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Change names of monomers (Peptides and CHEMs) #4781

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ljubica-milovic opened this issue Jun 6, 2024 · 2 comments · Fixed by #5178
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Change names of monomers (Peptides and CHEMs) #4781

ljubica-milovic opened this issue Jun 6, 2024 · 2 comments · Fixed by #5178
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feature request Monomer Library Test Cases Written Test cases has been written for that issue
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Ketcher 2.24.0-rc.1

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ljubica-milovic commented Jun 6, 2024 •
edited by AlexeyGirin
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Change the names of following peptides and CHEMs in the library (symbol, (new symbol), old name -> new name):

  • Az, Azide -> 4-azidobutyric acid
  • hxy, Hexynyl alcohol -> 5-hexyn-1-ol
  • SMCC, SMCC linker from Pierce -> SMCC 
  • SMPEG2, SM(PEG)2 linker from Pierce -> SM(PEG)2
  • Ala-ol, (2S)-2-aminopropan-1-ol -> L-Alaninol
  • Cya, 3-sulfoalanine -> Cysteic acid
  • D-2Nal, D-3-naphthylalanine -> D-3-(2-naphtyl)-alanine
  • D-2Thi, D-3-thienylalanine -> 3-(2-thienyl)-D-alanine
  • D-Cha, D-2-Amino-3-cyclohexyl-propionic acid -> 3-cyclohexyl-D-alanine
  • D-OAla, (2R)-2-hydroxypropanoic acid -> D-Lactic acid
  • DAlaol, (2R)-2-aminopropan-1-ol -> D-alaninol
  • Dha, 2-aminoprop-2-enoic acid -> Dehydroalanine
  • Nal, 2Nal, 3-naphthylalanine -> 3-(2-naphthyl)-alanine
  • Thi, 3-thienylalanine -> 3-(2-thienyl)-alanine
  • Tza, 3-thiazolyalanine -> 3-(4-Thiazolyl)-alanine
  • seC, U, SelenoCysteine -> Selenocysteine
  • Cys_Bn, (2R)-2-amino-3-(benyulsulfanyl)propanoic acid -> S-benzylcysteine
  • Cys_Me, (2R)-2-amino-3-(methylsulfanyl)propanoic acid -> S-methylcysteine
  • dSec, dU, D-SelenoCysteine -> D-selenocysteine
  • AspOH, D*, Aspartic acid (OH) -> Aspartic acid*
  • AspOh2, Kyn, (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid -> Kynurenine
  • aMePhe, (2S)-2-amino-2-methyl-3-phenylpropanoic acid -> alpha-methyl-L-phenylalanine
  • DAPhe, PhLA, Deamino-Phenylalanine -> 3-phenyllactic acid
  • DPhe4F, (2R)-2-amino-3-(4-fluorophenyl)propanoic acid -> 4-fluoro-D-phenylalanine
  • Phe_2F, (2S)-2-amino-3-(2-fluorophenyl)propanoic acid -> 2-fluoro-L-phenylalanine
  • Phe_3F, (2S)-2-amino-3-(3-fluorophenyl)propanoic acid -> 3-fluoro-L-phenylalanine
  • Phe_4F, (2S)-2-amino-3-(4-fluorophenyl)propanoic acid -> 4-fluoro-L-phenylalanine
  • Phe_4I, (2S)-2-amino-3-(4-iodophenyl)propanoic acid -> 4-iodo-L-phenylalanine
  • Phe-ol, (2S)-2-amino-3-phenylpropan-1-ol -> L-phenylalaninol
  • Phe2Me, (2S)-2-amino-3-(2-methylphenyl)propanoic acid -> 2-methyl-L-phenylalanine
  • Phe34d, (2S)-2-amino-3-(3,4-dichlorophenyl)propanoic acid -> 3,4-dichloro-L-phenylalanine
  • Phe4Br, (2S)-2-amino-3-(4-bromophenyl)propanoic acid -> 4-bromo-L-phenylalanine
  • Phe4NO, (2S)-2-amino-3-(4-nitrophenyl)propanoic acid -> 4-nitro-L-phenylalanine
  • PheaDH, 2-amino-3-phenylprop-2-enoic acid -> Dehydrophenylalanine
