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 theuser_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.
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.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 pressR
), typingcmd
, and pressingEnter
. Now type the following on the command prompt and pressEnter
:conda create --name my-chemapp-env python=3.11.3
When prompted to install default packages, type
yes
and pressEnter
. You can choose your own name instead ofmy-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.chemapp826.2.0-win-chemapp8.2.6-python3.11.3.tar.gz
. In this example you need to use Python 3.11.3 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 pressEnter
: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 pressingEnter
. You can ignore the lines that start withREM
. 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 chemapp826.2.0-win-chemapp8.2.6-python3.11.3.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 pressEnter
: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 826.2.0 <pip> pip 10.0.1 py36_0 pymongo 3.7.0 <pip> python 3.11.3 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 yourhome
directory (~
). For further instructions, please refer to theInstall-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=3.11.3
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.chemapp8.2.6-linux-chemapp8.2.6-python3.11.3.tar.gz
. In this example you need to use Python 3.11.3 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 pressEnter
: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 pressingEnter
:# change directory cd ~/Downloads # install chemapp pip install chemapp826.2.0-linux-chemapp8.2.6-python3.11.3.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 pressEnter
: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 826.2.0 <pip> pip 10.0.1 py36_0 pymongo 3.7.0 <pip> python 3.11.3 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 toC:\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
andpip
(a Python package manager) must be installed. These are installed by entering the following commands into theCommand Prompt
. The command prompt can be opened by pressingWindows-R
(hold down the Windows key and pressR
), typingcmd
, and pressingEnter
.install pip:
curl https://bootstrap.pypa.io/get-pip.py | python
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. Thencd
to thePython-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. Thefile_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\``chemapp826.2.0-win-chemapp8.2.6-python3.11.3.tar.gz``'
pip list
can be used to ensure that thechemapp
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 specificfile_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 rundeactivate
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 ``chemapp826.2.0-linux-chemapp8.2.6-python3.11.3.tar.gz``