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 biggest cluster by default (most fragments)

      3. Show all ligands in 3D viewer

      4. Show complex of first ligand

      5. (lazy loading of ligands?)

  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,


  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)