  • D-Phg, D-2-phenylglycine -> D-phenylglycine
  • DAGlyT, 2-(thiophen-2-yl)aceti acid -> 2-thiopheneacetic acid
  • DAPhg4, 2-(4-chlorophenyl)acetic acid -> 4-chlorophenylacetic acid
  • DPhgol, 2-amino-2-methylpropan-1-ol -> D-phenylglycinol
  • Phg, 2-phenylglycine -> L-phenylglycine
  • Phg-ol, (2S)-2-amino-phenylethan-1-ol -> L-phenylglycinol
  • Sar, meG, sarcosine (N-methylglycine -> Sarcosine 
  • His1Me, (2S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid -> 1-methyl-L-histidine
  • His3Me, (2S)-2-amino-3-(1-methyl-1H-imidazol-5-yl)propanoic acid -> 3-methyl-L-histidine
  • DALys, Deamino-Lysine -> 6-amino-2-hydroxyhexanoic acid
  • dPyl, dO, DPyl -> D-pyrrolysine
  • Lys_Ac, (2S)-2-amino-6-acetamidohexanoic acid -> N-epsilon-acetyl-L-lysine
  • Pyl, O, Pyl -> Pyrrolysine
  • DALeu, Deamino-Leucine -> 4-methylpentanoic acid
  • Leu-ol, (2S)-2-amino-4-methylpentan-1-ol -> L-leucinol
  • OLeu, (2S)-2-hydroxy-4-methylpentanoic acid -> L-leucic acid
  • DMetSO, (2R)-2-amino-4-[(S)-metanesulfinyl]butanoic acid  -> L-methionine (S)-S-oxide
  • Met_O, (2S)-2-amino-4-methanesulfinylbutanoic acid -> L-methionine sulfoxide
  • Met_O2, (2S)-2-amino-4-methanesulfonylbutanoic acid -> L-methionine sulfone
  • aHyp, L-allo-4-hydroxyproline -> cis-4-hydroxy-L-proline
  • aMePro, (2S)-2-methylpyrrolidine-2-carboxylic acid -> alpha-methyl-L-proline
  • D-aHyp, D-allo-4-hydroxyproline -> cis-4-hydroxy-D-proline
  • D-Hyp, D-4-hydroxyproline -> trans-4-hydroxy-D-proline
  • DProol, [(2R)-pyrrolidin-2-yl]methanol -> D-prolinol
  • Hyp, 4-hydroxyproline -> trans-4-hydroxy-L-proline
  • Mhp, 4-methyl-3-hydroxyproline -> 3-hydroxy-4-methylproline
  • Pro-ol, [(2S)-pyrrolidin-2-yl]methanol -> L-prolinol
  • xiHyp, (2S)-4-hydroxypyrrolidine-2-carboxylic acid -> 4-hydroxy-L-proline
  • Arg-al, N"-[(4S)-4-amino-5-oxopentyl]guanidine -> Argininal
  • D-hArg, (2R)-2-amino-6-[(diaminomethylidene)amino]hexanoic acid -> D-homoarginine
  • SerPO3, (2S)-2-amino-3-(phosphonooxy)propanoic acid -> O-phospho-L-serine
  • DThrol, (2R,3R)-2-aminobutane-1,3-diol -> L-threoninol
  • Thr-ol, (2S,3S)-2-aminobutane-1,3-diol -> D-threoninol
  • ThrPO3, (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid -> O-phospho-L-threonine
  • D-OVal, (2R)-2-hydroxy-3-methylbutanoic acid -> D-2-hydroxyisovaleric acid
  • D-Pen, D-penicillamine (3-mercaptovaline) -> D-penicillamine
  • L-OVal, (2S)-2-hydroxy-3-methylbutanoic acid -> 2-hydroxyisovaleric acid
  • Pen, penicillamine (3-mercaptovaline) -> Penicillamine
  • Tle, tLeu, 3-methylvaline -> L-tert-leucine
  • Val-ol, (2S)-2-amino-3-methylbutan-1-ol -> L-valinol
  • Val3OH, (2S)-2-amino-3-hydroxy-3-methylbutanoic acid -> 3-hydroxy-L-valine
  • DTrp2M, (2R)-2-amino-3-(2-methyl-1H-indol-3-yl)propanoic acid -> 2-methyl-D-tryptophan
  • DTrpFo, (2R)-2-amino-3-(1-formyl-1H-indol-3-yl)propanoic acid -> 1-formyl-D-tryptophan
  • Trp_Me, (2S)-2-amino-3-(1-methyl-1H-indol-3-yl)propanoic acid -> 1-methyl-L-tryptophan
  • Trp5OH, (2S)-2-amino-3-(5-hydroxy-1H-indol-3-yl)propanoic acid -> 5-hydroxy-L-tryptophan
  • -Bn, C-Terminal toluene -> C-Terminal benzyl
