Install and Run Molywood in Windows

As some of the conda dependencies of our packages are not fully compatible with Windows, those dependencies must be installed manually. Here you have a quick guide for installing in Windows 10.

Install Anaconda

Although the installation can be done without using Anaconda, we strongly recommend it as it contains numpy and matplotlib as a pre-installed package.

1. Go to the official Anaconda website:
   
   https://www.anaconda.com/distribution/#windows
2. Be sure that the Windows tab is selected and Download Python 3.x version.
   
   
3. Double click on the *.exe file and follow the instructions:
   
   
4. The process of installation can last several minutes:
   
   
5. When the execution is finished, try to execute conda in the Anaconda prompt. If it doesn't work, the path must be exported:
   
   

   export PATH=/home/USER/anaconda3/bin:$PATH

Create conda environment

Environment creation

Please follow the next steps for creating a new conda environment from scratch:

1. Let's create a new conda environment executing the following instruction in the Anaconda prompt:
   
   

   conda create --name molywood python=3

2. Once the molywood conda environment is created, activate it:
   
   

   conda activate molywood

Packages installation

Once the environment has been successfully created, please follow the next steps for installing all the dependencies needed for the execution of :

VMD (Visual Molecular Dynamics)

1. Please go to the following URL and download the *.msi file:
   
   https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
   
   
2. Note that although VMD software is free for academic use, it is mandatory to be registered for downloading it. You must agree to the terms of the license:
   
   
3. Execute the downloaded file.
4. The process of installation can last several minutes:
   
   

ImageMagick and FFmpeg

1. Please go to the following URL and download the *.exe file:
   
   https://imagemagick.org/script/download.php#windows
   
   
2. Execute the downloaded file.
3. Please be sure that the Install FFmpeg checkbox is checked:
   
   

Molywood

Run the Python Package Installer to install manually the last dependency:

pip install molywood

Run molywood

Now you can run molywood just typing molywood in your terminal.

(molywood) C:\Users\user\molywood>molywood

 Warning: no input data was provided.

 To run Molywood, provide the name of the input file, e.g. 'molywood script.txt'.

 To run a sample visualization, type 'y'.

 To generate a sample input, type 'i'.

 Pressing 'Enter' (or entering any other command) will terminate the script.
 >>> i

(molywood) C:\Users\user\molywood>molywood sample_molywood_input.txt

Note that even if the dependencies are not in PATH, the application find them:

vmd not found in PATH
ffmpeg not found in PATH
imagemagick not found in PATH
will try harder looking for vmd, magick, ffmpeg
vmd found in dir C:\Program Files (x86)\University of Illinois\VMD
magick found in dir C:\Program Files\ImageMagick-7.0.10-Q16
ffmpeg found in dir C:\Program Files\ImageMagick-7.0.10-Q16