Installing Software

ChemApp for Python with Anaconda

Windows

To complete this procedure, you will require Administrator privileges on your computer. To install Anaconda, Python and ChemApp for Python on a Windows computer, follow these steps:

Install Anaconda.

Once you have the installer file, named something like Anaconda3-2021.11-Windows-x86_64.exe, you can simply double-click on it to start the installation, and follow the prompts to complete it.

Note: The Anaconda installation uses C:\Users\user_name\Anaconda3 as installation destination by default. If the user_name contains spaces, e.g. C:\Users\John Doe\Anaconda3 it causes problems when using Anaconda. It is therefore recommended that Anaconda is installed directly onto a drive at, for example, C:\Anaconda3, D:\Anaconda3. This ensures that the path contains no spaces.

Also, both advanced options must be selected on the final installation prompt, as shown in the figure below. This is very important, since the conda commands in the terminal will not work otherwise.
Install development environment.
1. Install PyCharm.
  
  Once you have the installer file, named something like pycharm-community-2021.3.1.exe, you can simply double-click to start the installation, and follow the prompts to complete it.
  
  Note: It is important to select the 64 bit installer, and select .py when asked about “create associations”, seen in the figure below.
2. Install VSCode.
  
  Once you have the installer file, named something like VSCodeUserSetup-x64-1.64.2.exe, you can simply double-click to start the installation, and follow the prompts to complete it.
Create a conda environment.

Open the Windows command prompt by pressing Windows-R (hold down the Windows key and press R), typing cmd, and pressing Enter. Now type the following on the command prompt and press Enter:
```
conda create --name my-chemapp-env python=3.12.7
```
When prompted to install default packages, type yes and press Enter. You can choose your own name instead of my-chemapp-env. The Python version number must correspond to the Python version number in your ChemApp for Python distribution package’s file name, e.g. chemapp831.2.0-win-chemapp8.3.1-python3.12.7.tar.gz. In this example you need to use Python 3.12.7 with the distribution package.

Great! Now you have a Python environment in which you can use ChemApp for Python. Keep the Windows command prompt open for the next steps.
Activate the conda environment.

Now you need to activate your new conda environment so that you can work inside it. Type the following in the command prompt and press Enter:
```
activate my-chemapp-env
```
Now you are ready to install ChemApp for Python!
Install ChemApp for Python.

In the command prompt, change into the directory that contains the ChemApp for Python distribution package. Let’s assume it is located in D:\temp. Type the following, ending each line by pressing Enter. You can ignore the lines that start with REM. These are just comments that explain what the commands do.
```
REM Change current drive to 'D:'.
D:

REM This changes the current directory to 'D:\temp'.
cd D:\temp

REM install chemapp.
pip install chemapp831.2.0-win-chemapp8.3.1-python3.12.7.tar.gz
```
The name of the .tar.gz file must correspond to your distribution package file name.

Confirm successful installation in the conda environment.

To confirm that ChemApp for Python is now available in the conda environment, type the following in the command prompt and press Enter:

conda list

This should return a list of installed packages, with chemapp as one of them, with the version number corresponding with the version number of your ChemApp for Python distribution file, as follows:

# packages in environment at C:\Users\user\Anaconda3\envs\my-chemapp-env:
#
certifi                   2018.4.16                py36_0
chemapp                 831.2.0                     <pip>
pip                       10.0.1                   py36_0
pymongo                   3.7.0                     <pip>
python                    3.12.7               h09676a0_15
setuptools                39.2.0                   py36_0
vc                        14                   h0510ff6_3
vs2015_runtime            14.0.25123                    3
wheel                     0.31.1                   py36_0
wincertstore              0.2              py36h7fe50ca_0

Linux

To complete this procedure, you will require root privileges on your computer. To install Anaconda, PyCharm and ChemApp for Python on a Linux computer, follow these steps:

Install Anaconda.

Once you have the installer file, named something like Anaconda3-5.2.0-Linux-x86_64.sh, you need to change file permissions to allow execution. Open a console, and change into the directory where the installer file is located (in our case ~/Downloads).
```
cd ~/Downloads  # change directory
chmod +x Anaconda3-5.2.0-Linux-x86_64.sh  # allow execution
./Anaconda3-5.2.0-Linux-x86_64.sh  # install anaconda
```
Complete the installation by answering the questions posed by the installer. You should be able to safely accept the default values.
Install PyCharm.