  • -NHBn, C-Terminal 1-phenylmethaneamine -> C-Terminal benzylamino
  • 2Abz, 2-Aminobenzoic acid -> Anthranilic acid
  • Aad, 2-aminoadipic acid -> L-2-aminoadipic acid
  • Abu, 2-aminobutanoic acid -> L-2-aminobutyric acid
  • Abu23D, 2-aminobut-2-enoic acid -> (2Z)-2-aminobut-2-enoic acid
  • ac, Ac-, N-Terminal Acetic Acid -> N-Terminal acetyl
  • Ac6c, 1-aminocyclohexane-1-carboxylic acid -> Homocycloleucine
  • Aca, 2-aminocapric acid -> L-decyline
  • Aib, alpha-aminoisobutyric acid (2-aminoalanine) -> 2-aminoisobutyric acid
  • am, Am-, C-Terminal amine -> C-Terminal amino
  • Amp, 2-aminopimelic acid -> L-2-aminopimelic acid
  • App, gamma-amino-beta-hydroxybenzeneptanoic acid -> (3R,4S)-4-amino-3-hydroxy-5-phenylpentanoic acid
  • Asu, 2-aminosuberic acid -> (R)-2-aminooctanedioic acid
  • Aze, 2-carboxyazetidine -> L-azetidine-2-carboxylic acid
  • Bip, (2S)-2-amino-3-{[1,1'-biphenyl]-4-yl}propanoic acid -> Biphenylalanine
  • Bmt, (2S,3R,4R)-2-amino-3-hydroxy-4-methyloct-6-enoic acid -> (2S,3R,4R,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid
  • Bn-, N-Terminal toluene -> N-Terminal benzyl
  • Boc, Boc-, Tert-butyloxycarbonyl -> N-Terminal tert-butyloxycarbonyl
  • Bpa, (2S)-2-amino-3-(4-benzoylphenyl)propanoic acid -> 4-benzoylphenylalanine
  • Bua, Bua-, butanoic acid -> N-Terminal butanoyl
  • Bux, 4-amino-3-hydroxybutanoic acid -> (3S)-4-amino-3-hydroxybutanoic acid
  • Bz, Bz-, Benzaldehyde -> N-Terminal benzoyl
  • Cap, gamma-amino-beta-hydroxycyclohexanepentanoic acid -> (2R,3S)-3-amino-2-hydroxy-5-cyclohexylpentanoic acid
  • Cbz, Cbz-, Carboxybenzyl -> N-Terminal carboxybenzyl
  • Cit, citrullin -> Citrulline
  • D-3-Pal, D-3-(2-pyridyl)-alanine -> D-3-(3-pyridyl)-alanine
  • D-Bmt, (2R,3S,4S)-2-amino-3-hydroxy-4-methyloct-6-enoic acid -> (2R,3S,4S,6E)-2-amino-3-hydroxy-4-methyloct-6-enoic acid
  • D-Cit, D-Citrullin -> D-citrulline
  • D-Dap, D-2,3-diaminopropanoic acid -> 3-amino-D-alanine
  • D-Dip, (2R)-2-amino-3,3-diphenylpropanoic acid -> 3,3-diphenyl-D-alanine
  • D-Thz, (4S)-1,3-thiazolidine-4-carboxylic acid -> D-thioproline
  • Dab, 2,4-diaminobutanoic acid -> L-2,4-diaminobutanoic acid
  • DANcy, 2-sulfanylacetic acid -> Thioglycolic acid
  • Dip, (2S)-2-amino-3,3-diphenylpropanoic acid -> 3,3-diphenylalanine
  • Dpr, Dap, 2,3-diaminopropanoic acid -> 3-aminoalanine
  • Dsu, 2,7-diaminosuberic acid (2,7-diaminooctanedioic acid) -> 2,7-diaminosuberic acid
  • fmoc, fmoc-, fmoc N-Terminal Protection Group -> N-Terminal fluorenylmethoxycarbonyl 
  • Hsl, (3S)-3-aminooxolan-2-one -> L-homoserine lactone
  • Hva, 2-hydroxypentanoic acid -> (2S)-2-hydroxypentanoic acid
  • Mba, mercaptobutanoic acid (GMBA) -> (2S)-2-mercaptobutyric acid
  • Mpa, mercaptopropanoic acid -> Thiolactic acid
  • MsO, MsO-, Mesylate -> N-Terminal methanesulfonyl
  • NHBn-, N-Terminal 1-phenylmethanamine -> N-Terminal benzylamino
  • NHEt, -NHEt, Ethaneamine -> C-Terminal ethylamino
  • NMe, -NMe, C-Termial NMe -> C-Terminal methylamino
  • OBn-, N-Terminal phenylmethanol -> N-Terminal benzyloxy
  • OBz, -OBn, C-Terminal OBz -> C-Terminal benzyloxy
  • OEt,  -OEt, Ethanol -> C-terminal ethoxy
