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Macro: N- C-ends /5' - 3' - ends display in peptide /RNA chains #3545

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olganaz opened this issue Nov 7, 2023 · 5 comments · Fixed by #3851
Closed

Macro: N- C-ends /5' - 3' - ends display in peptide /RNA chains #3545

olganaz opened this issue Nov 7, 2023 · 5 comments · Fixed by #3851

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@olganaz
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olganaz commented Nov 7, 2023

Background
It is useful for chemists and biologists to see the beginning and the end of the chain. For peptide chain usually N/C designations are used, for RNA chains - 5'/3'.
Ketcher will only display the beginnings of the chains so as not to overload the visual presentation.
"N- end" of the peptide chain should be marked.
"5' - end" of the RNA chain should be marked.

Requirements

In addition to current rules for numbering monomers #3222:

  1. For the peptide chain (made from at list two monomers), the first monomer (numbered 1) should be marked as the N-terminus (Symbol 'N' at the left side of monomer - near the R1 AP).
  2. For RNA chain, the sugar, connected to the base numbered 1, should be marked as 5' (Mark "5' " at the left side of monomer - near the R1 AP).
  3. Single nucleotide (sugar+base+phosphate) should not be marked with 5'
  4. If any monomer is connected to single nucleotide (for example, phosphate or CHEM), then this nucleotide should be marked with 5'.
  5. For mixed chains each monomer, numbered 1, should be marked as N for a peptide monomer, or as 5' for RNA according to the rules described in 1-3.

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for development

@olganaz olganaz added this to the Macromolecules Milestone 4 milestone Nov 7, 2023
@olganaz olganaz self-assigned this Nov 7, 2023
@olganaz olganaz changed the title N- C- и 5' - 3' - chains - draft [Macro] N- C- и 5' - 3' - chains - draft Nov 7, 2023
@olganaz olganaz changed the title [Macro] N- C- и 5' - 3' - chains - draft Macro: N- C-ends /5' - 3' - ends display in peptide /RNA chains - draft Dec 4, 2023
@olganaz olganaz changed the title Macro: N- C-ends /5' - 3' - ends display in peptide /RNA chains - draft Macro: N- C-ends /5' - 3' - ends display in peptide /RNA chains Dec 22, 2023
@olganaz olganaz assigned Andrey-Antonov and unassigned olganaz Dec 29, 2023
@Andrey-Antonov
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image

@Andrey-Antonov
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Andrey-Antonov commented Jan 5, 2024

image

StarlaStarla added a commit that referenced this issue Jan 9, 2024
@Zhirnoff
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Zhirnoff commented Jan 9, 2024

Tests added to automation table.

@Zhirnoff
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Pretested. No comments.

rrodionov91 added a commit that referenced this issue Jan 12, 2024
…ns (#3851)

Co-authored-by: Roman Rodionov <roman_rodionov@epam.com>
@Zhirnoff
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Tested.

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5 participants