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Introduce to .ket file specification attachment point information for super atoms #2765

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kaluginserg opened this issue Jun 13, 2023 · 0 comments · Fixed by #2823 or #2919
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kaluginserg commented Jun 13, 2023

Background

In this task - the main area is .ket format upgradation and it's Ketcher implementation.
Connected task: #2467 - support SAP instruction for format mol v2000 by Ketcher (+internal data model and Ketcher behavior)

Solution

  • update the specification for .ket file format
    • on the sgroup level we need to store information about attachment points.
    • attachment point id
    • attachment point leaving atom id
    • attachment point additional information
  • update .ket serializer in Ketcher (save file)
  • update .ket deserializer in Ketcher (open file)

Refs

As an example of the attachment point attributes:
Link to the CTFiles format explanation: http://c4.cabrillo.edu/404/ctfile.pdf (2005)
Section: "Superatom Attachment Point", page 33

Acceptance criteria

  1. Ketcher should be able to open mol200 file with sgroup attachment point and then save the struct to .ket format (the "attachmentPoints" instruction should exist in the result file)
  2. Ketcher should be able to open .ket file with the "attachmentPoints" instruction and should display attachment point correctly in the contracted sgroup tooltip and also this attachment point should be the used as a connection with other structures.
@Nitvex Nitvex added this to the Ketcher 2.13.0-rc.1 milestone Jun 28, 2023
even1024 added a commit that referenced this issue Jul 2, 2023
…ntpoints

#2765 Introduce to .ket file specification attachment point information for super atoms
@even1024 even1024 reopened this Jul 2, 2023
@kaluginserg kaluginserg assigned kaluginserg and unassigned Nitvex Jul 3, 2023
kaluginserg added a commit that referenced this issue Jul 13, 2023
Nitvex added a commit that referenced this issue Jul 18, 2023
Nitvex added a commit that referenced this issue Jul 18, 2023
…int_information_for_super_atoms' of https://github.com/epam/ketcher into #2765-introduce_to_ket_file_specification_attachment_point_information_for_super_atoms
Nitvex added a commit that referenced this issue Jul 18, 2023
…tion for super atoms (#2919)

* #2765 - introduce to .ket file specification attachment point information for super atoms

* #2765 - refactor import statements for sGroupAttachmentPoint

* #2765 – Introduce to .ket file specification attachment point information for super atoms

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Co-authored-by: Nikita_Vozisov <Nikita_Vozisov@epam.com>
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