  • Oic, 2-carboxyocthydroindole -> (2S)-perhydroindolic acid
  • Oic3aR, (2S,3aR,7aS)-octaxydro-1H-indole-2-carboxylic acid -> (2S,3aR,7aS)-perhydroindolic acid
  • Oic3aS, Perhydroindolic acid -> (2S,3aS,7aS)-perhydroindolic acid
  • OMe, -OMe, C-Terminal OMe -> C-Terminal methoxy
  • OMe-, N-Terminal methanol -> N-Terminal methoxy
  • OtBu, -OtBu, C-Terminal OtBu -> C-Terminal tert-butoxy
  • Oxa, C-Terminal Oxa -> 2‑oxazoline
  • Ph, -Ph, Phenyl -> C-terminal phenyl
  • Pqa, Piperazine quinazolinone acetic acid, 2-(4-oxo-6-piperazin-1-yl-quinazolin-3-yl)acetic acid -> 2-(4-xxo-6-(piperazin-1-yl)quinazolin-3(4H)-yl)acetic acid
  • Spg, Ar5c, 1-amino-1-carboxycyclopentane -> Cycloleucine
  • Sta, statin (4-amino-3-hydroxy-6-methylheptanoic acid) -> Statine
  • Thz, (4R)-1,3-thiazolidine-4-carboxylic acid -> L-thioproline
  • Tos, Tos-, Tosyl -> N-Terminal tosyl
  • Wil, alpha-amino-2,4-dioxopyrimidenepropanoic acid -> Willardiine
  • aMeTy3, (2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid -> L-methyldopa
  • aMeTyr, (2S)-2-amino-3-(4-hydroxyphenyl)-2-methylpropanoic acid -> L-metyrosine
  • D-nTyr, (2R)-2-amino-2-(4-hydroxyphenyl)acetic acid -> D-4-Hydroxyphenylglycine
  • DAnTyr, 2-(4-methoxyphenyl)acetic acid -> 4-methoxyphenylacetic acid
  • DTyr3O, (2R)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid -> D-methyldopa
  • DTyrEt, (2R)-2-amino-3-(4-ethoxyphenyl)propanoic acid -> O-ethyl-D-tyrosine
  • DTyrMe, (2R)-2-amino-3-(4-methoxyphenyl)propanoic acid -> O-methyl-D-tyrosine
  • nTyr, (2S)-2-amino-2-(4-hydroxyphenyl)acetic acid -> L-4-Hydroxyphenylglycine
  • Tyr_3I, (2S)-2-amino-3-(4-hydroxy-3-iodophenyl)propanoic acid -> 3-iodo-L-tyrosin
  • Tyr_Me, (2S)-2-amino-3-(4-methoxyphenyl)propanoic acid -> O-methyl-L-tyrosine
  • Tyr26d, (2S)-2-amino-3-(4-hydroxy-2,6-dimethylphenyl)propanoic acid -> 2,6-dimethyl-L-tyrosine
  • Tyr35d, (2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acid -> 3,5-diiodo-L-tyrosine
  • Try3NO, (2S)-2-amino-3-(4-hydroxy-3-nitrophenyl)propanoic acid -> 3-nitro-L-tyrosine
  • Tyr3OH, (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid -> 3-hydroxy-L-tyrosine
  • TyrabD, 2-amino-3-(4-methoxyphenyl)-prop-2-enoic acid -> (2E)-2-amino-3-(4-methoxyphenyl)-prop-2-enoic acid
  • TyrPO3, (2S)-2-amino-3-[4-(phosphonooxy)phenyl]propanoic acid -> O-phospho-L-tyrosine
  • TyrSO3, (2S)-2-amino-3-[4-(sulfooxy)phenyl]propanoic acid -> O-sulfo-L-tyrosine
@ljubica-milovic ljubica-milovic changed the title Monomers with incorrect names (priority: high) (IN PROGRESS) Monomers with incorrect names Jun 14, 2024
@ljubica-milovic ljubica-milovic changed the title Monomers with incorrect names Change names of monomers with incorrect names Jul 17, 2024
@ljubica-milovic ljubica-milovic changed the title Change names of monomers with incorrect names Change names of monomers (Peptides and CHEMs) Jul 24, 2024
@ljubica-milovic ljubica-milovic self-assigned this Jul 24, 2024
rrodionov91 added a commit that referenced this issue Jul 26, 2024
@rrodionov91
#4780 - Remove monomers form the library (Peptides and CHEMs)
e89120e 
#4781 - Change names of monomers (Peptides and CHEMs)

