Structural distortion occurs during multi expand and multi collapse of macromolecule abbreviations in Micro mode

[Zhirnoff]

Steps to Reproduce

1. Open file in Macro mode (Flex mode) monomers-cycled.zip
2. Switch to Micro mode
3. Select all monomers and expand it

Actual behavior
During the multi expand of macromolecule abbreviations, the resulting structure is severely distorted, with overlapping bonds, misplaced functional groups, and general structural misalignment, as shown in the attached screenshot. This makes the expanded structure unusable and difficult to interpret.

Same in not cycled chain:

After multi-collapse, abbreviations do not return to their original places but are crowded together

Expected behavior
The expanded macromolecules should retain their proper structure and alignment, with all components clearly displayed and positioned correctly.

Desktop:

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

Ketcher version
[Version 2.26.0-rc.1]
Indigo version
[Version 1.25.0-rc.1]
Bug found during testing: #5400

[Zhirnoff]

With multi-expand, the appearance has improved, but the structures are still disorganized, and bonds overlap with one another. The collapsing functionality, however, has been fixed—abbreviations now return to their original positions.

2025-01-02_12h27_25.mp4

2025-01-02_12h28_02.mp4

Desktop:

• OS: Windows 11
• Browser Chrome
• Version 131.0.6778.205 (Official Build) (64-bit)

Ketcher version
[Version 3.0.0-rc.1]
Indigo version
[Version 1.28.0-rc.1]

[svvald]

The refined algorithm for expanding monomers now utilizes the concept of "lines," which is the predominant method for representing monomers in micromolecular mode, particularly for RNA/DNA/Peptide sequences generated in macromolecular mode. The algorithm begins by traversing the monomer graph, starting from a designated monomer marked for expansion, and assesses whether each monomer aligns with the initial monomer. Monomers are considered aligned if their vertical coordinates are either equal to or within a specified delta (0.5 angstroms) of the initial monomer.

If a monomer is aligned with the initial monomer, it is shifted either to the left or right by half the width of the bounding box:

If a monomer is not aligned with the initial monomer, it is repositioned above or below it.

The following steps delineate the specifics of the vertical movement:
Identify the largest bounding box among already expanded monomers in the line.
Depending on its size relative to the bounding box of the monomer being expanded:

• If larger or equal, no vertical movement occurs to prevent creating unnecessary gaps between lines.

- If smaller, adjust the vertical movement distance based on the absolute difference in height between the two bounding boxes to fit exactly the new expanded monomer between lines without creating unnecessary space. - If no expanded monomers exist in the line, set the vertical movement distance to half the height of the monomer's bounding box to fit the expanded monomer between lines.

This method also applies to cyclic chains. Despite their circular structure, monomers can still be categorized by "lines" and manipulated according to the same algorithm as linear structures:

For RNA/DNA sequences, this algorithm also accommodates "complementary lines," focusing on bases that are complementary to the sugars. A base is considered part of a "complementary line" if its vertical coordinate differs by a larger delta (2 angstroms) and it is connected only once to a monomer from the "main line":

Complementary line monomers are not moved vertically if its main line monomer is expanded except for the case when monomer is placed directly below the monomer being expanded to avoid overlapping sugar and the base connected to it.
Complementary line monomers are moved horizontally when main line monomers are expanded to ensure the vertical alignment of bases and sugars persists.

(Note: This method currently has limitations and may not consistently produce accurate results for RNA/DNA sequences, specifically when applying multiple monomers expansion. Further improvements are necessary to stabilize its performance.)

For multiple monomers expansion the algorithm is applied for each selected monomer one by one.

In addition to expanding monomers, the algorithm is responsible for collapsing them. It uses the inverse of the movement used during expansion, ensuring that monomers revert to their original positions.