "monomerTemplate-Dpm___diaminopimelic acid" + }, + { + "$ref": "monomerTemplate-Dpr___2,3-diaminopropanoic acid" + }, + { + "$ref": "monomerTemplate-Dsu___2,7-diaminosuberic acid (2,7-diaminooctanedioic acid)" + }, + { + "$ref": "monomerTemplate-E___Glutamic acid" + }, + { + "$ref": "monomerTemplate-Edc___S-ethylthiocysteine" + }, + { + "$ref": "monomerTemplate-F___Phenylalanine" + }, + { + "$ref": "monomerTemplate-G___Glycine" + }, + { + "$ref": "monomerTemplate-Ggu___gamma-glutamic acid" + }, + { + "$ref": "monomerTemplate-Gla___gamma-carboxyglutamic acid" + }, + { + "$ref": "monomerTemplate-Glc___glycolic acid" + }, + { + "$ref": "monomerTemplate-Glp___pyroglutamic acid" + }, + { + "$ref": "monomerTemplate-H___Histidine" + }, + { + "$ref": "monomerTemplate-Har___homoarginine" + }, + { + "$ref": "monomerTemplate-Hcy___homocysteine" + }, + { + "$ref": "monomerTemplate-Hhs___homohistidine" + }, + { + "$ref": "monomerTemplate-Hiv___2-hydroxyisovaleric acid" + }, + { + "$ref": "monomerTemplate-Hse___homoserine" + }, + { + "$ref": "monomerTemplate-Hva___2-hydroxypentanoic acid" + }, + { + "$ref": "monomerTemplate-Hyl___5-hydroxylysine" + }, + { + "$ref": "monomerTemplate-Hyp___4-hydroxyproline" + }, + { + "$ref": "monomerTemplate-I___Isoleucine" + }, + { + "$ref": "monomerTemplate-Iva___isovaline" + }, + { + "$ref": "monomerTemplate-K___Lysine" + }, + { + "$ref": "monomerTemplate-L___Leucine" + }, + { + "$ref": "monomerTemplate-Lac___lactic acid" + }, + { + "$ref": "monomerTemplate-M___Methionine" + }, + { + "$ref": "monomerTemplate-Maa___mercaptoacetic acid" + }, + { + "$ref": "monomerTemplate-Mba___mercaptobutanoic acid (GMBA)" + }, + { + "$ref": "monomerTemplate-Mhp___4-methyl-3-hydroxyproline" + }, + { + "$ref": "monomerTemplate-Mpa___mercaptopropanoic acid" + }, + { + "$ref": "monomerTemplate-N___Asparagine" + }, + { + "$ref": "monomerTemplate-Nal___3-naphthylalanine" + }, + { + "$ref": "monomerTemplate-Nle___norleucine" + }, + { + "$ref": "monomerTemplate-Nty___nitrotyrosine" + }, + { + "$ref": "monomerTemplate-Nva___norvaline" + }, + { + "$ref": "monomerTemplate-Oic___2-carboxyocthydroindole" + }, + { + "$ref": "monomerTemplate-Orn___L-ornithine" + }, + { + "$ref": "monomerTemplate-P___Proline" + }, + { + "$ref": "monomerTemplate-Pen___penicillamine (3-mercaptovaline)" + }, + { + "$ref": "monomerTemplate-Phg___2-phenylglycine" + }, + { + "$ref": "monomerTemplate-Pqa___Piperazine quinazolinone acetic acid, 2-(4-oxo-6-piperazin-1-yl-quinazolin-3-yl)acetic acid" + }, + { + "$ref": "monomerTemplate-Q___Glutamine" + }, + { + "$ref": "monomerTemplate-R___Arginine" + }, + { + "$ref": "monomerTemplate-S___Serine" + }, + { + "$ref": "monomerTemplate-Sar___sarcosine (N-methylglycine)" + }, + { + "$ref": "monomerTemplate-Spg___1-amino-1-carboxycyclopentane" + }, + { + "$ref": "monomerTemplate-Sta___statin (4-amino-3-hydroxy-6-methylheptanoic acid)" + }, + { + "$ref": "monomerTemplate-T___Threonine" + }, + { + "$ref": "monomerTemplate-Thi___3-thienylalanine" + }, + { + "$ref": "monomerTemplate-Tic___1,2,3,4-tetrahydro-3-isoquinolinecarboxylic acid" + }, + { + "$ref": "monomerTemplate-Tle___3-methylvaline" + }, + { + "$ref": "monomerTemplate-Tml___epsilon-N-trimethyllysine" + }, + { + "$ref": "monomerTemplate-Tza___3-thiazolylalanine" + }, + { + "$ref": "monomerTemplate-V___Valine" + }, + { + "$ref": "monomerTemplate-W___Tryptophan" + }, + { + "$ref": "monomerTemplate-Wil___alpha-amino-2,4-dioxopyrimidinepropanoic acid" + }, + { + "$ref": "monomerTemplate-Y___Tyrosine" + }, + { + "$ref": "monomerTemplate-ac___N-Terminal Acetic Acid" + }, + { + "$ref": "monomerTemplate-am___C-Terminal amine" + }, + { + "$ref": "monomerTemplate-dA___D-Alanine" + }, + { + "$ref": "monomerTemplate-dC___D-Cysteine" + }, + { + "$ref": "monomerTemplate-dD___D-Aspartic acid" + }, + { + "$ref": "monomerTemplate-dE___D-Glutamic acid" + }, + { + "$ref": "monomerTemplate-dF___D-Phenylalanine" + }, + { + "$ref": "monomerTemplate-dH___D-Histidine" + }, + { + "$ref": "monomerTemplate-dK___D-Lysine" + }, + { + "$ref": "monomerTemplate-dL___D-Leucine" + }, + { + "$ref": "monomerTemplate-dM___D-Methionine" + }, + { + "$ref": "monomerTemplate-dN___D-Asparagine" + }, + { + "$ref": "monomerTemplate-dP___D-Proline" + }, + { + "$ref": "monomerTemplate-dQ___D-Glutamine" + }, + { + "$ref": "monomerTemplate-dR___D-Arginine" + }, + { + "$ref": "monomerTemplate-dS___D-Serine" + }, + { + "$ref": "monomerTemplate-dV___D-Valine" + }, + { + "$ref": "monomerTemplate-dI___D-Isoleucine" + }, + { + "$ref": "monomerTemplate-dT___D-Threonine" + }, + { + "$ref": "monomerTemplate-dW___D-Tryptophan" + }, + { + "$ref": "monomerTemplate-dY___D-Tyrosine" + }, + { + "$ref": "monomerTemplate-fmoc___fmoc N-Terminal Protection Group" + }, + { + "$ref": "monomerTemplate-meA___N-Methyl-Alanine" + }, + { + "$ref": "monomerTemplate-meC___N-Methyl-Cysteine" + }, + { + "$ref": "monomerTemplate-meD___N-Methyl-Aspartic acid" + }, + { + "$ref": "monomerTemplate-meE___N-Methyl-Glutamic acid" + }, + { + "$ref": "monomerTemplate-meF___N-Methyl-Phenylalanine" + }, + { + "$ref": "monomerTemplate-meH___N-Methyl-Histidine" + }, + { + "$ref": "monomerTemplate-meI___N-Methyl-Isoleucine" + }, + { + "$ref": "monomerTemplate-meK___N-Methyl-Lysine" + }, + { + "$ref": "monomerTemplate-meL___N-Methyl-Leucine" + }, + { + "$ref": "monomerTemplate-meM___N-Methyl-Methionine" + }, + { + "$ref": "monomerTemplate-meN___N-Methyl-Asparagine" + }, + { + "$ref": "monomerTemplate-meQ___N-Methyl-Glutamine" + }, + { + "$ref": "monomerTemplate-meR___N-Methyl-Arginine" + }, + { + "$ref": "monomerTemplate-meS___N-Methyl-Serine" + }, + { + "$ref": "monomerTemplate-meT___N-Methyl-Threonine" + }, + { + "$ref": "monomerTemplate-meV___N-Methyl-Valine" + }, + { + "$ref": "monomerTemplate-meW___N-Methyl-Tryptophan" + }, + { + "$ref": "monomerTemplate-meY___N-Methyl-Tyrosine" + }, + { + "$ref": "monomerTemplate-pnA___PNA Adenine" + }, + { + "$ref": "monomerTemplate-pnC___PNA Cytosine" + }, + { + "$ref": "monomerTemplate-pnG___PNA Guanine" + }, + { + "$ref": "monomerTemplate-pnT___PNA Thymine" + }, + { + "$ref": "monomerTemplate-seC___SelenoCysteine" + }, + { + "$ref": "monomerTemplate-Test-6-Ch___Test-6-AP-Chem" + }, + { + "$ref": "monomerTemplate-A6OH___6-amino-hexanol" + }, + { + "$ref": "monomerTemplate-Az___Azide" + }, + { + "$ref": "monomerTemplate-EG___Ethylene Glycol" + }, + { + "$ref": "monomerTemplate-MCC___4-(N-maleimidomethyl)cyclohexane-1-carboxylate" + }, + { + "$ref": "monomerTemplate-PEG2___Diethylene Glycol" + }, + { + "$ref": "monomerTemplate-SMCC___SMCC linker from Pierce" + }, + { + "$ref": "monomerTemplate-SMPEG2___SM(PEG)2 linker from Pierce" + }, + { + "$ref": "monomerTemplate-SS3___Dipropanol-disulfide" + }, + { + "$ref": "monomerTemplate-hxy___Hexynyl alcohol" + }, + { + "$ref": "monomerTemplate-sDBL___Symmetric