Once you have the installer file, named something like pycharm-community-2021.3.1.tar.gz, you can simply extract it into your home directory (~). For further instructions, please refer to the Install-Linux-tar.txt file in the root of the directory into which you extracted the installer.
Create conda environment.

Type the following in the console:
```
conda create --name my-chemapp-env python=3.12.7
```
You can choose your own name instead of my-chemapp-env. The Python version number must correspond to the Python version number in your ChemApp for Python distribution package’s file name, e.g. chemapp8.3.1-linux-chemapp8.3.1-python3.12.7.tar.gz. In this example you need to use Python 3.12.7 with the distribution package.

Great! Now you have a Python environment in which you can use ChemApp for Python. Keep the Linux command prompt open for the next steps.
Activate the conda environment.

Now you need to activate your new conda environment so that you can work inside it. Type the following on the command prompt and press Enter:
```
source activate my-chemapp-env
```
Now you are inside your new conda environment, ready to install ChemApp for Python!
Install the libgfortran3 library.

ChemApp is dependent on this library on Linux machines. Use the following command:
```
sudo apt install libgfortran3
```
Install ChemApp for Python.

In the command prompt, change into the directory that contains the ChemApp for Python distribution package. Let’s assume it is located in ~/Downloads. Type the following, ending each line by pressing Enter:
```
# change directory
cd ~/Downloads

# install chemapp
pip install chemapp831.2.0-linux-chemapp8.3.1-python3.12.7.tar.gz
```
The name of the .tar.gz file must correspond to your distribution package file name.

Confirm successful installation in the conda environment.

To confirm that ChemApp for Python is now available in the conda environment, type the following in the command prompt and press Enter:

conda list

This should return a list of installed packages, with chemapp as one of them, with the version number corresponding with the version number of your ChemApp for Python distribution file, as follows:

# packages in environment at C:\Users\user\Anaconda3\envs\my-chemapp-env:
#
certifi                   2018.4.16                py36_0
chemapp                 831.2.0                     <pip>
pip                       10.0.1                   py36_0
pymongo                   3.7.0                     <pip>
python                    3.12.7               h09676a0_15
setuptools                39.2.0                   py36_0
vc                        14                   h0510ff6_3
vs2015_runtime            14.0.25123                    3
wheel                     0.31.1                   py36_0
wincertstore              0.2              py36h7fe50ca_0

ChemApp for Python with a Bare Python Installation

This procedure explains how to install ChemApp for Python into a bare Python installation.

Windows

Download the relevent version of Python. For the current ChemApp for Python version, you need to download Python 3.9.1..
Install Python.

Double-click on the downloaded python-3.9.5-amd64 file. In the installation window, tick the “Add Python 3.9 to PATH” and choose customise installation and click next. On the Optional Features window, make sure that all of the checkboxes are ticked and as seen in the Figure below, and click next.

On the Advanced Options window seen in the Figure below, click on the “Install for all users” checkbox. This will change the install directory to C:\Program Files\Python39. This should be changed to C:\Python39 for simplification purposes.

After the installation, the window can be closed.
Additional installations.

To be able to install the ChemApp for Python package, setuptools and pip (a Python package manager) must be installed. These are installed by entering the following commands into the Command Prompt. The command prompt can be opened by pressing Windows-R (hold down the Windows key and press R), typing cmd, and pressing Enter.
1. install pip:
```
curl https://bootstrap.pypa.io/get-pip.py | python
```
2. install setuptools:
```
pip install setuptools
```
  If you are unsuccessful with the installation, a more detailed procedure can be found here. Or consider to switch to one of the IDE installation methods.
Install new packages using pip.

In the command prompt, new packages can be installed with the following command: pip install <new-package>. Try it out by installing the numpy package:
```
pip install numpy
```
Display packages installed on Python.

The following command can be used to see the packages installed on Python.
```
pip list
```
Download ChemApp for Python’s free Light edition.

ChemApp for Python Light can be downloaded from the GTT website. The dowloaded file should be stored in an easily accessible location. In this example, the file is downloaded to
```
C:\Python36\Scripts\python-packages\
```
The “python-packages” folder was created manually.
Install ChemApp for Python Light.

