Progress Reports

Client Meeting Notes:

  • Meeting 9-24-25:
    Right-click context menu for periodic table (other functions?)
        Override default right-click menu with an application focused one

    Manual Coordinate Inputting

    Molecule Weight to Sphere Size
        (ratio of atomic weight to sphere radius, this gets more complicated when you 
         consider distance in the scene scale)

  • Meeting Notes 10-1-25:
    ---Meeting with Prof Tosaporn, chemist from University from Hawaii---

    > chemcompute.org - a similar web app that can build molecules in an environment
    > openbabel.org - A chem toolbox to maybe understand the different chemical calculations that might occur within our application?

    > .inp Files need to be able to be read by the GAMESS software to do the calculations
        - The calculations that will happen seem to heavily depend on the BASIS declarations that are written before the molecule is     written?
        - Maybe focus on the MacMolPlt input builder tab to learn more about how to properly build the GAMESS files.
        - By default, use C1 to use the cartesian coordinates.

    > We will hopefully be receiving a few files to better explain GAMESS files and the ways in which we would like to be building them out.

    --> Recommendations <--

    > How many bonds they will be able to have, display their coordinations?
        - Which ones have a coordination of which, either find a lib for it or maybe make it as a field of itself?

    > The distance between the atom will have an impact on the bonds they create, and how the geometry will be affected
        - For example, a carbon atom with four hydrogens connected will be of a tetrahedral geometry, maybe look into getting it to     automatically adjust?
    > Make our own input builder to aid in creating the proper output for GAMESS files, they use energy and some of the BASIS sets to build
    out the header section to inform the file how to be written.

  • Meeting Notes 11-5-25:

    Work to be done:
    Change atom tab to use atomic symbol
    Change output file to reflect atomic number in 2nd column
    scale atoms to atomic mass
    input builder functionality, add canvas and default GAMESS variables.
    molview.org - tool with more implementation examples

    Future Features:
    fragment molecules - pymol has this for example
    transpose fragmentation formats into standard XYZ
    highlighting specific areas of the canvas, hide atoms outside of that area

  • Meeting Notes 11-12-25
    WHAT WAS PRESENTED:

    -> Export displayed atomic mass, not atomic number and was updated.
    -> Looked into more about creating stricter molecular geometry and editing coordination of atoms.
    -> Coordinate Controller now displays atomic symbol.
    -> A new header added to display the Chemistry Connector name, upon request.
    -> Fixed input function, as it had some errors working upon our last demonstration.


    TODO LIST:

    -> Input builder tab for GAMESS file.
    -> Coordination for atoms, a limit for # of bonds it can create/share with other atoms.
    -> View tab to enable/disable grid, axes helper, and change color of atoms.
       -> With coloring of atoms, features such as these will be stored in cookies, rather than in some database.
       -> Either add a dynamic grid to span outwards as molecules get placed in further coordinates, or include a feature to increase the size manually.
    Double/triple bond logic?
    -> Molecular Geometry implementation.
    -> Add a moto to website per Dr. Cohen's request "Bringing molecules together".