alphaParser

alphaParser is a python software that parses AlphaFold/ColabFold results into a PyMOL .pse file of the best predicted model and a .png visualization of the Predicted Alignment Error matrix. More details relative to the .pse and .png files will be explained below.

Installing alphaParser

Requirements for alphaParser are listed below:

setuptools~=61.2.0
numpy~=1.21.5
matplotlib~=3.5.1
seaborn~=0.11.2
pymol-open-source~=2.5.0

Linux and macOS Installation

Using git or wget you can download alphaParser via

git clone https://github.com/mabdulqader172/alphaParser.git

or

wget https://github.com/mabdulqader172/alphaParser.git

Once downloaded, move the dot .pyz program to your bin

mv alphaParser/alphaParser.pyz /usr/local/bin

If you don't have sudo access simply mv to your local bin.

mkdir ~/bin # do this only if you don't have one yet
mv <location of the repository>/alphaParser/alphaParser.pyz ~/bin
echo 'export PATH="$HOME/bin:$PATH"' >> ~/.profile
source ~/.profile

Once in your path, call alphaParser

alphaParser.pyz -h

You should get the following help message back

usage: alphaParser [-h] [-o OUTPUT] [-t TITLE] results

A python software to parse AlphaFold results into PyMOL PSE and PAE plots.

positional arguments:
  results               the `results` directory or zipfile produced from your AlphaFold prediction. Files will have same 
                        name as the zipfile/directory given. To change the output file names for the pse and png files 
                        use '-o'/'--output' metavar.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        name of the output pse and png files to use.
  -t TITLE, --title TITLE
                        The desired title for your PAE plot, remember to wrap the title in quotations. 
                        Example: "PAE Plot"

Running alphaParser

Creating .pse and .png Files

Create your annotated .pse and .png file by calling

alphaParser.pyz <path to your zipfile>

If you wish to input a directory just call

alphaParser.pyz <path to your directory>

Note that all the files produced will have the name of the zipfile or the directory name as a prefix.

Adding a target directory for your output

If you wish to output your data to a specific target call the -o metavar.

alphaParser.pyz <path to your directory or zipfile> -o <output dir>

Adding a title to your PAE plot.

The default title is "PAE Plot" so if you wish to add a more descriptive name, use the -t metavar

alphaParser.pyz <path to your directory or zipfile> -t <your descriptive title>

Reaching Out/Feedback

If alphaParser is running into an error, or if you have any feedback on any features to add just raise an issue and will get back to you soon!