Installing Anaconda and the LabBorg Python Module
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Computer Systems Tested
- Windows 10
- Mac OS Ventura 13.2 (Apple M1)
- Download and Install Anaconda
- This takes a while about 10-15 minutes.
- Install Anaconda in your user directory and not as administrator.
- If you have a Mac with an ARM processor, click the apple and about. It will say either Apple M1 or M2. Use the X86_64.pkg at the end of the Anaconda installer (not the arm64.pkg). At the end, the installer will say that it failed but ignore that.
- Open Anaconda Navigator
- On the left side, click
- Click the
- In the Create Environment Dialog, put some name like Jupyter37 and be sure that the Python version is 3.7. something.
- Download YYMMDD-Installer.zip from ELC New and put it somewhere where you can find it. The name might be something like 230123-Installer.zip.
- You should be able to repeat this procedure for any other versions.
- Unzip YYMMDD-Installer.zip. This will produce a folder called Installer.
- Put a folder called PHRM8010 on your Desktop or some other location that you can find it.
- Navigate to the Installer that you unzipped. In Windows, an Installer directory might be in an Installer directory.
- Navigate to the LabBorg folder, then Examples, and copy the Jupyter Folder and put it into the PHRM8010 directory that you created.
- These examples will be useful for you to try out different things in Python.
- If the Anaconda program is not already open, open it. Click environments on the left hand side.
- Select the environment that you created. In this example, it is Jupyter37.
- Click the and select Open Terminal...
- Navigate to the Installer folder that you unzipped on the command line.
- For Windows, you will use two DOS commands: cd and dir for change directory and list directory, respectively.
- For Mac, you will use two Linux commands: cd and ls for change directory and list directory, respectively.
- For example, from the command prompt, I typed the following:
- Check to see if setup.py is in the directory list. If it is, type: python setup.py install
- At the end, you should get the following dialog box:
- Select the PHRM8010 folder that you made.
- Exit and restart Anaconda Navigator.
- Select Environment on the left and the environment that you created. In my case, it was Jupyter37.
- Select Home
- should be under the Icon. If it is not, restart the Anaconda program.
- JupyterLab should appear like the following in your browser:
- Double click the Jupyter folder on the left. If you do not see it, click
- When you double click the Jupyter folder, you should see the following:
- Each of these folders represents a different Python module and they contain short working Jupyter programs.
- Now, let us double click on the folder nglview. This Python module allows you to visualize macromolecules.
- Double click on nglview01
- Double click on
- If you did it correctly, you should get the following:
- At the top left, click
- When get prompted to restart the kernel, click Yes.
- rdkit is another Python module to test to see if your install worked properly.
- if you want to use the rpy2 Python module, you need to install R and R-studio separately from anaconda..