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Change symbols of monomers (Peptides and CHEMs) #5166

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ljubica-milovic opened this issue Jul 24, 2024 · 2 comments · Fixed by #5178
Closed
33 tasks done

Change symbols of monomers (Peptides and CHEMs) #5166

ljubica-milovic opened this issue Jul 24, 2024 · 2 comments · Fixed by #5178
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@ljubica-milovic
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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
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ljubica-milovic commented Jul 24, 2024 •
edited by AlexeyGirin

Change the symbols of following peptides and CHEMs in the library (name, (new name), old symbol-> new symbol):

  • beta-Alanine, Bal -> bAla
  • 3-naphthylalanine, 3-(2-naphthyl)-alanine, Nal -> 2Nal
  • SelenoCysteine, Selenocysteine, seC -> U
  • D-SelenoCysteine, D-selenocysteine, dSec -> dU
  • Aspartic acid (OH), Aspartic acid*, AspOH -> D*
  • (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid, Kynurenine, AspOh2 -> Kyn
  • gamma-glutamic acid, Ggu -> gGlu
  • Deamino-Phenylalanine, 3-phenyllactic acid, DAPhe -> PhLA
  • sarcosine (N-methylglycine), Sarcosine, Sar -> meG
  • DPyl, D-pyrrolysine, dPyl -> dO
  • 5-hydroxylysine, Hyl -> Hyl5xi
  • Pyl, Pyrrolysine, Pyl -> O
  • epsilon-N-trimethyllysine, Tml -> LysMe3
  • 3-methylvaline, L-tert-leucine, Tle -> tLeu
  • N-Terminal Acetic Acid, N-Terminal acetyl, ac -> Ac-
  • C-Terminal amine, C-Terminal amino, am -> Am-
  • Tert-butyloxycarbonyl, N-Terminal tert-butyloxycarbonyl, Boc -> Boc-
  • butanoic acid, N-Terminal butanoyl, Bua -> Bua-
  • Benzaldehyde, N-Terminal benzoyl, Bz -> Bz-
  • Carboxybenzyl, N-Terminal carboxybenzyl, Cbz -> Cbz-
  • 2,3-diaminopropanoic acid, 3-aminoalanine, Dpr -> Dap
  • fmoc N-Terminal Protection Group, N-Terminal fluorenylmethoxycarbonyl, fmoc -> fmoc-
  • lactic acid, Lac -> L-OAla
  • Mesylate, N-Terminal methanesulfonyl, MsO ->MsO-
  • Ethaneamine, C-Terminal ethylamino, NHEt -> -NHEt
  • C-Termial NMe, C-Terminal methylamino, NMe -> -NMe
  • C-Terminal OBz, C-Terminal benzyloxy , OBz -> -OBn
  • Ethanol, C-terminal ethoxy, OEt -> -OEt
  • C-Terminal OMe, C-Terminal methoxy, OMe -> -OMe
  • C-Terminal OtBu, C-Terminal tert-butoxy, OtBu -> -OtBu
  • Phenyl, C-terminal phenyl, Ph -> -Ph
  • 1-amino-1-carboxycyclopentane, Cycloleucine, Spg -> Ar5c
  • Tosyl, N-Terminal tosyl, Tos -> Tos-
@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
Merged
9 tasks
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
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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 Jul 31, 2024
@AlexeyGirin
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No test cases needed for that particular case

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