Doubler" + }, + { + "$ref": "monomerTemplate-dPyl___D-Pyl" + }, + { + "$ref": "monomerTemplate-dSec___D-SelenoCysteine" + }, + { + "$ref": "monomerTemplate-Pyl___Pyl" + }, + { + "$ref": "monomerTemplate-NMe___C-Terminal NMe" + }, + { + "$ref": "monomerTemplate-OMe___C-Terminal OMe" + }, + { + "$ref": "monomerTemplate-OtBu___C-Terminal OtBu" + }, + { + "$ref": "monomerTemplate-Oxa___C-Terminal Oxa" + }, + { + "$ref": "monomerTemplate-OBz___C-Terminal OBz" + }, + { + "$ref": "monomerTemplate--Me___C-Terminal methyl" + }, + { + "$ref": "monomerTemplate-aIle___L-allo-Isoleucine" + }, + { + "$ref": "monomerTemplate-D-gGlu___D-Gamma glutamic acid" + }, + { + "$ref": "monomerTemplate-D-Nle___D-Norleucine" + }, + { + "$ref": "monomerTemplate-D-hPhe___D-Homophenylalanine" + }, + { + "$ref": "monomerTemplate-D-Hyp___D-4-Hydroxyproline" + }, + { + "$ref": "monomerTemplate-D-Nva___D-Norvaline" + }, + { + "$ref": "monomerTemplate-D-Orn___D-Ornithine" + }, + { + "$ref": "monomerTemplate-Pyr___Pyroglutamic acid" + }, + { + "$ref": "monomerTemplate-D-Pyr___D-Pyroglutamic acid" + }, + { + "$ref": "monomerTemplate-Phe3Cl___3-Chloro-L-phenylalanine" + }, + { + "$ref": "monomerTemplate-Phe4Cl___4-Chloro-L-phenylalanine" + }, + { + "$ref": "monomerTemplate-Phe4NH___p-Aminophenylalanine" + }, + { + "$ref": "monomerTemplate-SertBu___O-tert-Butyl-L-serine" + }, + { + "$ref": "monomerTemplate-Tyr_Bn___O-Benzyl-L-tyrosine" + }, + { + "$ref": "monomerTemplate-1Nal___3-(1-naphthyl)-alanine" + }, + { + "$ref": "monomerTemplate-LysBoc___N-epsilon-tert-Boc-L-lysine" + }, + { + "$ref": "monomerTemplate-aThr___L-allo-Threonine" + }, + { + "$ref": "monomerTemplate-D-2Nal___D-3-naphthylalanine" + }, + { + "$ref": "monomerTemplate-D-2Thi___D-3-thienylalanine" + }, + { + "$ref": "monomerTemplate-D-aHyp___D-allo-4-hydroxyproline" + }, + { + "$ref": "monomerTemplate-D-aIle___D-allo-Isoleucine" + }, + { + "$ref": "monomerTemplate-D-Phg___D-2-phenylglycine" + }, + { + "$ref": "monomerTemplate-DSertB___O-tert-Butyl-D-serine" + }, + { + "$ref": "monomerTemplate-Phe4Me___p-Methylphenylalanine" + }, + { + "$ref": "monomerTemplate-Ser_Bn___O-Benzyl-L-serine" + }, + { + "$ref": "monomerTemplate-TyrtBu___O-tert-Butyl-L-tyrosine" + }, + { + "$ref": "monomerTemplate-aHyp___L-allo-4-hydroxyproline" + }, + { + "$ref": "monomerTemplate-hPhe___Homophenylalanine" + }, + { + "$ref": "monomerTemplate-D-1Nal___D-3-(1-naphthyl)-alanine" + }, + { + "$ref": "monomerTemplate-D-aThr___D-allo-Threonine" + }, + { + "$ref": "monomerTemplate-D-Cha___D-2-Amino-3-cyclohexyl-propionic acid" + }, + { + "$ref": "monomerTemplate-D-Pen___D-penicillamine (3-mercaptovaline)" + }, + { + "$ref": "monomerTemplate-DPhe4C___4-Chloro-D-phenylalanine" + }, + { + "$ref": "monomerTemplate-DSerBn___O-Benzyl-D-serine" + }, + { + "$ref": "monomerTemplate-MsO___Mesylate" + }, + { + "$ref": "monomerTemplate-Oic3aS___Perhydroindolic acid" + }, + { + "$ref": "monomerTemplate-Pip___Pipecolic acid" + }, + { + "$ref": "monomerTemplate-3Pal___3-(2-pyridyl)-alanine" + }, + { + "$ref": "monomerTemplate-4Pal___3-(4-Pyridyl)-alanine" + }, + { + "$ref": "monomerTemplate-Chg___Alpha-cyclohexylglycine" + }, + { + "$ref": "monomerTemplate-D-3Pal___D-3-(2-pyridyl)-alanine" + }, + { + "$ref": "monomerTemplate-DaMeAb___D-Isovaline" + }, + { + "$ref": "monomerTemplate-D-Chg___D-Alpha-cyclohexylglycine" + }, + { + "$ref": "monomerTemplate-D-Cit___D-Citrullin" + }, + { + "$ref": "monomerTemplate-D-Dab___D-2,4-diaminobutanoic acid" + }, + { + "$ref": "monomerTemplate-D-Pip___D-Pipecolic acid" + }, + { + "$ref": "monomerTemplate-D-Tic___D-1,2,3,4-tetrahydro-3-isoquinolinecarboxylic acid" + }, + { + "$ref": "monomerTemplate-D-2Pal___D-3-(2-Pyridyl)-alanine" + }, + { + "$ref": "monomerTemplate-D-Abu___D-2-aminobutanoic acid" + }, + { + "$ref": "monomerTemplate-D-Dap___D-2,3-diaminopropanoic acid" + }, + { + "$ref": "monomerTemplate-Cbz___Carboxybenzyl" + }, + { + "$ref": "monomerTemplate--Et___C-Terminal ethyl" + }, + { + "$ref": "monomerTemplate-NHEt___Ethanamine" + }, + { + "$ref": "monomerTemplate-OEt___Ethanol" + }, + { + "$ref": "monomerTemplate-Tos___Tosyl" + }, + { + "$ref": "monomerTemplate-D-Thz___(4S)-1,3-thiazolidine-4-carboxylic acid" + }, + { + "$ref": "monomerTemplate-DACys___Deamino-Cysteine" + }, + { + "$ref": "monomerTemplate-DADab___4-aminobutanoic acid" + }, + { + "$ref": "monomerTemplate-DAGlyC___2-cyanoacetic acid" + }, + { + "$ref": "monomerTemplate-DAGlyP___2-cyclopentylacetic acid" + }, + { + "$ref": "monomerTemplate-DAGlyO___2-hydroxyacetic acid" + }, + { + "$ref": "monomerTemplate-DAGlyT___2-(thiophen-2-yl)acetic acid" + }, + { + "$ref": "monomerTemplate-DTrpFo___(2R)-2-amino-3-(1-formyl-1H-indol-3-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-DANcy___2-sulfanylacetic acid" + }, + { + "$ref": "monomerTemplate-DAPhe___Deamino-Phenylalanine" + }, + { + "$ref": "monomerTemplate-DAPhg3___2-(3,5-dimethylphenyl)acetic acid" + }, + { + "$ref": "monomerTemplate-DALeu___Deamino-Leucine" + }, + { + "$ref": "monomerTemplate-D-OAla___(2R)-2-hydroxypropanoic acid" + }, + { + "$ref": "monomerTemplate-L-OVal___(2S)-2-hydroxy-3-methylbutanoic acid" + }, + { + "$ref": "monomerTemplate-NHBn-___N-Terminal 1-phenylmethanamine" + }, + { + "$ref": "monomerTemplate-Bz___Benzaldehyde" + }, + { + "$ref": "monomerTemplate-Et-___N-Terminal ethyl" + }, + { + "$ref": "monomerTemplate-Me-___N-Terminal methyl" + }, + { + "$ref": "monomerTemplate-DTyrEt___(2R)-2-amino-3-(4-ethoxyphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Lys_Ac___(2S)-2-amino-6-acetamidohexanoic acid" + }, + { + "$ref": "monomerTemplate-OMe-___N-Terminal methanol" + }, + { + "$ref": "monomerTemplate-AspOMe___(2S)-2-amino-4-methoxy-4-oxobutanoic acid" + }, + { + "$ref": "monomerTemplate-NMe23A___3-(dimethylamino)benzoic acid" + }, + { + "$ref": "monomerTemplate-PheaDH___2-amino-3-phenylprop-2-enoic acid" + }, + { + "$ref": "monomerTemplate-Sta3xi___4-amino-3-hydroxy-6-methylheptanoic acid" + }, + { + "$ref": "monomerTemplate-TyrabD___2-amino-3-(4-methoxyphenyl)prop-2-enoic acid" + }, + { + "$ref": "monomerTemplate-DAlaol___(2R)-2-aminopropan-1-ol" + }, + { + "$ref": "monomerTemplate-DPhgol___2-amino-2-methylpropan-1-ol" + }, + { + "$ref": "monomerTemplate-DThrol___(2R,3R)-2-aminobutane-1,3-diol" + }, + { + "$ref": "monomerTemplate-Gly-ol___aminomethanol" + }, + { + "$ref": "monomerTemplate-Ala-ol___(2S)-2-aminopropan-1-ol" + }, + { + "$ref": "monomerTemplate-Lys-ol___(2S)-2,6-diaminohexan-1-ol" + }, + { + "$ref": "monomerTemplate-Phg-ol___(2S)-2-amino-2-phenylethan-1-ol" + }, + { + "$ref": "monomerTemplate-Pro-ol___[(2S)-pyrrolidin-2-yl]methanol" + }, + { + "$ref": "monomerTemplate-Val-ol___(2S)-2-amino-3-methylbutan-1-ol" + }, + { + "$ref": "monomerTemplate-Ala-al___(2S)-2-aminopropanal" + }, + { + "$ref": "monomerTemplate-Arg-al___N''-[(4S)-4-amino-5-oxopentyl]guanidine" + }, + { + "$ref": "monomerTemplate-Asp-al___(3S)-3-amino-4-oxobutanoic