#8898 Selection ignored in Ketcher API calls

[Copilot]

How the feature works? / How did you fix the issue?

Selection data in KET files is preserved through the initiallySelected flag on atoms/bonds during deserialization. The UI's "Open as New Project" workflow restores this selection after loading, but the API methods (setMolecule, addFragment) did not.

Changes:

• Added getSelectionFromStruct() helper that extracts selection from entities with initiallySelected flags
• Updated setMolecule() and addFragment() to restore selection after loading and clean up flags

Before:

await ketcher.setMolecule(ketFileWithSelection);
// Selection is lost - initiallySelected flags set but never used

After:

await ketcher.setMolecule(ketFileWithSelection);
// Selection properly restored and flags cleaned up

Check list

• unit-tests written
• e2e-tests written
• documentation updated
• PR name follows the pattern #1234 – issue name
• branch name doesn't contain '#'
• PR is linked with the issue
• base branch (master or release/xx) is correct
• task status changed to "Code review"
• reviewers are notified about the pull request

Original prompt

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This section details on the original issue you should resolve

<issue_title>Selection ignored in Ketcher API calls</issue_title>
<issue_description>Steps to Reproduce

1. Open Ketcher
2. Open browser dev tools
3. Call Ketcher setMolecule or addFragment api and pass ket file with selected atoms and bonds to it.
   example.ket.zip

Actual behavior
Molecule drawn on canvas, but atoms and bonds are not selected.

Expected behavior
Atoms and bonds are selected.

Ketcher version [e.g. v2.4.2].
3.11.0-rc.2

Additional context
It works as expected with same ket file if it is opened through Ketcher UI "Open file" > "Open as New Project"</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Selection ignored in Ketcher API calls #8898

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