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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
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1 revision
As | I want | so that |
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Ketcher polymer editor user | to select RNA monomer from the monomer library | I can use it as an element for building the RNA structure |
This user story represents the first step of the process of peptide creation in the Ketcher peptide editor.
Glossary: Peptide Glossary
ID | Assumption |
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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 |
# | User Group | GIVEN | WHEN | THEN |
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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 |
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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 |
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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 |
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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 |
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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 |
- Polymer Editor - Glossary
- Polymer Editor - Business Rules
- Polymer Editor - HELM Mapping Rules
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Polymer Editor - HELM RNA monomers numeration
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Polymer Editor - Monomer Representation
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Polymer Editor - Long Chain Polymer Representation
- Polymer Editor Save file
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Polymer Editor Open file
- Monomer Library - Peptide Monomers
- Monomer Library - RNA Monomers
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Monomer Library - Chem Monomers
- Monomer Peptide - Adding to the canvas
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Monomer Peptide - Adding bonds between Peptide monomers
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RNA Structure - Adding to the canvas
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RNA Structure - Adding bonds between RNA monomers
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RNA Structure - Adding hydrogen bonds between RNA monomers
- Chem Structure - Adding to the canvas
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Chem Structure - Adding bonds between CHEM monomers
- Complex Polymers - Adding bonds between monomers of different types