acid" + }, + { + "$ref": "monomerTemplate-Lys-al___(2S)-2,6-diaminohexanal" + }, + { + "$ref": "monomerTemplate-Pro-al___(2S)-pyrrolidine-2-carbaldehyde" + }, + { + "$ref": "monomerTemplate--NHBn___C-Terminal 1-phenylmethanamine" + }, + { + "$ref": "monomerTemplate-Met_O2___(2S)-2-amino-4-methanesulfonylbutanoic acid" + }, + { + "$ref": "monomerTemplate-Phe2Me___(2S)-2-amino-3-(2-methylphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe34d___(2S)-2-amino-3-(3,4-dichlorophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe4Br___(2S)-2-amino-3-(4-bromophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe_4I___(2S)-2-amino-3-(4-iodophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe4SD___(2S)-2-amino-3-{4-[(4S)-2,6-dioxo-1,3-diazinane-4-amido]phenyl}propanoic acid" + }, + { + "$ref": "monomerTemplate-SerPO3___(2S)-2-amino-3-(phosphonooxy)propanoic acid" + }, + { + "$ref": "monomerTemplate-ThrPO3___(2S,3R)-2-amino-3-(phosphonooxy)butanoic acid" + }, + { + "$ref": "monomerTemplate-Thz___(4R)-1,3-thiazolidine-4-carboxylic acid" + }, + { + "$ref": "monomerTemplate-Trp_Me___(2S)-2-amino-3-(1-methyl-1H-indol-3-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Tyr26d___(2S)-2-amino-3-(4-hydroxy-2,6-dimethylphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Tyr_3I___(2S)-2-amino-3-(4-hydroxy-3-iodophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Tyr3NO___(2S)-2-amino-3-(4-hydroxy-3-nitrophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-TyrPh4___(2S)-2-amino-3-[4-(4-hydroxyphenoxy)phenyl]propanoic acid" + }, + { + "$ref": "monomerTemplate-TyrSO3___(2S)-2-amino-3-[4-(sulfooxy)phenyl]propanoic acid" + }, + { + "$ref": "monomerTemplate-Val3OH___(2S)-2-amino-3-hydroxy-3-methylbutanoic acid" + }, + { + "$ref": "monomerTemplate-xiIle___(2S)-2-amino-3-methylpentanoic acid" + }, + { + "$ref": "monomerTemplate-NMe2Ab___2-(methylamino)benzoic acid" + }, + { + "$ref": "monomerTemplate-NMebAl___3-(methylamino)propanoic acid" + }, + { + "$ref": "monomerTemplate-aMePhe___(2S)-2-amino-2-methyl-3-phenylpropanoic acid" + }, + { + "$ref": "monomerTemplate-aMePro___(2S)-2-methylpyrrolidine-2-carboxylic acid" + }, + { + "$ref": "monomerTemplate-aMeTy3___(2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid" + }, + { + "$ref": "monomerTemplate-Bmt___(2S,3R,4R)-2-amino-3-hydroxy-4-methyloct-6-enoic acid" + }, + { + "$ref": "monomerTemplate-Cys_Bn___(2R)-2-amino-3-(benzylsulfanyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-His1Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Glyall___(2S)-2-aminopent-4-enoic acid" + }, + { + "$ref": "monomerTemplate-GlycPr___(2S)-2-amino-2-cyclopropylacetic acid" + }, + { + "$ref": "monomerTemplate-Hsl___(3S)-3-aminooxolan-2-one" + }, + { + "$ref": "monomerTemplate-AspPh2___(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid" + }, + { + "$ref": "monomerTemplate-Azi___(2S)-aziridine-2-carboxylic acid" + }, + { + "$ref": "monomerTemplate-2Abz___2-Aminobenzoic acid" + }, + { + "$ref": "monomerTemplate-3Abz___3-Aminobenzoic acid" + }, + { + "$ref": "monomerTemplate-4Abz___4-Aminobenzoic acid" + }, + { + "$ref": "monomerTemplate-Ac3c___1-aminocyclopropane-1-carboxylic acid" + }, + { + "$ref": "monomerTemplate-Ac6c___1-aminocyclohexane-1-carboxylic acid" + }, + { + "$ref": "monomerTemplate-D-Bmt___(2R,3S,4S)-2-amino-3-hydroxy-4-methyloct-6-enoic acid" + }, + { + "$ref": "monomerTemplate-D-hArg___(2R)-2-amino-6-[(diaminomethylidene)amino]hexanoic acid" + }, + { + "$ref": "monomerTemplate-DPhe4F___(2R)-2-amino-3-(4-fluorophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-DTrp2M___(2R)-2-amino-3-(2-methyl-1H-indol-3-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-DTyr3O___(2R)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-DTyrMe___(2R)-2-amino-3-(4-methoxyphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-DxiIle___(2R)-2-amino-3-methylpentanoic acid" + }, + { + "$ref": "monomerTemplate-LysiPr___(2S)-2-amino-6-[(propan-2-yl)amino]hexanoic acid" + }, + { + "$ref": "monomerTemplate--Bn___C-Terminal toluene" + }, + { + "$ref": "monomerTemplate-Ph___Phenyl" + }, + { + "$ref": "monomerTemplate-Boc___Tert-butyloxycarbonyl" + }, + { + "$ref": "monomerTemplate-DAChg___2-cyclohexylacetic acid" + }, + { + "$ref": "monomerTemplate-DADip___3,3-diphenylpropanoic acid" + }, + { + "$ref": "monomerTemplate-DAGlyB___3,3-dimethylbutanoic acid" + }, + { + "$ref": "monomerTemplate-DAhPhe___4-phenylbutanoic acid" + }, + { + "$ref": "monomerTemplate-DAnTyr___2-(4-methoxyphenyl)acetic acid" + }, + { + "$ref": "monomerTemplate-DAPhg4___2-(4-chlorophenyl)acetic acid" + }, + { + "$ref": "monomerTemplate-D-OVal___(2R)-2-hydroxy-3-methylbutanoic acid" + }, + { + "$ref": "monomerTemplate-OLeu___(2S)-2-hydroxy-4-methylpentanoic acid" + }, + { + "$ref": "monomerTemplate-Bn-___N-Terminal toluene" + }, + { + "$ref": "monomerTemplate-OBn-___N-Terminal phenylmethanol" + }, + { + "$ref": "monomerTemplate-DALys___Deamino-Lysine" + }, + { + "$ref": "monomerTemplate-NMe24A___4-(dimethylamino)benzoic acid" + }, + { + "$ref": "monomerTemplate-PheNO2___2-amino-3-(3-nitrophenyl)prop-2-enoic acid" + }, + { + "$ref": "monomerTemplate-Aib-ol___2-amino-2-methylpropan-1-ol" + }, + { + "$ref": "monomerTemplate-DProol___[(2R)-pyrrolidin-2-yl]methanol" + }, + { + "$ref": "monomerTemplate-Leu-ol___(2S)-2-amino-4-methylpentan-1-ol" + }, + { + "$ref": "monomerTemplate-Phe-ol___(2S)-2-amino-3-phenylpropan-1-ol" + }, + { + "$ref": "monomerTemplate-Thr-ol___(2S,3S)-2-aminobutane-1,3-diol" + }, + { + "$ref": "monomerTemplate-Gly-al___2-aminoacetaldehyde" + }, + { + "$ref": "monomerTemplate-Leu-al___(2S)-2-amino-4-methylpentanal" + }, + { + "$ref": "monomerTemplate-Phe-al___(2S)-2-amino-3-phenylpropanal" + }, + { + "$ref": "monomerTemplate-LhArgE___(2S)-2-amino-6-{[bis(ethylamino)methylidene]amino}hexanoic acid" + }, + { + "$ref": "monomerTemplate-Met_O___(2S)-2-amino-4-methanesulfinylbutanoic acid" + }, + { + "$ref": "monomerTemplate-nTyr___(2S)-2-amino-2-(4-hydroxyphenyl)acetic acid" + }, + { + "$ref": "monomerTemplate-Oic3aR___(2S,3aR,7aS)-octahydro-1H-indole-2-carboxylic acid" + }, + { + "$ref": "monomerTemplate-Phe_2F___(2S)-2-amino-3-(2-fluorophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe_3F___(2S)-2-amino-3-(3-fluorophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe_4F___(2S)-2-amino-3-(4-fluorophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phe4NO___(2S)-2-amino-3-(4-nitrophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Phebbd___(2S)-2-amino-3-methyl-3-phenylbutanoic acid" + }, + { + "$ref": "monomerTemplate-Trp5OH___(2S)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-TrpOme___(2S)-2-amino-3-(1-methoxy-1H-indol-3-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Tyr35d___(2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Tyr3OH___(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Tyr_Me___(2S)-2-amino-3-(4-methoxyphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-TyrPO3___(2S)-2-amino-3-[4-(phosphonooxy)phenyl]propanoic