In the command prompt, type-in the following command to install ChemApp for Python Light
```
pip install C:\Python36\Scripts\python-packages\chemapp-0.3.2-gtt-win-chemapp7.2.0-python3.6.2.tar.gz
```
The name of the downloaded file could differ depending on the ChemApp for Python release version.
Open python.

Python can be opened by typing “python” in the command prompt. An alternative method is to press the Windows button, search for “python” and clicking on “Python 3.9 (64-bit)” under Apps.

Linux

The following procedure must be used to use ChemApp for Python in bare Python.

Install Python.

Install Python 3.9 through the terminal with the following command:
```
sudu apt-get install python3
```
Ensure that Python 3.9.1 is installed by downloading it here. Unzip the file, with a name like Python-3.9.1.tgz in an easy to locate location. Then cd to the Python-3.9.1 file in the terminal and run the following commands:
```
sudo make
```
And,
```
sudo make install
```
Verify that Python 3.9.1 was installed correctly by executing the following command:
```
python3 -V
```
Install ChemApp for Python.

For this installation it is required to have obtained the ChemApp for Python *.tar.gz file. cd to where the ChemApp for Python package is stored and install ChemApp for Python through the terminal with the following command:
```
pip install chemapp_816-linux-chemapp_8.1.6-python3.9.1.tar.gz
```
Ensure that ChemApp for Python installed successfully by running the following command in the terminal:
```
pip list
```
A list of all the installed packages will appear. Below is an example of the list showing that chemapp is installed.
```
certifi                            2017.7.27.1
cffi                               1.10.0
chardet                            3.0.4
chemapp                            816
click                              6.7
cloudpickle                        0.4.0
clyent                             1.2.2
colorama                           0.3.9
```
Running a Python file.

In order to run a *.py file run the command, shown below, in therminal. The file_path to the *.py file must be entered correctly in the terminal.
```
python file_path/*.py
```

ChemApp for Python with Python virtualenv

The following procedures were written for Windows and Linux users that prefer using Python virtual environments without the use of an IDE.

Windows

Download Python and Pip.

Download and install Python as explained in the “ChemApp for Python with a Bare Python Installation” section. Also complete the “Additional installations” mentioned in this section to install “pip” and “setuptools”.
Make a virtual environment.

A step-by-step guide on creating a virtual environment can be found here. In this example, we will name our virtual environment “chemapp-light”.
Download ChemApp for Python’s free Light edition.

Download and install ChemApp for Python Light as explained in the “Installing ChemApp for Python on Bare Python” section. In this example, ChemApp for Python was downloaded to
```
C:\Python\Scripts\python-packages\
```
Install ChemApp for Python in a virtual environment.

Activate the newly created virtual environment with the following command:
```
.\chemapp-light\Scripts\activate
```
ChemApp for Python can now be installed using
```
pip install C:\Python\Scripts\python-packages\``chemapp831.2.0-win-chemapp8.3.1-python3.12.7.tar.gz``'
```
pip list can be used to ensure that the chemapp package was successfully installed.

Linux

The procedure for installing ChemApp for Python on Linux using a Python virtual environment is as follows:

Install virtualenv.

In the terminal, run the following installation command:
```
pip install virtualenv
```
Add a new virtual environment.

Once the virtualenv installtion is completed it is required to create a virtual environment. The name of the virtual environment is determined by the user, for simplicity, my-chemapp-env is used to name the environment. The environment can be created in any directory with its specific file_path.
```
virtualenv file_path/my-chemapp-env
```
It is not necessary to add a file_path, then by default, the virtual environment will be created in the /home directory.
Activate the virtual environment.

To activate the virtual environment run the following command in the terminal.
```
source file_path/my-chemapp-env/bin/activate
```
Once the virtual environment is active, the name of the virtual environment will be displayed in closed brackets on the left-hand side of the terminal command line, e.g. (my-chemapp-env). To deactivate the environment simply run deactivate in the terminal command line.
Install the Python version.

To install the correct Python version type the following command in the terminal with the virtual environment active:
```
virtualenv --download python3.9.1
```
Install ChemApp for Python.

ChemApp for Python Light can be downloaded from the GTT Technologies website for the Linux version. You will need to cd file_path to the directory where the ChemApp for Python distribution package is stored. Install the ChemApp for Python package with the following command in the terminal:
```
pip install ``chemapp831.2.0-linux-chemapp8.3.1-python3.12.7.tar.gz``
```