Fragalysis beta bugs/features - priorities

Release (if possible)

1. Header bar:

   

   1. Report: two prominent buttons, “Report error” (red), “Submit idea” (green)

   2. Target name big and bold

   3. Order along top: menu || Fragalysis: <target name> || session buttons (later “project”) || report buttons || logos etc.

   4. Logos that are links should change the pointer (to a hand)

      

2. Site info in cluster navigator

   1. Defaults on entry:

      1. White background

      2. Activate some cluster by default (first or biggest)

      3. Activate first hit of first cluster, display all

3. Remove download YANK button

   

4. “Clear selection” button: clear the filters

5. Viewer controls:

   1. popup behaviour - like Office property editor

      

   2. get rid of header,

   3. 3 buttons tight together

6. Automatic depth queuing - (pass them the backend code?)

   

   1. orientation algorithm - v1: look down vector from centre of mass through centre of site

   2. whatever the algorithm: should be consistent for a site regardless of which hit I click on

7. Hit navigator: layout

   1. (another mock-up)

      

   2. quality metrics - MUCH narrower, squish into single icon-let

   3. Compound much bigger, at least 2x wider

   4. Change properties into table: only one header at top, single row

   5. Remove target name from label

   6. Numbers - decimal points. none: MW, TPSA. one: logP

   7. #cpd - make it work - move to backend

   8. #vectors - total (pickable)

   9. Velec - wrong number?

   10. add electron density selector

   11. display toggles: better contrast (check ICM, suggest you copy)

8. Hit navigator: drop-down to colour red the value outside rule of 3 or 5 or none - left of sort/filter button. Default: rule-of-3.

9. Sort-filter behaviour:

   

   1. slide out modal over 3D pane, without inactivating whole page

   2. apply changes instantly, not on “apply”

   3. everything should remain active - just slide in-out.

   4. third the width (less than half): squish all icons, labels two rows if necessary, sliders far narrower

10. Hide all button in hit navigator - stay in site and 3D view

11. Compound picker

    1. First compound in list: spinning wheel

       

    2. Highlight constant part - RDkit command

    3. Header text: “<vector label>: <#cpds> available (total for molecule: <#total cpds>”

    4. Vector label: backend, for now human readable atom label straight from RDkit if that exists

       1. if not: “vector 5” by whatever arbitrary sequence

       2. ideally: can RDkit generate “alpha imine” or similar?

       3. (the least amount of work possible)

    5. Convert to table - exact same layout (and data) as hit navigator - including sort/filter

       1. except quality things and label

       2. sort/filter - slide out to left, but over 3D view)

       3. display options: all, ligand, complex, vectors (hooks at least)

       4. check-box on left - keep highlight of row if checked

       5. by all means leave colours.

    6. 3D view - make it work

12. Header bar:

    1. Janssen logo

    2. “supported by” - pop out a modal

    3. (back-button from “supported by” resets the view - BUG. but eliminate through modal)

    4. update logos in “supported by page”: ULTRA-DD, IMI, Horizon 2020,

Wishlist

1. Landing page, Target List - more columns

   1. target info (Uniprot, anything) - auto-generate starting from reference structure sequence

   2. link to pdb group deposition page (if it is a thing - else something similar - might be query)

   3. wiki page (if exists)

   4. (Brian will have suggestions)

2. Display electron density - extra display selector

3. Colour compound properties - backend for implementing rules

   1. future: customise on the fly (conditional formatting, or like sort/filter thingy)

   2. move filters into backend

4. Compound navigator

   1. Convert to tree-view to navigate sub-vectors

5. Download CSV button

6. Richer display of 2D compounds - map RDkit properties onto 2D view

7. Ligand interaction diagram - comparison tools. (Needs thinking)