acid" + }, + { + "$ref": "monomerTemplate-xiHyp___(2S)-4-hydroxypyrrolidine-2-carboxylic acid" + }, + { + "$ref": "monomerTemplate-xiThr___(2S)-2-amino-3-hydroxybutanoic acid" + }, + { + "$ref": "monomerTemplate-NMe4Ab___4-(methylamino)benzoic acid" + }, + { + "$ref": "monomerTemplate-aMeTyr___(2S)-2-amino-3-(4-hydroxyphenyl)-2-methylpropanoic acid" + }, + { + "$ref": "monomerTemplate-Aoda___(2S)-2-amino-8-oxodecanoic acid" + }, + { + "$ref": "monomerTemplate-Bpa___(2S)-2-amino-3-(4-benzoylphenyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Cys_Me___(2R)-2-amino-3-(methylsulfanyl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Dip___(2S)-2-amino-3,3-diphenylpropanoic acid" + }, + { + "$ref": "monomerTemplate-hArg___(2S)-2-amino-6-[(diaminomethyl)amino]hexanoic acid" + }, + { + "$ref": "monomerTemplate-His1Bn___(2S)-2-amino-3-(1-benzyl-1H-imidazol-4-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-His3Me___(2S)-2-amino-3-(1-methyl-1H-imidazol-5-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-Hyl5xi___(2S)-2,6-diamino-5-hydroxyhexanoic acid" + }, + { + "$ref": "monomerTemplate-Bip___(2S)-2-amino-3-{[1,1'-biphenyl]-4-yl}propanoic acid" + }, + { + "$ref": "monomerTemplate-Abu23D___2-aminobut-2-enoic acid" + }, + { + "$ref": "monomerTemplate-D-Dip___(2R)-2-amino-3,3-diphenylpropanoic acid" + }, + { + "$ref": "monomerTemplate-Dha___2-aminoprop-2-enoic acid" + }, + { + "$ref": "monomerTemplate-DhArgE___(2R)-2-amino-6-{[bis(ethylamino)methylidene]amino}hexanoic acid" + }, + { + "$ref": "monomerTemplate-DMetSO___(2R)-2-amino-4-[(S)-methanesulfinyl]butanoic acid" + }, + { + "$ref": "monomerTemplate-DHis1B___(2R)-2-amino-3-(1-benzyl-1H-imidazol-4-yl)propanoic acid" + }, + { + "$ref": "monomerTemplate-D-nTyr___(2R)-2-amino-2-(4-hydroxyphenyl)acetic acid" + }, + { + "$ref": "monomerTemplate-DPhe4u___(2R)-2-amino-3-[4-(carbamoylamino)phenyl]propanoic acid" + }, + { + "$ref": "monomerTemplate-oC3o___1,3 Propanediol" + }, + { + "$ref": "monomerTemplate-tCo___1,3-Diaza-2-oxophenoxazin" + }, + { + "$ref": "monomerTemplate-dhp___1,3-Dihydroxy-2-propoxymethyl (ganciclovir sugar)" + }, + { + "$ref": "monomerTemplate-oC4o___1,4 Butanediol" + }, + { + "$ref": "monomerTemplate-oC5o___1,5 Pentanediol" + }, + { + "$ref": "monomerTemplate-oC6o___1,6 Hexanediol" + }, + { + "$ref": "monomerTemplate-oC7o___1,7 Heptanediol" + }, + { + "$ref": "monomerTemplate-oC11o___1,11 Undecanediol" + }, + { + "$ref": "monomerTemplate-oC12o___1,12 Dodecanediol" + }, + { + "$ref": "monomerTemplate-m1Yra___1-Methyl-pseudouracil" + }, + { + "$ref": "monomerTemplate-m1A___1-Methyladenine" + }, + { + "$ref": "monomerTemplate-m1G___1-Methylguanine" + }, + { + "$ref": "monomerTemplate-nC62r___2-O-(6-aminohexyl)ribose" + }, + { + "$ref": "monomerTemplate-m22G___2,2-Dimethylguanine" + }, + { + "$ref": "monomerTemplate-ox23ar___2,3-Oxetanearabinose" + }, + { + "$ref": "monomerTemplate-bnanc___2,4-BNANC (oxyamino-BNA)" + }, + { + "$ref": "monomerTemplate-bnancm___2,4-BNANCMe (N-Methyl-oxyamino BNA)" + }, + { + "$ref": "monomerTemplate-n2A___2-Aminoadenine" + }, + { + "$ref": "monomerTemplate-mon2ln___2-(Methoxy)amino LNA" + }, + { + "$ref": "monomerTemplate-moeon2___2-(Methoxyethoxy)amino LNA (N-MOE)" + }, + { + "$ref": "monomerTemplate-Rmclna___2-(R)-Methyl-cLNA" + }, + { + "$ref": "monomerTemplate-impr6n___2-Amino-N6-imidazoylpropyladenine" + }, + { + "$ref": "monomerTemplate-n2r___2-Aminoribose" + }, + { + "$ref": "monomerTemplate-Bcm2r___2-C-Methylribose" + }, + { + "$ref": "monomerTemplate-cl2cyp___2-Chloro-N6-cyclopentyladenine" + }, + { + "$ref": "monomerTemplate-cl2A___2-Chloroadenine" + }, + { + "$ref": "monomerTemplate-mopr2d___2-Deoxy-2-methoxypropyl" + }, + { + "$ref": "monomerTemplate-fl2A___2-Fluoroadenine" + }, + { + "$ref": "monomerTemplate-io2A___2-Iodoadenine" + }, + { + "$ref": "monomerTemplate-mo2A___2-Methoxyadenine" + }, + { + "$ref": "monomerTemplate-moen___2-Methoxyethylamino" + }, + { + "$ref": "monomerTemplate-m2A___2-Methyladenine" + }, + { + "$ref": "monomerTemplate-m2G___2-Methylguanine" + }, + { + "$ref": "monomerTemplate-se2r___2-Methylseleno-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-ms2r___2-Methylthio-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-ms2A___2-Methylthioadenine" + }, + { + "$ref": "monomerTemplate-mnc2r___2-N-Methylcarbamoylribose" + }, + { + "$ref": "monomerTemplate-imbu2r___2-O-4-(Imidazo-1-yl) butylribose" + }, + { + "$ref": "monomerTemplate-fl5pr2___2-O-(2,2,3,3,3-Pentafluoropropyl)ribose" + }, + { + "$ref": "monomerTemplate-nac2r___2-O-(2-Acetamide)ribose" + }, + { + "$ref": "monomerTemplate-ne2r___2-O-(2-Amino)ethylribose" + }, + { + "$ref": "monomerTemplate-fle2r___2-O-(2-Fluoroethyl)ribose" + }, + { + "$ref": "monomerTemplate-menoe2___2-O-(2-Formaldoximino)ethylribose" + }, + { + "$ref": "monomerTemplate-phoe2r___2-O-(2-Phenoxyethyl)ribose" + }, + { + "$ref": "monomerTemplate-fl3e2r___2-O-(2-Trifluoro)ethylribose" + }, + { + "$ref": "monomerTemplate-fl3pr2___2-O-(3,3,3-Trifluoropropyl)ribose" + }, + { + "$ref": "monomerTemplate-nbu2r___2-O-(4-Aminobutyl)ribose" + }, + { + "$ref": "monomerTemplate-GalNAc___2-O-(6-(N-glutaryl-GalNAc3)aminohexylribose" + }, + { + "$ref": "monomerTemplate-nma___2-O-(N-Methylacetamide)ribose" + }, + { + "$ref": "monomerTemplate-pyren1___2-O-(Pyren-1-yl)methylribose" + }, + { + "$ref": "monomerTemplate-Sm2moe___2-O-(S)-Methyl MOE" + }, + { + "$ref": "monomerTemplate-dmaoe___2-O-[(dimethylaminooxy)ethyl]ribose (DMAOE)" + }, + { + "$ref": "monomerTemplate-allyl2___2-O-Allylribose" + }, + { + "$ref": "monomerTemplate-aoe2r___2-O-Aminooxyethylribose (AOE)" + }, + { + "$ref": "monomerTemplate-nC52r___2-O-Aminopentylribose" + }, + { + "$ref": "monomerTemplate-npr2r___2-O-Aminopropylribose" + }, + { + "$ref": "monomerTemplate-bnoe2r___2-O-Benzyloxyethylribose" + }, + { + "$ref": "monomerTemplate-bn2r___2-O-Benzylribose" + }, + { + "$ref": "monomerTemplate-bu2r___2-O-Butylribose" + }, + { + "$ref": "monomerTemplate-m2nc2r___2-O-Dimethylaminocarbamoylribose" + }, + { + "$ref": "monomerTemplate-m2e2r___2-O-Dimethylaminoethylribose" + }, + { + "$ref": "monomerTemplate-eom2r___2-O-Ethoxymethylribose" + }, + { + "$ref": "monomerTemplate-e2r___2-O-Ethylribose" + }, + { + "$ref": "monomerTemplate-ipr2r___2-O-Isopropylribose" + }, + { + "$ref": "monomerTemplate-c4m___2-O-Methyl carbocyclic ribose" + }, + { + "$ref": "monomerTemplate-s4m___2-O-Methyl-4-thioribose" + }, + { + "$ref": "monomerTemplate-mne2r___2-O-Methylaminoethylribose (MMAE)" + }, + { + "$ref": "monomerTemplate-mseac___2-O-N-[2-(methylsulfanyl)ethyl]acetamidoribose" + }, + { + "$ref": "monomerTemplate-C92r___2-O-Nonylribose" + }, + { + "$ref": "monomerTemplate-C52r___2-O-Pentylribose" + }, + { + "$ref": "monomerTemplate-ph2r___2-O-Phenylribose" + }, + { + "$ref": "monomerTemplate-prparg___2-O-Propargylribose" + }, + { + "$ref": "monomerTemplate-pr2r___2-O-Propylribose" + }, + { + "$ref": "monomerTemplate-ime2r___2-O-[2-(1-Imidizolyl)ethyl] ribose" + }, + { + "$ref": "monomerTemplate-trimoe___2-O-[2-(2-Methoxyethoxy)ethoxy]ethylribose (TriMOE)" + }, + { + "$ref": "monomerTemplate-e2noe2___2-O-[2-((N,N-diethyl)aminooxy)ethyl]ribose" + }, + { + "$ref": "monomerTemplate-iprmno___2-O-[2-((N-Isopropyl-N-methyl)aminooxy)ethyl]ribose" + }, + { + "$ref": "monomerTemplate-guane2___2-O-[2-(Guanidinium)ethyl]ribose" + }, + { + "$ref": "monomerTemplate-mse2r___2-O-[2-(Methylthio)ethyl]ribose" + }, + { + "$ref": "monomerTemplate-msoe2r___2-O-[2-(methylsulfinyl)ethyl]ribose" + }, + { + "$ref": "monomerTemplate-dmaeoe___2-O-[2-[2-(N,N-dimethyl)aminoethoxy]ethyl]ribose" + }, + { + "$ref": "monomerTemplate-m2npr2___2-O-[3-(N,N-Dimethyl)aminopropyl]ribose" + }, + { + "$ref": "monomerTemplate-s4moe___2-O-[(2-Methoxy)ethyl]-4-thioribose" + }, + { + "$ref": "monomerTemplate-m2nenc___2-O-[(Dimethylamino)ethylcarbamoyl]ribose" + }, + { + "$ref": "monomerTemplate-dmac___2-O-[(N,N-dimethyl)acetamido]ribose" + }, + { + "$ref": "monomerTemplate-dmaeac___2-O-[N-[2-(Dimethylamino)ethyl]acetamido]ribose" + }, + { + "$ref": "monomerTemplate-phs2r___2-Phenylthio-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-s2lna___2-Thio LNA" + }, + { + "$ref": "monomerTemplate-Rs2cEt___2-Thio-(R)-cEt" + }, + { + "$ref": "monomerTemplate-Ss2cEt___2-Thio-(S)-cEt" + }, + { + "$ref": "monomerTemplate-s2C___2-Thiocytosine" + }, + { + "$ref": "monomerTemplate-s2T___2-Thiothymine" + }, + { + "$ref": "monomerTemplate-s2U___2-Thiouracil" + }, + { + "$ref": "monomerTemplate-Ae2d___2-alpha-C-Ethyl-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-Am2d___2-alpha-C-Methyl-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-m2nprn___3-(Dimethylamino)propylaminoadenine" + }, + { + "$ref": "monomerTemplate-clhna___3-Chloro HNA" + }, + { + "$ref": "monomerTemplate-c3ally___3-Deaza-3-allylguanine" + }, + { + "$ref": "monomerTemplate-c3A___3-Deazaadenine" + }, + { + "$ref": "monomerTemplate-c3G___3-Deazaguanine" + }, + { + "$ref": "monomerTemplate-n3m___3-Deoxy-3-amino-2-O-methylribose" + }, + { + "$ref": "monomerTemplate-n3d___3-Deoxy-3-amino-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-n3fl2r___3-Deoxy-3-amino-2-fluororibose" + }, + { + "$ref": "monomerTemplate-n3co4d___3-Deoxy-3-amino-4-carboxyl-deoxyribose" + }, + { + "$ref": "monomerTemplate-me3m___3-Deoxy-3-methylene-2-O-methylribose" + }, + { + "$ref": "monomerTemplate-me3d___3-Deoxy-3-methylene-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-me3fl2___3-Deoxy-3-methylene-2-fluororibose" + }, + { + "$ref": "monomerTemplate-me3r___3-Deoxy-3-methyleneribose" + }, + { + "$ref": "monomerTemplate-s3d___3-Deoxy-3-thio-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-25d3r___3-Deoxyribose (2,5 connectivity)" + }, + { + "$ref": "monomerTemplate-fhna___3-Fluoro HNA" + }, + { + "$ref": "monomerTemplate-m3ALln___3-Methyl-alpha-L-LNA" + }, + { + "$ref": "monomerTemplate-m3C___3-Methylcytosine" + }, + { + "$ref": "monomerTemplate-m3U___3-Methyluracil" + }, + { + "$ref": "monomerTemplate-mo4bn3___3-N-(p-Methoxybenzyl)thymine" + }, + { + "$ref": "monomerTemplate-fleana___3-O-FEt ANA" + }, + { + "$ref": "monomerTemplate-moe3an___3-O-MOE-ANA" + }, + { + "$ref": "monomerTemplate-m3ana___3-O-Methyl-ANA" + }, + { + "$ref": "monomerTemplate-25moe3___3-O-methoxyethyl ribose (2,5 connectivity)" + }, + { + "$ref": "monomerTemplate-afhna___3-ara FHNA" + }, + { + "$ref": "monomerTemplate-Bcm3d___3-beta-C-Methyl-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-Bcm3r___3-beta-C-Methylribose" + }, + { + "$ref": "monomerTemplate-h456U___4,5,6-Trihydrouracil" + }, + { + "$ref": "monomerTemplate-acn4d___4-Acetylamino-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-ac4C___4-Acetylcytosine" + }, + { + "$ref": "monomerTemplate-cnes4T___4-Cyanoethylthiothymidine" + }, + { + "$ref": "monomerTemplate-d4U___4-Deoxouracil" + }, + { + "$ref": "monomerTemplate-oC64m5___4-Hexan-6-ol-5-methylcytosine" + }, + { + "$ref": "monomerTemplate-m4C___4-Methylcytosine" + }, + { + "$ref": "monomerTemplate-oh4C___4-N-Hydroxcytosine" + }, + { + "$ref": "monomerTemplate-s4d___4-Thio-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-s4T___4-Thiothymidine" + }, + { + "$ref": "monomerTemplate-s4U___4-Thiouracil" + }, + { + "$ref": "monomerTemplate-h56T___5,6-Dihydrothymine" + }, + { + "$ref": "monomerTemplate-m6T___5,6-Dimethyluracil" + }, + { + "$ref": "monomerTemplate-pr56U___5,6-Propylene uracil" + }, + { + "$ref": "monomerTemplate-brviny___5-(2-Bromovinyl)uracil" + }, + { + "$ref": "monomerTemplate-npry5C___5-(Propargylamine)cytosine" + }, + { + "$ref": "monomerTemplate-5R6Rm5___5-(R)-Methyl-(R)-cEt BNA" + }, + { + "$ref": "monomerTemplate-5R6Sm5___5-(R)-Methyl-(S)-cEt BNA" + }, + { + "$ref": "monomerTemplate-5S6Rm5___5-(S)-Methyl-(R)-cEt BNA" + }, + { + "$ref": "monomerTemplate-5S6Sm5___5-(S)-Methyl-(S)-cEt BNA" + }, + { + "$ref": "monomerTemplate-allyl5___5-Allyluracil" + }, + { + "$ref": "monomerTemplate-nC65C___5-Aminohexylcytosine" + }, + { + "$ref": "monomerTemplate-nC65U___5-Aminohexyluracil" + }, + { + "$ref": "monomerTemplate-npr5U___5-Aminopropyluracil" + }, + { + "$ref": "monomerTemplate-br5C___5-Bromocytosine" + }, + { + "$ref": "monomerTemplate-br5U___5-Bromouracil" + }, + { + "$ref": "monomerTemplate-cl5C___5-Chlorocytosine" + }, + { + "$ref": "monomerTemplate-cl5U___5-Chlorouracil" + }, + { + "$ref": "monomerTemplate-CN5U___5-Cyanouracil" + }, + { + "$ref": "monomerTemplate-DBCOnC___5-DBCO-U (ethylene carbamoyl hexylamino linker)" + }, + { + "$ref": "monomerTemplate-d5m___5-Deoxy-2-O-methylribose" + }, + { + "$ref": "monomerTemplate-d5moe___5-Deoxy-2-O-methyoxyethylribose" + }, + { + "$ref": "monomerTemplate-n5m___5-Deoxy-5-amino-2-O-methylribose" + }, + { + "$ref": "monomerTemplate-n5d___5-Deoxy-5-amino-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-n5fl2r___5-Deoxy-5-amino-2-fluororibose" + }, + { + "$ref": "monomerTemplate-n5r___5-Deoxy-5-aminoribose" + }, + { + "$ref": "monomerTemplate-s5d___5-Deoxy-5-thioribose" + }, + { + "$ref": "monomerTemplate-e5U___5-Ethyluracil" + }, + { + "$ref": "monomerTemplate-ethy5C___5-Ethynylcytosine" + }, + { + "$ref": "monomerTemplate-fl5C___5-Fluorocytosine" + }, + { + "$ref": "monomerTemplate-5formD___5-Formyl-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-form5C___5-Formylcytosine" + }, + { + "$ref": "monomerTemplate-form5U___5-Formyluracil" + }, + { + "$ref": "monomerTemplate-oh5C___5-Hydroxycytosine" + }, + { + "$ref": "monomerTemplate-hm5C___5-Hydroxymethylcytosine" + }, + { + "$ref": "monomerTemplate-oh5U___5-Hydroxyuracil" + }, + { + "$ref": "monomerTemplate-ohm5U___5-Hyroxymethyluracil" + }, + { + "$ref": "monomerTemplate-io5C___5-Iodocytosine" + }, + { + "$ref": "monomerTemplate-ipr5U___5-Isopropyluracil" + }, + { + "$ref": "monomerTemplate-mo5U___5-Methoxyuracil" + }, + { + "$ref": "monomerTemplate-m5m___5-Methyl-2-O-methylribose" + }, + { + "$ref": "monomerTemplate-m5d___5-Methyldeoxyribose" + }, + { + "$ref": "monomerTemplate-thiz5C___5-Thiazolecytidine" + }, + { + "$ref": "monomerTemplate-thiz5U___5-Thiazoleuridine" + }, + { + "$ref": "monomerTemplate-thien5___5-Thienyl-6-azauracil" + }, + { + "$ref": "monomerTemplate-fl3mC___5-Trifluoromethylcytosine" + }, + { + "$ref": "monomerTemplate-vinyl5___5-Vinyluracil" + }, + { + "$ref": "monomerTemplate-mnm5U___5-[(Methylamino)methyl]uridine" + }, + { + "$ref": "monomerTemplate-nobn6p___6-(p-Nitrobenzylthio)purine" + }, + { + "$ref": "monomerTemplate-nC6n2G___6-Aminohexyl-2-aminoguanine" + }, + { + "$ref": "monomerTemplate-nC6n8A___6-Aminohexyl-8-aminoadenine" + }, + { + "$ref": "monomerTemplate-z6pry5___6-Aza-5-propynyluracil" + }, + { + "$ref": "monomerTemplate-z5C___6-Azacytosine" + }, + { + "$ref": "monomerTemplate-z5T___6-Azathymine" + }, + { + "$ref": "monomerTemplate-z6U___6-Azauracil" + }, + { + "$ref": "monomerTemplate-cl6G___6-Chloroguanine" + }, + { + "$ref": "monomerTemplate-cl6pur___6-Chloropurine" + }, + { + "$ref": "monomerTemplate-cyh6A___6-Cyclohexyladenine" + }, + { + "$ref": "monomerTemplate-cyp6A___6-Cyclopentyladenine" + }, + { + "$ref": "monomerTemplate-e6A___6-Ethyladenine" + }, + { + "$ref": "monomerTemplate-mo6pur___6-Methoxypurine" + }, + { + "$ref": "monomerTemplate-m6G___6-Methylguanine" + }, + { + "$ref": "monomerTemplate-m6pur___6-Methylpurine" + }, + { + "$ref": "monomerTemplate-ms6G___6-Methylthioguanine" + }, + { + "$ref": "monomerTemplate-ms6pur___6-Methylthiopurine" + }, + { + "$ref": "monomerTemplate-m6U___6-Methyluracil" + }, + { + "$ref": "monomerTemplate-s6G___6-Thioguanine" + }, + { + "$ref": "monomerTemplate-s6puri___6-Thiopurine" + }, + { + "$ref": "monomerTemplate-Bcoh4d___6-beta-Hydroxycarbo-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-z7G___7-Azaguanine" + }, + { + "$ref": "monomerTemplate-c7cn7A___7-Deaza-7-cyanoadenine" + }, + { + "$ref": "monomerTemplate-c7io7n___7-Deaza-7-iodo-2-aminoadenine" + }, + { + "$ref": "monomerTemplate-c7io7A___7-Deaza-7-iodoadenine" + }, + { + "$ref": "monomerTemplate-c7io7G___7-Deaza-7-iodoguanine" + }, + { + "$ref": "monomerTemplate-c7py7N___7-Deaza-7-propyne-2-aminoadenine" + }, + { + "$ref": "monomerTemplate-c7py7A___7-Deaza-7-propynyladenine" + }, + { + "$ref": "monomerTemplate-c7A___7-Deazaadenine" + }, + { + "$ref": "monomerTemplate-c7G___7-Deazaguanine" + }, + { + "$ref": "monomerTemplate-m7h8G___7-Methyl 8-dihydroguanine" + }, + { + "$ref": "monomerTemplate-m7G___7-Methylguanine" + }, + { + "$ref": "monomerTemplate-tCnitr___7-Nitro-1,3-diaza-2-oxophenothiazin" + }, + { + "$ref": "monomerTemplate-n8A___8-Aminoadenine" + }, + { + "$ref": "monomerTemplate-n8G___8-Aminoguanine" + }, + { + "$ref": "monomerTemplate-z8c3G___8-Aza-3-deazaguanine" + }, + { + "$ref": "monomerTemplate-z8A___8-Azaadenine" + }, + { + "$ref": "monomerTemplate-br8A___8-Bromoadenine" + }, + { + "$ref": "monomerTemplate-br8G___8-Bromoguanine" + }, + { + "$ref": "monomerTemplate-cl8A___8-Chloroadenine" + }, + { + "$ref": "monomerTemplate-o8s9G___8-Oxo-9-thioguanine" + }, + { + "$ref": "monomerTemplate-o8A___8-Oxoadenine" + }, + { + "$ref": "monomerTemplate-o8G___8-Oxoguanine" + }, + { + "$ref": "monomerTemplate-s8G___8-Thioguanine" + }, + { + "$ref": "monomerTemplate-allyl9___9-Allylguanine" + }, + { + "$ref": "monomerTemplate-Smclna___(2S)-methyl-cLNA" + }, + { + "$ref": "monomerTemplate-Rm5lna___(5R)-5-Methyl-LNA" + }, + { + "$ref": "monomerTemplate-Rm5ALl___(5R)-5-methyl-alpha-L-LNA" + }, + { + "$ref": "monomerTemplate-Rm5moe___(5R)-Me-2O-MOE" + }, + { + "$ref": "monomerTemplate-Sm5fl2___(5S)-2-Fluoro-5-methylribose" + }, + { + "$ref": "monomerTemplate-Sm5ALl___(5S)-5-Methyl-alpha-L-LNA" + }, + { + "$ref": "monomerTemplate-Svinyl___(5S)-5-Vinyl-BNA" + }, + { + "$ref": "monomerTemplate-Sm5lna___(5S)-5-methyl-LNA" + }, + { + "$ref": "monomerTemplate-Sm5moe___(5S)-Methyl-2O-MOE" + }, + { + "$ref": "monomerTemplate-Sm6fhn___(6S)-6-methyl-FHNA" + }, + { + "$ref": "monomerTemplate-Sm6ALl___(6S)-6-methyl-alpha-L-LNA" + }, + { + "$ref": "monomerTemplate-nen___(Aminoethyl)amino" + }, + { + "$ref": "monomerTemplate-Diprgl___(D)-2-O-(2,3-Isopropylidene glycer-1-yl)ribose" + }, + { + "$ref": "monomerTemplate-m2nen___(Dimethylaminoethyl)amino" + }, + { + "$ref": "monomerTemplate-Liprgl___(L)-2-O-(2,3-Isopropylidene glycer-1-yl)ribose" + }, + { + "$ref": "monomerTemplate-h456UR___(R)-4,5,6-Trihydrouracil" + }, + { + "$ref": "monomerTemplate-Rm5fl2___(R)-2-Fluoro-5-methylribose" + }, + { + "$ref": "monomerTemplate-Rm5d___(R)-5-Methyldeoxyribose" + }, + { + "$ref": "monomerTemplate-Rhe5d___(R)-5-hydroxyethyl 2-deoxyribose" + }, + { + "$ref": "monomerTemplate-Rflcln___(R)-F-cLNA" + }, + { + "$ref": "monomerTemplate-Rso2ln___(R)-Sulfoxide BNA" + }, + { + "$ref": "monomerTemplate-Rcet___(R)-cEt BNA" + }, + { + "$ref": "monomerTemplate-Rcmoe___(R)-cMOE BNA" + }, + { + "$ref": "monomerTemplate-RSpabC___(RC5,SP)-a,b-CNA" + }, + { + "$ref": "monomerTemplate-Rmp___(Rp)-Methylphosphonate" + }, + { + "$ref": "monomerTemplate-Rsp___(Rp)-Phosphorothioate" + }, + { + "$ref": "monomerTemplate-She5d___(S)-5-Hydroxyethyl-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-Sm5d___(S)-5-Methyldeoxyribose" + }, + { + "$ref": "monomerTemplate-cet___(S)-cEt BNA" + }, + { + "$ref": "monomerTemplate-Scmoe___(S)-cMOE BNA" + }, + { + "$ref": "monomerTemplate-ScPr___(S)-cPr-BNA" + }, + { + "$ref": "monomerTemplate-SRpabC___(SC5,RP)-a,b-CNA" + }, + { + "$ref": "monomerTemplate-Smp___(Sp)-Methylphosphonate" + }, + { + "$ref": "monomerTemplate-Ssp___(Sp)-Phosphorothioate" + }, + { + "$ref": "monomerTemplate-ana___ANA" + }, + { + "$ref": "monomerTemplate-hn___Amino" + }, + { + "$ref": "monomerTemplate-Smn2ce___Amino(S)-cEt (N-methyl)" + }, + { + "$ref": "monomerTemplate-Rmn2ce___Amino(R)-cEt (N-methyl)" + }, + { + "$ref": "monomerTemplate-nC6n5U___Amino-Modier C6 dT" + }, + { + "$ref": "monomerTemplate-nC6n5C___Amino-Modier C6 dC" + }, + { + "$ref": "monomerTemplate-az8A___Azidoadenine" + }, + { + "$ref": "monomerTemplate-bnn___Benzylamino" + }, + { + "$ref": "monomerTemplate-bcdna___BicycloDNA" + }, + { + "$ref": "monomerTemplate-c4d___Carbocyclic-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-co___Carbonyl" + }, + { + "$ref": "monomerTemplate-cm___Carbonylmethyl" + }, + { + "$ref": "monomerTemplate-cena___CeNA" + }, + { + "$ref": "monomerTemplate-fl2me___Difluoromethylene" + }, + { + "$ref": "monomerTemplate-hU___Dihydrouracil" + }, + { + "$ref": "monomerTemplate-en___Ethylamino" + }, + { + "$ref": "monomerTemplate-eop___Ethylphosphate" + }, + { + "$ref": "monomerTemplate-fcena___Fluoro-CeNA" + }, + { + "$ref": "monomerTemplate-gclamp___G-clamp (9-(aminoethoxy)phenoxazine)" + }, + { + "$ref": "monomerTemplate-ggclam___G-clamp (9-(guanylethoxy)phenoxazine)" + }, + { + "$ref": "monomerTemplate-Oro___Orotic