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[RNA Structure] As Ketcher user I want to select RNA monomers from the monomer library

Alena Guznischeva edited this page Dec 16, 2021 · 1 revision
As I want so that
Ketcher polymer editor user to select RNA monomer from the monomer library I can use it as an element for building the RNA structure

1. Context

This user story represents the first step of the process of peptide creation in the Ketcher peptide editor.

Glossary: Peptide Glossary

3. Assumptions

ID Assumption
1 RNA monomers are used to create long chains
2 5 basic nucleotides are used to create the chain mostly. Then the chain can be modified to reflect the expected user's result.
3 It should be possible to immediately add RNA monomer from the library to the chain in the canvas when the special mode in enabled

4. Additional information (optional)

8. Acceptance Criteria

# User Group GIVEN WHEN THEN
1 Ketcher peptide editor User Peptide editor mode of the Ketcher enabled
AND
RNA monomer library section is selected
viewing on the tool panel I see the 5 basic Nucleotides in the Nucleotide section
AND
I can navigate to Nucleobase, Sugar, and Phosphate sections.
2 clicking on the monomer in the Nucleotides section of the RNA monomer library panel section this monomer is highlighted in the library panel
AND
is displayed in the Nucleotides section header
AND
short name of it's parts (Nucleobase, Sugar, Phosphate) are displayed in the headers of corresponding sections of RNA monomer library
3 Peptide editor mode of the Ketcher enabled
AND
RNA monomer library section is selected
AND
Nucleobase (or Sugar, or Phosphate) section is selected
clicking on the monomer in the Nucleobase (Sugar, Phosphate) section this monomer is highlighted in the list of monomers in the library panel
AND
is displayed in the Nucleobase (Sugar, Phosphate) section header
AND
corresponding part is replaced with newly selected monomer (Nucleobase, Sugar, Phosphate) in the header of Nucleotide section
4 Peptide editor mode of the Ketcher enabled
AND
there is selected Nucleotide in the RNA monomer library panel
AND
Nucleotide section is selected
clicking on the empty place of the canvas Ketcher adds to the canvas Nucleotide with the parts presented in the headers of the RNA library sections
AND
Ketcher displays all 3 parts of the Nucleotide separately on the canvas with bonds from Nucleobase to Sugar & bond from Phosphate to Sugar in accordance with the alignment rules
AND
the same monomer stays highlighted in the monomer library
AND
this newly added monomer is considered a chain with type RNA and this chain receives the number in accordance with the rules
AND
this monomer receives number 1 in the chain
5 Peptide editor mode of the Ketcher enabled
AND
there is selected Nucleotide in the RNA monomer library panel
AND
Nucleobase (or Sugar or Phosphate) section is selected
clicking on the empty place of the canvas Ketcher adds to the canvas Nucleobase (or Sugar or Phosphate) as single object similar to presented in the header of the section selected
AND
the same monomer stays highlighted in the monomer library
AND
this newly added monomer is considered a chain with type RNA and this chain receives the number in accordance with the rules
AND
this monomer receives number 1 in the chain
6 Peptide editor mode of the Ketcher enabled
AND
there is selected any section in the RNA monomer library panel
clicking on the simple RNA monomer on the canvas Ketcher replaces simple RNA monomer on the canvas with the element that is displayed in the header of the simple RNA monomer section
AND
all other canvas elements are staying the same, including the bonds for this replaced monomer
AND
newly replaced monomer receives the same connection points in the same status as the replaced one had
AND
chains and their enumeration stays the same
AND
monomer's enumeration stays the same
7 clicking on the monomer of different from RNA type on the canvas Ketcher does not change the objects on the canvas
AND
Ketcher shows the indication that this kind of replacement is not available
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