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Add ambiguous monomers to the library and allow their addition to the canvas #5186

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ljubica-milovic opened this issue Jul 29, 2024 · 1 comment · Fixed by #5358
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Requirements Done Test Cases Written Test cases has been written for that issue variant_monomers

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@ljubica-milovic
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ljubica-milovic commented Jul 29, 2024

Background
In addition to importing/exporting ambiguous monomers and supporting them on the canvas, some standard ambiguous monomers should be added to the library and the users should be able to add them to the canvas form the library.

Requirements

  1. In the peptides section of the library a new subsection should be added with the title "Ambiguous Amino Acids"
    1.1. The subsection should be placed on the bottom of all the other subsections (bellow tyrosine).
    1.2. The ambiguous monomers from the table bellow should be be added.
    1.3. The first monomer is X, and the others are arranged alphabetically.
    1.4. Class of these monomers is "AminoAcid"
    1.5. These monomers are "Alternatives".
Symbol Monomers that make up the ambiguous monomer
B D (aspartic acid), N (asparagine)
J L (leucine), I (isoleucine)
Z E (glutamic acid), Q (glutamine)
X Any Amino Acid, A (Alanine), C (cysteine), D (aspartic acid), E (glutamic acid), F (phenylalanine), G (glycine), H (histidine), I (isoleucine), K (lysine), L (leucine), M (methionine), N (asparagine), O (pyrrolysine), P (proline), Q (glutamine), R (arginine), S (serine), T (threonine), U (selenocysteine), V (valine), W (tryptophan), Y (tyrosine)
  1. In the bases section of the library (under RNA tab) a new subsections should be added with the title "Ambiguous Bases", "Ambiguous DNA Bases" and "Ambiguous RNA Bases" (in that order).
    2.1. The subsections should be placed on the bottom of all the other subsections (bellow bases with natural analogue X).
    2.2. The ambiguous monomers from the table bellow should be be added to appropriate sections (DNA bases to "Ambiguous DNA Bases", RNA bases to "Ambiguous RNA Bases", and Both bases to "Ambiguous Bases").
    2.3. The first monomer in RNA and DNA sections is N, every other monomer should be arranged alphabetically.
    2.4. Class of these monomers is "Base"
    2.5. These monomers are "Alternatives".
Symbol Monomers that make up the ambiguous DNA/RNA/Both
R A (adenine), G (guanine) Both
Y C (cytosine), T (thymine) DNA
Y C (cytosine), U (uracil) RNA
S G (guanine), C (cytosine) Both
W A (adenine), T (thymine) DNA
W A (adenine), U (uracil) RNA
K G (guanine), T (thymine) DNA
K G (guanine), U (uracil) RNA
M A (adenine), C (cytosine) Both
B C (cytosine), G (guanine), T (thymine) DNA
B C (cytosine), G (guanine), U (uracil) RNA
D A (adenine), G (guanine), T (thymine) DNA
D A (adenine), G (guanine), U (uracil) RNA
H A (adenine), C (cytosine), T (thymine) DNA
H A (adenine), C (cytosine), U (uracil) RNA
V A (adenine), C (cytosine), G (guanine) Both
N Any base, A (adenine), C (cytosine), G (guanine), T (thymine) DNA
N Any base, A (adenine), C (cytosine), G (guanine), U (uracil) RNA
  1. The user should be able to add the ambiguous monomers to the canvas just like all other monomers in the library, and preform all canvas operations (Related issue: #4554)

UX
355820472-b11d6e03-148e-460e-a3d2-9918f1988c4e

@ljubica-milovic ljubica-milovic added this to the Ketcher 2.25.0-rc.1 milestone Jul 29, 2024
@Zhirnoff Zhirnoff added the Test Cases Written Test cases has been written for that issue label Aug 13, 2024
@rrodionov91 rrodionov91 self-assigned this Aug 14, 2024
@ljubica-milovic ljubica-milovic changed the title Add variant monomers to the library and allow their addition to the canvas Add ambiguous monomers to the library and allow their addition to the canvas Aug 26, 2024
rrodionov91 added a commit that referenced this issue Aug 26, 2024
…n to the canvas

- added ambiguous monomers to the library
rrodionov91 added a commit that referenced this issue Aug 26, 2024
…n to the canvas

- added ambiguous monomers to the library
rrodionov91 added a commit that referenced this issue Aug 27, 2024
…n to the canvas

- added ambiguous monomers to the library
rrodionov91 added a commit that referenced this issue Aug 27, 2024
…n to the canvas (#5358)

- added ambiguous monomers to the library
- updated screenshots
@Zhirnoff
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Zhirnoff commented Sep 6, 2024

Tested.
2024-09-06_11h24_11
2024-09-06_11h24_41
2024-09-06_11h25_29

Desktop:

  • OS: Windows 11
  • Browser Chrome
  • Version 128.0.6613.120 (Official Build) (64-bit)

Ketcher version
[Version 2.25.0-rc.1]
Indigo version
[Version 1.24.0-rc.1]

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3 participants