Acid" + }, + { + "$ref": "monomerTemplate-ibun___Isobutylamino" + }, + { + "$ref": "monomerTemplate-isoG___Isoguanine" + }, + { + "$ref": "monomerTemplate-Ld___L-2-deoxyribose" + }, + { + "$ref": "monomerTemplate-mn___Methylamino" + }, + { + "$ref": "monomerTemplate-me___Methylene" + }, + { + "$ref": "monomerTemplate-meclna___Methylene cLNA" + }, + { + "$ref": "monomerTemplate-mepo2___Methylenephosphonate" + }, + { + "$ref": "monomerTemplate-mp___Methylphosphonate" + }, + { + "$ref": "monomerTemplate-msp___Methylthiophosphonate" + }, + { + "$ref": "monomerTemplate-nen2G___N2-(2-Amino)ethyl guanine" + }, + { + "$ref": "monomerTemplate-npr2G___N2-(3-Aminopropyl) guanine" + }, + { + "$ref": "monomerTemplate-nen2A___N2-(Aminoethyl)aminoadenine" + }, + { + "$ref": "monomerTemplate-moprn2___N2-(Methoxypropylamino)adenine" + }, + { + "$ref": "monomerTemplate-impr2G___N2-Imidazoylpropylguanine" + }, + { + "$ref": "monomerTemplate-phen2A___N2-Phenethylaminoadenine" + }, + { + "$ref": "monomerTemplate-2imen2___N2-[(Imidazo-2-yl)ethylamino]adenine" + }, + { + "$ref": "monomerTemplate-4imen2___N2-[(Imidazol-4-yl)ethyl]guanine" + }, + { + "$ref": "monomerTemplate-cneT___N3-(2-Cyanoethyl)thymine" + }, + { + "$ref": "monomerTemplate-4ime6A___N6-[2-(4-Imidazoyl)ethyl]adenine" + }, + { + "$ref": "monomerTemplate-imprn2___N-(Aminopropyl)imidazoleadenine" + }, + { + "$ref": "monomerTemplate-mnobna___N-(Methyl)aminooxy BNA" + }, + { + "$ref": "monomerTemplate-gly___N-Hydroxyglycine" + }, + { + "$ref": "monomerTemplate-mn2lna___N-Methylamino LNA" + }, + { + "$ref": "monomerTemplate-npomT___NPOM-caged thymine" + }, + { + "$ref": "monomerTemplate-afl2Nm___North-2-ara-fluoro-methanocarbocycle" + }, + { + "$ref": "monomerTemplate-fl2Nmc___North-2-fluoro-methanocarbocycle" + }, + { + "$ref": "monomerTemplate-Nmc___North-methanocarbocycle" + }, + { + "$ref": "monomerTemplate-oxy___Oxy (ether)" + }, + { + "$ref": "monomerTemplate-Sp18___PEG/HEG 18 atom spacer" + }, + { + "$ref": "monomerTemplate-pna___PNA (peptide nucleic acid)" + }, + { + "$ref": "monomerTemplate-Dlyspn___PNA D-Lysine (peptide nucleic acid)" + }, + { + "$ref": "monomerTemplate-Llyspn___PNA L-Lysine (peptide nucleic acid)" + }, + { + "$ref": "monomerTemplate-cmp___Phosphonoacetate" + }, + { + "$ref": "monomerTemplate-m2np___Phosphorodiamidate" + }, + { + "$ref": "monomerTemplate-s2p___Phosphorodithioate" + }, + { + "$ref": "monomerTemplate-prn___Propylamino" + }, + { + "$ref": "monomerTemplate-psiU___Pseudouracil" + }, + { + "$ref": "monomerTemplate-purine___Purine" + }, + { + "$ref": "monomerTemplate-Smc___South-methanocarbacycle" + }, + { + "$ref": "monomerTemplate-trina1___Tricyclic Nucleoside (TriNA1)" + }, + { + "$ref": "monomerTemplate-trina2___Tricyclic Nucleoside (TriNA2)" + }, + { + "$ref": "monomerTemplate-tcdna___TricycloDNA" + }, + { + "$ref": "monomerTemplate-Xan___Xanthine" + }, + { + "$ref": "monomerTemplate-ALmecl___alpha-L-Methylene cLNA" + }, + { + "$ref": "monomerTemplate-ALtri1___alpha-L-TriNA1" + }, + { + "$ref": "monomerTemplate-ALtri2___alpha-L-TriNA2" + }, + { + "$ref": "monomerTemplate-ciPr___ciPr BNA" + }, + { + "$ref": "monomerTemplate-25mo3r___3-O-Methylribose (2,5 connectivity)" + }, + { + "$ref": "monomerGroupTemplate-A" + }, + { + "$ref": "monomerGroupTemplate-C" + }, + { + "$ref": "monomerGroupTemplate-G" + }, + { + "$ref": "monomerGroupTemplate-T" + }, + { + "$ref": "monomerGroupTemplate-U" + }, + { + "$ref": "monomerGroupTemplate-MOE(A)P" + }, + { + "$ref": "monomerGroupTemplate-MOE(5meC)P" + }, + { + "$ref": "monomerGroupTemplate-MOE(G)P" + }, + { + "$ref": "monomerGroupTemplate-MOE(T)P" + }, + { + "$ref": "monomerGroupTemplate-dR(U)P" + } + ] + }, + "monomerTemplate-12ddR___1',2'-Di-Deoxy-Ribose": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "O", + "location": [ + -0.8526, + 1.541, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.3405, + 0.131, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 0.3301, + 2.4636, + 0 + ] + }, + { + "label": "C", + "location": [ + 1.1586, + 0.1823, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.5731, + 1.6239, + 0 + ] + }, + { + "label": "O", + "location": [ + 2.0777, + -1.0008, + 0 + ] + }, + { + "label": "C", + "location": [ + -1.1818, + -1.1087, + 0 + ] + }, + { + "label": "O", + "location": [ + -2.6787, + -1.0008, + 0 + ] + }, + { + "label": "H", + "location": [ + -3.3525, + -1.9937, + 0 + ] + }, + { + "label": "H", + "location": [ + 3.2666, + -0.8378, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + "type": 1, + "atoms": [ + 0, + 2 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 3 + ] + }, + { + "type": 1, + "atoms": [ + 1, + 6 + ], + "stereo": 1 + }, + { + "type": 1, + "atoms": [ + 2, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 4 + ] + }, + { + "type": 1, + "atoms": [ + 3, + 5 + ], + "stereo": 6 + }, + { + "type": 1, + "atoms": [ + 5, + 9 + ] + }, + { + "type": 1, + "atoms": [ + 6, + 7 + ] + }, + { + "type": 1, + "atoms": [ + 7, + 8 + ] + } + ], + "class": "Sugar", + "classHELM": "RNA", + "id": "12ddR___1',2'-Di-Deoxy-Ribose", + "fullName": "1',2'-Di-Deoxy-Ribose", + "alias": "12ddR", + "attachmentPoints": [ + { + "attachmentAtom": 7, + "leavingGroup": { + "atoms": [ + 8 + ] + }, + "type": "left" + }, + { + "attachmentAtom": 5, + "leavingGroup": { + "atoms": [ + 9 + ] + }, + "type": "right" + } + ], + "naturalAnalogShort": "R" + }, + "monomerTemplate-25R___2,5-Ribose": { + "type": "monomerTemplate", + "atoms": [ + { + "label": "O", + "location": [ + -0.6295, + -1.1398, + 0 + ] + }, + { + "label": "C", + "location": [ + -0.8657, + 0.3416, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 0.8523, + -1.3729, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 0.4701, + 1.024, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "C", + "location": [ + 1.5319, + -0.0356, + 0 + ], + "stereoLabel": "abs" + }, + { + "label": "O", + "location": [ + 0.6566, + 2.2094, + 0 + ] + }, + { + "label": "O", + "location": [ + 3.0119, + 0.1971, + 0 + ] + }, + { + "label": "C", + "location": [ + -2.2027, + 1.0176, + 0 + ] + }, + { + "label": "O", + "location": [ + 1.3982, + -2.4414, + 0 + ] + }, + { + "label": "O", + "location": [ + -3.4595, + 0.1971, + 0 + ] + }, + { + "label": "H", + "location": [ + -4.5303, + 0.7385, + 0 + ] + }, + { + "label": "H", + "location": [ + 3.7667, + -0.7357, + 0 + ] + } + ], + "bonds": [ + { + "type": 1, + "atoms": [ + 0, + 1 + ] + }, + { + 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"$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-C": { + "type": "monomerGroupTemplate", + "id": "C", + "name": "C", + "class": "RNA", + "templates": [ + { + "$ref": "monomerTemplate-R___Ribose" + }, + { + "$ref": "monomerTemplate-C___Cytosine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-G": { + "type": "monomerGroupTemplate", + "id": "G", + "name": "G", + "class": "RNA", + "templates": [ + { + "$ref": "monomerTemplate-R___Ribose" + }, + { + "$ref": "monomerTemplate-G___Guanine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-T": { + "type": "monomerGroupTemplate", + "id": "T", + "name": "T", + "class": "RNA", + "templates": [ + { + "$ref": "monomerTemplate-R___Ribose" + }, + { + "$ref": "monomerTemplate-T___Thymine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-U": { + "type": "monomerGroupTemplate", + "id": "U", + "name": "U", + "class": "RNA", + "templates": [ + { + "$ref": "monomerTemplate-R___Ribose" + }, + { + "$ref": "monomerTemplate-U___Uracil" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-MOE(A)P": { + "type": "monomerGroupTemplate", + "id": "MOE(A)P", + "name": "MOE(A)P", + "class": "RNA", + "idtAliases": { + "base": "2MOErA" + }, + "templates": [ + { + "$ref": "monomerTemplate-MOE___2'-O-Methoxyethyl ribose" + }, + { + "$ref": "monomerTemplate-A___Adenine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-MOE(5meC)P": { + "type": "monomerGroupTemplate", + "id": "MOE(5meC)P", + "name": "MOE(5meC)P", + "class": "RNA", + "idtAliases": { + "base": "2MOErC" + }, + "templates": [ + { + "$ref": "monomerTemplate-MOE___2'-O-Methoxyethyl ribose" + }, + { + "$ref": "monomerTemplate-5meC___5-methyl-cytidine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-MOE(G)P": { + "type": "monomerGroupTemplate", + "id": "MOE(G)P", + "name": "MOE(G)P", + "class": "RNA", + "idtAliases": { + "base": "2MOErG" + }, + "templates": [ + { + "$ref": "monomerTemplate-MOE___2'-O-Methoxyethyl ribose" + }, + { + "$ref": "monomerTemplate-G___Guanine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-MOE(T)P": { + "type": "monomerGroupTemplate", + "id": "MOE(T)P", + "name": "MOE(T)P", + "class": "RNA", + "idtAliases": { + "base": "2MOErT" + }, + "templates": [ + { + "$ref": "monomerTemplate-MOE___2'-O-Methoxyethyl ribose" + }, + { + "$ref": "monomerTemplate-T___Thymine" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + }, + "monomerGroupTemplate-dR(U)P": { + "type": "monomerGroupTemplate", + "id": "dR(U)P", + "name": "dR(U)P", + "class": "RNA", + "idtAliases": { + "base": "deoxyU" + }, + "templates": [ + { + "$ref": "monomerTemplate-dR___Deoxy-Ribose" + }, + { + "$ref": "monomerTemplate-U___Uracil" + }, + { + "$ref": "monomerTemplate-P___Phosphate" + } + ] + } +} \ No newline at end of file diff --git a/api/wasm/indigo-ketcher/test/test.js b/api/wasm/indigo-ketcher/test/test.js index 54e77138c4..e2ee55b655 100644 --- a/api/wasm/indigo-ketcher/test/test.js +++ b/api/wasm/indigo-ketcher/test/test.js @@ -952,10 +952,14 @@ M END test("IDT", "basic", () => { var fs = require('fs'); let options = new indigo.MapStringString(); + const monomersLib = fs.readFileSync("monomer_library.ket"); options.set("output-content-type", "application/json"); options.set("input-format", "chemical/x-idt"); - const idt = "mA*mGC"; - const res_ket = JSON.parse(indigo.convert(idt, "ket", options)).struct; + options.set("monomerLibrary",monomersLib); + const idt = "/5Phos/mA*mGC/i2MOErA//3Phos/"; + const res = indigo.convert(idt, "ket", options); + const res_ket = JSON.parse(res).struct; + // fs.writeFileSync("idt_maxmgc.ket", res_ket); const res_ket_ref = fs.readFileSync("idt_maxmgc.ket"); assert.equal(res_ket, res_ket_ref.toString().trim()); let save_options = new indigo.MapStringString(); diff --git a/core/indigo-core/molecule/monomers_lib.h b/core/indigo-core/molecule/monomers_lib.h index 1e0c193c85..e666b86bff 100644 --- a/core/indigo-core/molecule/monomers_lib.h +++ b/core/indigo-core/molecule/monomers_lib.h @@ -212,10 +212,10 @@ namespace indigo MonomerTemplate() = delete; + MonomerTemplate(const MonomerTemplate& other); + MonomerTemplate(const std::string& id, MonomerClass mt_class, const std::string& class_HELM, const std::string& full_name, const std::string& alias, - const std::string& natural_analog, int tgroup_id, BaseMolecule& mol) - : _id(id), _class(mt_class), _class_HELM(class_HELM), _full_name(full_name), _alias(alias), _natural_analog(natural_analog), _tgroup_id(tgroup_id), - _mol(mol){}; + const std::string& natural_analog, int tgroup_id, BaseMolecule& mol); MonomerTemplate(const std::string& id, const std::string& mt_class, const std::string& class_HELM, const std::string& full_name, const std::string& alias, const std::string& natural_analog, int tgroup_id, BaseMolecule& mol); @@ -274,11 +274,6 @@ namespace indigo return _natural_analog; } - inline int TGroupId() const - { - return _tgroup_id; - } - inline void setIdtAlias(const IdtAlias& idt_alias) { _idt_alias = idt_alias; @@ -296,8 +291,7 @@ namespace indigo std::map _attachment_points; std::string molecule; IdtAlias _idt_alias; - int _tgroup_id; - BaseMolecule& _mol; + TGroup _tgroup; }; class DLLEXPORT MonomerGroupTemplate @@ -322,7 +316,7 @@ namespace indigo inline bool hasTemplateClass(MonomerClass monomer_class) { - for (auto id_template : _monomer_templates) + for (auto& id_template : _monomer_templates) { if (id_template.second.monomerClass() == monomer_class) return true; diff --git a/core/indigo-core/molecule/src/monomers_lib.cpp b/core/indigo-core/molecule/src/monomers_lib.cpp index ae44a5c478..e93aa71014 100644 --- a/core/indigo-core/molecule/src/monomers_lib.cpp +++ b/core/indigo-core/molecule/src/monomers_lib.cpp @@ -235,11 +235,25 @@ namespace indigo return MonomerClass::Unknown; } + MonomerTemplate::MonomerTemplate(const std::string& id, MonomerClass mt_class, const std::string& class_HELM, const std::string& full_name, + const std::string& alias, const std::string& natural_analog, int tgroup_id, BaseMolecule& mol) + : _id(id), _class(mt_class), _class_HELM(class_HELM), _full_name(full_name), _alias(alias), _natural_analog(natural_analog) + { + _tgroup.copy(mol.tgroups.getTGroup(tgroup_id)); + } + MonomerTemplate::MonomerTemplate(const std::string& id, const std::string& mt_class, const std::string& class_HELM, const std::string& full_name, const std::string& alias, const std::string& natural_analog, int tgroup_id, BaseMolecule& mol) - : _id(id), _class(StrToMonomerClass(mt_class)), _class_HELM(class_HELM), _full_name(full_name), _alias(alias), _natural_analog(natural_analog), - _tgroup_id(tgroup_id), _mol(mol) + : _id(id), _class(StrToMonomerClass(mt_class)), _class_HELM(class_HELM), _full_name(full_name), _alias(alias), _natural_analog(natural_analog) + { + _tgroup.copy(mol.tgroups.getTGroup(tgroup_id)); + } + + MonomerTemplate::MonomerTemplate(const MonomerTemplate& other) + : _id(other._id), _class(other._class), _class_HELM(other._class_HELM), _full_name(other._full_name), _alias(other._alias), + _natural_analog(other._natural_analog), _idt_alias(other._idt_alias) { + _tgroup.copy(other._tgroup); } void MonomerTemplate::AddAttachmentPoint(const std::string& id, const std::string& ap_type, int att_atom, std::vector& leaving_group) @@ -270,7 +284,7 @@ namespace indigo const TGroup& MonomerTemplate::getTGroup() const { - return _mol.tgroups.getTGroup(_tgroup_id); + return _tgroup; } bool MonomerTemplate::hasIdtAlias(const std::string& alias, IdtModification mod)