Indigo issues

Isoelectric Point calculation should take into account occupied leaving groups (exclude them)

**Steps to Reproduce** 1. Go to Macromolecules mode - Flex canvas (empty) 2. Load from HELM: `PEPTIDE1{C}|PEPTIDE2{C}|PEPTIDE3{C}|PEPTIDE4{C}|PEPTIDE5{C.C}|PEPTIDE6{C}|PEPTIDE7{C}$PEPTIDE2,PEPTIDE1,1:R3-1:R3|PEPTIDE4,PEPTIDE3,1:R2-1:R2|PEPTIDE6,PEPTIDE7,1:pair-1:pair$$$V2.0` ![Image](https://github.com/user-attachments/assets/76345bf7-f7ad-4cd1-834d-ef3eb37e4214) 3. Open Calculate properties (press `Alt+C`) 4. Select each chain **Actual behavior**...

AlexeyGirin

Priority: Medium

Severity: Medium

Atom weights in indigo should be updated according to last IUPAC data

1

**Steps to Reproduce** 1. Go to Macromolecules mode - Flex canvas (empty) 2. Load from HELM: `CHEM1{[CCC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(CNC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(C(NC(CNC(C(NC(C(NC(C(N)CC1NC=NC=1)=O)(C)C)=O)CCC(O)=O)=O)=O)C(O)C)=O)CC1C=CC=CC=1)=O)C(O)C)=O)CO)=O)CC(O)=O)=O)C(C)C)=O)CO)=O)CO)=O)CC1C=CC(O)=CC=1)=O)CC(C)C)=O)CCC(O)=O)=O)=O)CCC(N)=O)=O)C)=O)C)=O)CCCCNC(COCCOCCNC(COCCOCCNC(CCC(NC(CCCCCCCCCCCCCCCCC(O)=O)=O)C(O)=O)=O)=O)=O)=O)CCC(O)=O)=O)CC1C=CC=CC=1)=O)C(NC(C(NC(C(NC(C(NC(C(NC(C(NCC(NC(C(NCC(O)=O)=O)CCCNC(N)=N)=O)=O)CCCNC(N)=N)=O)C(C)C)=O)CC(C)C)=O)CC1C2C(=CC=CC=2)NC=1)=O)C)=O)C]}$$$$V2.0` ![Image](https://github.com/user-attachments/assets/ddcb0f9d-f9cd-4027-a1aa-3c368f77988e) 3. Open Calculate properties (press `Alt+C`) **Actual behavior** Molecular mass is `4113.578`...

AlexeyGirin

Priority: Medium

Severity: Medium

System shouldn't allow to export molecules to 3-letter sequence format

**Steps to Reproduce** 1. Go to Macromolecules mode - Flex canvas (empty) 2. Load from KET: [System shouldn't allow to export molecules to 3-letter sequence format.zip](https://github.com/user-attachments/files/20552958/System.shouldn.t.allow.to.export.molecules.to.3-letter.sequence.format.zip) ![Image](https://github.com/user-attachments/assets/34cc0b10-ec9c-4c4a-9d62-abce74899f94) 3. Export canvas...

AlexeyGirin

Priority: Medium

Export to Sequence

Ljubica found bugs

Severity: Medium

System loads base as sugar

**Steps to Reproduce** 1. Go to Macromolecules mode - Flex mode (empty canvas) 2. Load from HELM: `RNA1{(A)}$$$$V2.0` **Actual behavior** System loads base as sugar ![Image](https://github.com/user-attachments/assets/681bbdee-2066-4362-ae82-ae9d0fe249c4) **Expected behavior** System loads...

AlexeyGirin

Priority: Medium

HELM

Severity: Medium

Reaction data support in KET-format

**Background** In the current version of the KET format, reactions are represented as a collection of saved molecules, arrows, and plus signs, without retaining information about the specific roles of...

even1024

Test Cases Written

Support new colours of nucleobases and nucleotides on SVG export

**Background** [Issue on Ketchers side.](https://github.com/epam/ketcher/issues/7221) **Requirements** 1. Adenine, and all bases and nucleotides with the natural analogue A, should have their colour changed to [TBD1]. 2. Cytosine, and all bases...

ljubica-milovic

Export to SVG/PNG

Bump h11 from 0.14.0 to 0.16.0 in /api/http

1

Bumps [h11](https://github.com/python-hyper/h11) from 0.14.0 to 0.16.0. Commits 1c5b075 this time for surer d9c3699 this time for sure... d91b9dd blacken 5a4683c Soothe mypy 9c9567f Bump version to 0.16.0 114803a Merge commit...

dependabot[bot]