#8856 – Defining other monomer properties - presets in the monomer creation wizard

[Copilot]

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

Implements auto-property assignment for RNA preset components when mandatory fields are not user-provided (requirement 2.3.2.2).

Core Logic

Property Auto-Assignment

• Code: {presetCode}{suffix} where suffix = B (base), S (sugar), P (phosphate)
• Name: Defaults to Code
• Natural Analogue: Defaults to 'X' for bases
• Only triggered when mandatory fields are empty or whitespace-only

Hidden vs Visible Monomers

• Monomers marked hidden: true only when properties are auto-assigned
• User-filled properties → normal visible monomer in library
• Hidden monomers already filtered from UI (existing librarySlice.ts:482)

Attachment Point Leaving Groups

// Auto-assigns correct leaving atoms per component type
Base R1:       H
Sugar R2:      H  (phosphate connection)
Sugar R3:      O  (base connection, represents OH)
Phosphate R1:  O  (represents OH)

Implementation

Added helper functions:

• hasAllMandatoryPropertiesFilled(): Checks Code + Natural Analogue (if required)
• autoAssignPropertiesForHiddenMonomer(): Generates defaults
• getLeavingAtomForAttachmentPoint(): Maps component type + AP → leaving atom

Modified:

• validateRnaPresetWizard(): Skips validation when properties absent (allows auto-assignment)
• assignConnectionPointAtom(): Added leavingAtomLabel parameter

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>Defining other monomer properties - presets in the monomer creation wizard</issue_title>
<issue_description>## Background

This is an improvement to the previous logic contained in this ticket.

Requirements

$\color{Red}{\textbf{Entering the wizard}}$

❗ The requirements for this section contained in a separate ticket. ❗

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$\color{Red}{\textbf{Defining the monomers}}$

$\color{Pink}{\textbf{Defining the monomer structure}}$

❗ The requirements for this section contained in a separate ticket. ❗

$\color{Pink}{\textbf{Highlighting}}$

❗ The requirements for this section contained in a separate ticket. ❗

$\color{Pink}{\textbf{Additions to the structure}}$

❗ The requirements for this section contained in a separate ticket. ❗

$\color{Pink}{\textbf{Defining other monomer properties}}$

2.3. The user can choose not to define some (all except the structure) properties for some (or all) components.

2.3.1. If for a monomer component all mandatory properties are filled, that monomer will also be saved to the library (in addition to the preset).

2.3.2. If all mandatory properties are not defined, that monomer gets saved to the library with user-assigned and default-assigned properties, but is "hidden" from the user.

2.3.2.1. Any properties of the "hidden" monomers should not be used for uniqueness, or any other checks, in regards to creating and editing monomers.

2.3.2.2. The following monomer properties will be assigned automatically:

• Monomer type - based on if the user marked the monomer as base, sugar, or phosphate.

• Code - constructed from the preset code (for example abc) as abcB (for bases), abcS (for sugars), and abcP (for phosphates).

• Name - same as code.

• Natural analogue (for base only) - X by default.

• Attachment points:

  • If a base is present, the connection between sugar and base is formed between two APs: R1 with LGA H for the base, and R3 with LGA OH for the sugar.

  • If phosphate is present, the connection between sugar and phosphate is formed between two APs: R1 with LGA OH for the phosphate, and R2 with LGA H for the sugar.

• Structure - based on the structure marked as belonging to that monomer.

Expand for the step-by-step assignment of the APs

There are three types of presets: sugar(base)phosphate (1), sugar()phosphate (2), and sugar(base) (3).

1.1. Start by defining the phosphate and then base

Select the phosphate -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA OH.
Select the base -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA H.
Select the sugar -> it has two internal APs that we know are with the phosphate and the base -> Assign that AP with the phosphate as R2 with LGA H, and the AP with the base as R3 with LGA OH.

1.2. Start by defining the base and then phosphate

First and second steps from the previous workflow flipped.

1.3. Start by defining the phosphate then sugar

Select the phosphate -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA OH.
Select the sugar -> it has two internal APs, we know which is with the phosphate so we assign it as R2 with LGA H. The other one must be with a base so it is assigned as R3 with LGA OH.
Select the base -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA H.

1.4. Start by defining the base then sugar

Same logic as the previous workflow - we know what APs the sugar will have because one of the components is known.

1.5. Start by defining the sugar then phosphate

Select the sugar -> It has two internal APs, but we don't know which is used for base and which for phosphate. Assign the first one R2 with LGA H based on the number of the AA in the KET file, and the other one R3 with LGA OH.
Select the phosphate -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA OH.
If the bond between sugar and phosphate is not R2(H)-R1(OH), the APs of the sugar must be flipped.
Select the base -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA H.

1.6. Start by defining the sugar then base

Same logic from the previous workflow - the sugar APs are assigned by default, and then flipped after the base is defined if the bond between sugar and base is not R3(OH)-R1(H).

2.1. Start by defining the phosphate

Select the phosphate -> it has one internal AP that can only be with a sugar -> Assign that AP as R1 with LGA OH.
Select the sugar -> it has one internal AP that we know is with the phosphate -> Assign that AP as R2 with LGA H.

2.2. Star...

• Fixes Defining other monomer properties - presets in the monomer creation wizard #8775

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