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[Monomer library] As Ketcher Polymer Editor user I want to work with RNA monomers
Alena Guznischeva edited this page Feb 18, 2022
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As | I want | so that |
---|---|---|
Ketcher polymer editor user | to work with the monomer of RNA type in monomer library | I can view, explore, and select proper monomers to create peptides on the canvas |
Glossary: Peptide Glossary
Monomers of RNA type in Monomer library will represent the basic nucleotides that are participating in RNA and DNA combining among with the modifications available for nucleobase, sugar, and phosphate.
ID | Assumption |
---|---|
1 | 5 basic nucleotides would be the group of RNA monomers with the easiest access for users |
2 | |
3 |
RasMol color scheme description for Nucleosides: http://www.pdg.cnb.uam.es/cursos/Barcelona2002/pages/Farmac/CMU_course/ProtG/ShapelyColors.html
UIPAC nomenclature for nucleotides:
IUPAC nucleotide code | Base |
---|---|
A | Adenine |
C | Cytosine |
G | Guanine |
T (or U) | Thymine (or Uracil) |
# | User Group | GIVEN | WHEN | THEN |
---|---|---|---|---|
1 | Ketcher peptide editor User | Peptide editor mode of the Ketcher enabled | viewing on the Ketcher peptide editor | I immediately see the monomer library with RNA tab presented AND I can select the RNA tab |
2 | RNA tab of Monomer library is selected | I see 4 sections of the RNA library: Nucleotide, Nucleobase, Sugar, and Phosphate AND I immediately see on the header of each section what element is selected right now AND when hovering on the header of each section I see the tooltip with the name of the corresponding monomer type and the full name of currently selected monomer in this section |
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3 | Peptide editor mode of the Ketcher enabled AND RNA tab of Monomer library selected |
Nucleotide section is displayed | I see the list of basic Nucleotides with UIPAC code presented immediately (A, C, G, T, U) AND I can hover or select each of them |
|
4 | Sugar section is displayed | I see the list of Sugar elements with Ribose, Deoxyribose on the top AND other sugars sorted by the name with short name presented immediately on the screen for each one of them |
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5 | Phosphate group section is displayed | I see the list of Sugar elements with Phosphate on the top AND other phosphate groups sorted by the name with short name presented immediately on the screen for each one of them |
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6 | RNA tab of Monomer library is selected AND any section is displayed AND hovering over the element |
I see the hovering window with the information about the nucleotide element: 1) trivial name of the element 2) molecule structure picture representing the molecule with connection points specifically identified, enumerated, and presented and with a transcript of each connection end molecular formula (can be delayed) |
- 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