#5166 - Change symbols of monomers (Peptides and CHEMs)

#4787 - Change structure of monomers (Peptides and CHEMs)

#5167 - Change natural analogue of monomers Peptides and CHEMs)
@rrodionov91 rrodionov91 mentioned this issue Jul 26, 2024
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@rrodionov91 rrodionov91 linked a pull request Jul 26, 2024 that will close this issue
#4780 - Remove monomers form the library (Peptides and CHEMs) #5178
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rrodionov91 added a commit that referenced this issue Jul 29, 2024
@rrodionov91
#4780 - Remove monomers form the library (Peptides and CHEMs)
d6527c4 
#4781 - Change names of monomers (Peptides and CHEMs)

#5166 - Change symbols of monomers (Peptides and CHEMs)

#4787 - Change structure of monomers (Peptides and CHEMs)

#5167 - Change natural analogue of monomers Peptides and CHEMs)
rrodionov91 added a commit that referenced this issue Jul 29, 2024
@rrodionov91
#4780 - Remove monomers form the library (Peptides and CHEMs)
b7e6703 
#4781 - Change names of monomers (Peptides and CHEMs)

#5166 - Change symbols of monomers (Peptides and CHEMs)

#4787 - Change structure of monomers (Peptides and CHEMs)

#5167 - Change natural analogue of monomers Peptides and CHEMs)
rrodionov91 added a commit that referenced this issue Jul 29, 2024
@rrodionov91
#4780 - Remove monomers form the library (Peptides and CHEMs) (#5178)
4e504c5 
#4780 - Remove monomers form the library (Peptides and CHEMs)
#4781 - Change names of monomers (Peptides and CHEMs)
#5166 - Change symbols of monomers (Peptides and CHEMs)
#4787 - Change structure of monomers (Peptides and CHEMs)
#5167 - Change natural analogue of monomers Peptides and CHEMs)

- fixed tests and updated screenshots
- updated screenshots
@AlexeyGirin AlexeyGirin mentioned this issue Jul 31, 2024
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Fixed.

  • Ketcher Version 2.23.0-rc.3 Build at 2024-07-31; 05:31:01
  • Indigo Toolkit Version 1.23.0-dev.2.1-gd93b8ec4-wasm32-wasm-clang-12.0.0
  • Windows 10 Pro
  • Chrome Version 127.0.6533.89 (Official Build) (64-bit)

@AlexeyGirin AlexeyGirin added the Test Cases Written Test cases has been written for that issue label Aug 1, 2024
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Test cases are not needed for that issue

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#4780 - Remove monomers form the library (Peptides and CHEMs) epam/ketcher
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