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A model to build organic molecules from atoms of oxygen, nitrogen, carbon and hydrogen and visualize them in a 3D perspective with SAGE2 panel.
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README.md

Molecules Maker

A model to build organic molecules (currently 4 atoms available) and visualize them in a 3D perspective.

SAGE2

First of all you must install SAGE2 in order to use the application.

The tutorial and archives for installation are available at http://sage2.sagecommons.org/.

Once installed, configure and start the SAGE2 server side.

Installation

There are 3 ways of installing a new application in SAGE2 server:

  1. Go to your Documents/ folder system and find the directory SAGE2_Media/apps/, create a paste named molecules_maker and copy the archives to this directory.
  2. With your device connected in SAGE2 panel server, click and drag a zipped file containing the archives in the SAGE2 application client side.
  3. Go to your SAGE2 installed folder in your system and find dorectory public/uploads/apps/, create a paste named molecules_maker and copy the archives to this directory.

Note: Recommended to follow the first or second installation option.

Application

  • Language Button You may toggle the language between english and portuguese.

Language Button

  • Atoms Buttons Here you may spawn and object of the desired atom to build your molecules. Atoms available: Carbon, hydrogen, nitrogen, oxygen.

Atoms Buttons

  • Auxiliar Buttons
    • Complete with Hydrogen: It will complete the remaining connections with hydrogen atoms of all molecules that are in you working area (canvas 2D).
    • Create Benzene: Creates a benzene molecule with a better shape visualization.
    • 1/2/3 Connection: You may click in this button to change the amount of connections the atoms will make when you connect them.

Auxiliar Buttons

  • Trash To delete an atom or a molecule you just have to click and drag the same on trash. Be careful if you release the atom or molecule with any part of it crossing the trash, it will be deleted.

Trash

  • Building 2D Molecules Simple as dragging atoms near the side of another, it will automatically detect the side of collision and connect them in those sides.

Build 2D Molecule

  • Building 3D Model Just double click on the molecule you desire to build the 3D model Molecule marked in blue indicate the current molecule in 3D visualization.

Build 3D Model

  • Widget Menu Use the left button of mouse (or any other device) to open the widget menu, it has 3 options by sign:
    • + Zoom In: the plus sign zoom in the 3D model visualization.
    • - Zoom Out: the minus sign zoom out the 3D model visualization.
    • Loop: toggle the button to change the 3D model from auto rotation to manual rotation. Note: In manual rotation mode click and drag on 3D canvas to rotate the model.

Widget Menu

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