Introduce hydrogen bonds in macromolecules mode

[ljubica-milovic]

Background
It is hard to overestimate the importance of hydrogen bonds in macromolecules. They are crucial for the stability and function of macromolecules, and their existence allows the life to function as it does.

	Proteins	Nucleic acids
Primary structure	Linear sequence of amino acids linked by peptide bonds (R1-R2)	Linear sequence of nucleotides, linked by phosphodiester bonds (R1-R2 sugar-phosphate)
Secondary structure	Local folding patterns like alpha helices and beta sheets, stabilized by hydrogen bonds	Local nucleotide interactions like the double helix of DNA and hairpin loops of RNA, stabilized by hydrogen bonds of complementary nucleotides
Tertiary structure	Overall 3D structure of a single polypeptide chain, stabilized by disulfide bridges (R3-R3 cysteine-cysteine), salt bridges, hydrophilic/phobic interactions, and hydrogen bonds	Overall 3D structure of a single nucleotide chain, stabilized by ionic interactions, hydrophilic/phobic interactions, base stacking, and hydrogen bonds
Quaternary structure	Interactions between multiple polypeptide chains, stabilized by, among other interactions, hydrogen bonds	Interactions between multiple nucleic acid chains and/or polypeptide chains, stabilized by, among other interactions, hydrogen bonds

For these reasons, it is very important to introduce hydrogen bonds in Ketcher. Users will be able to represent macromolecules with a higher level of detail and precision.

Requirements

1. User should be able to save macromolecules structures with hydrogen bonds to a .ket file.

2. User should be able to load macromolecules structures with hydrogen bonds from a .ket file.

3. The user should be able to select "Hydrogen Bond" from the bond menu in the sidebar (the same behavior like in micromolecules mode).

4. User is able to establish hydrogen bonds between any two monomers who are not connected via a single bond.
   4.1. Hydrogen bonds do not require attachment points - they are ambiguous connections.
   4.2. Only one hydrogen bond is allowed to be established between two monomers.
   4.2.1. If the user tries to establish a hydrogen bond between two monomers who already have a hydrogen bond, they should get an error message: "Unable to establish multiple hydrogen bonds between two monomers".
   4.2.2. If the user tires to establish a hydrogen bond between two monomers who are connected via a single bond, they should get an error message: "Unbale to establish a hydrogen bond between two monomers connected with a single bond".
   4.3. Hydrogen bonds should be treated as side-chain connections for layout purposes.

5. Unlike single bonds, there should not be a "Edit Connection Points" dialogue for hydrogen bonds, or a bond preview.
   5.1. Hovering over the hydrogen bond should result only in highlighting of the hydrogen bond and the monomers, excluding the attachment points of those monomers.

For example: a hydrogen bond is between two bases -> hovering over the hydrogen bond should highlight the bond (single bond used for the exmple)

and the highlight of the monomer

6. When switching from macromolecules mode (where there are hydrogen bonds) to small molecules mode, and one of the monomers gets expanded, the hydrogen bond should temporarily disappear (switching back to macromolecules mode, the hydrogen bond should still be there).

7. User shouldn't be able to establish hydrogen bonds with small molecules in macromolecules mode (both between two small molecules and between a small molecule and a monomer).

Many functionalities covered by requirements 4, 5, 6 and 7 will be amended later. This is just the introduction of hydrogen bonds and in the simplest way that still makes sense.
First ticket that will ament certain behaviors descried here (the layouting): #5712

UX
TBD

[AlexeyGirin]

Verified.

• Ketcher Version 2.27.0-rc.1 Build at 2024-11-05; 14:55:18
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