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extend the color definition #7

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Commits on Feb 12, 2023

  1. add color of nitrogen

    Test-wise addition for / about nitrogen.  Tested on the example of
    pyridine by openbabel from the SMILES string (`c1ccncc1`), and
    diethylamine (`CCNCC`).
    nbehrnd committed Feb 12, 2023
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  2. add the color for oxygen

    Tested for the examples of diethylether (`CCOCC`), THF (`C1COCC1`),
    and propan-2-ol (`C(C)(O)(C)`) in .xyz files generated by obabel.
    nbehrnd committed Feb 12, 2023
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  3. add color about sulfur

    Tested with openbabel generated .xyz about diethyl thioether
    (`CCSCC`) and furfural (`O=Cc1cccs1`).  However, contrasting to
    e.g., the depiction with openbabel generated .pov, the C-S bonds
    no longer are visible.
    nbehrnd committed Feb 12, 2023
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  4. add color of fluorine

    Tested with openbabel SMILES string of fluoroethane (`CCF`).  The
    .pov/.ini and subsequent generation of .png seem fine.
    nbehrnd committed Feb 12, 2023
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  5. tentative addition for/about Cl

    Introduction of chlorine.  Tested with an .xyz about chloroethane
    (`CCCl`) generated by openbabel, the chlorine atom is depicted as
    sphere, separated from the backbone of the molecule.  Because of
    a similar observation for compounds with C-S bonds, and because the
    analogue CCF was rendered well, perhaps the assignment where to
    draw a bond faces an obstacle here.
    nbehrnd committed Feb 12, 2023
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Commits on Apr 25, 2023

  1. organize atom definition more like a dictionary

    The previous approach requires four lines each for every atom type
    as an instance of class Atom.  I think an approach which uses the
    element symbol as key to a the corresponding values of mass,
    radiosity, and rgb coordinates in a dictionary is - in comparison
    to this one - easier to read, and to maintain.  Lacking any better
    inspiration, atoms with atom types not yet explicitly defined in
    said dictionary default to hydrogen.  In such an instance, the
    conversion will not stop for good, however is going to issue one
    warning for each atom not fully defined (yet).
    nbehrnd committed Apr 25, 2023
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