Developer's Guide

This section gives function and class definitions used in the development of OrgoChemVisualizer.

If you are a first-time contributer: - Go to https://github.com/cjcrowder1/OrgoChemVisualizer - Click on the ‘Fork’ button in the top right of the screen

This creates your own copy of the project

-Go to your own Github repository and you will see a repository named OrgoChemVisualizer

Click into this repository and make a local copy of it by hitting the clone button Copy the URL shown

–If using Visual Studio Code:

Open Source control and push Clone Repository, this will open a window to type in the repository name Type in the repository name and select the repository If prompted to, sign into Github and return to VS Code -Remember, push requests must be fulfilled to push changes to Github

When you make changes and save the file, Source Code will show an alert that there is a pending change Navigate to Source Code, select the wanted changes, add a comment in the top textbox, and press the check button Then hit the arrow button in the blue bottom section of VS Code to fulfill the push requests

-To have the latest changes of the software from other contributers, press the same arrow button to pull the changes

–For general use (not using VS code):

Clone the project to your local computer using the copied URL Change the directory using: cd numpy Add the upstream repository: git remote add upstream [repository website] Now git remote -v will show two remote repositories named: origin and upstream -Pull latest changes:

Use: git checkout master, and git pull upstream master Create a branch for the feature you want to work on: git checkout -b [branch name]

-Push changes

Use: git push origin [branch name]

–To add new chemicals/molecules for a reaction:

-Navigate to the folder chemanim.py -Follow the format below for creating molecules:

class CO2(Chemical):

def __init__(self):

super(CO2, self).__init__()

pos = self.get_positions() adj = self.get_edges() sym = [strToSym(“O”), strToSym(“C”), strToSym(“O”)]

self.setData(pos=pos, adj=adj, pxMode=False,

symbol=sym, antialias=True)

def get_positions(self):

return np.array([

[-1, 13], [0, 13], [1, 13], ], dtype=float)

def get_edges(self):

return np.array([

[0, 1], [1, 2], ])

** similar formats are used for arrows and textboxes, these are also found in the chemanim.py file - Add the chemical/molecule created to the __main__.py file using the format: #self.mol2 = ca.CO2() and #self.addItem(mol2)

–To create the animations:

-Navigate to the __main__.py file -Make sure the chemical(s)/molecule(s) wanted for the animation and/or reaction have been added to the file -Follow the format for the reaction sequences (from the other reactions 1-3) *Naming the animation follows the format: Example from Reaction 2 self.R2S1 Where R2 stands for Reaction 2, and S1 indicates that it is the first chemical/molecule in the reaction

**Textboxes and arrows are animated in similar ways