Caretta

Caretta is a software-suite to perform multiple protein structure alignment and structure feature extraction.

Visit the demo server to see caretta's capabilities. The server only allows alignment of up to 50 proteins at once. The command-line tool and self-hosted web application do not have this restriction.

Installation

Requirements

Operating system support

1. Linux and Mac

• All capabilities are supported

2. Windows

• The external tool msms is not available in Windows. Due to this:
  • Feature extraction is not available.
  • extract-all-features argument in caretta-cli should be always False.
  • caretta-app is not available.

Software

Caretta works with Python 3.7+ Run the following commands to install required external dependencies (Mac and Linux only):

conda install -c salilab dssp
conda install -c bioconda msms

Download caretta

git clone https://git.wur.nl/durai001/caretta.git
cd caretta

Install both the command-line interface and the web-application (Mac and Linux only):

pip install -e ".[GUI]"

Install only the command-line interface:

pip install .

Environment variables:

export OMP_NUM_THREADS=1 # this should always be 1
export NUMBA_NUM_THREADS=20 # change to required number of threads

Usage

Command-line Usage

caretta-cli input_pdb_folder
# e.g. caretta-cli test_data  
# caretta-cli -h for more options

Web-application Usage (Mac and Linux only)

caretta-app <host-ip> <port> 
# e.g. caretta-app localhost 8091