NAME
INTERCAAT (Interface Contact definition with Adaptable Atom Types software)

SYNOPSIS
This program uses a PDB file to identify the residues present in the interface 
between a query chain and an interacting chain(s)

PRE-REQUISITES
1. Python 3.8 or newer is required.
3. Qhull is recommended since it is much faster. Qhull can be downloaded from here: http://www.qhull.org/download/.
4. If you wish not to use Qhull, the Python package pyHull is used instead.
INSTALL
Intercaat can be installed using the pip package manager by running:
pip install intercaat 

TEST
We included a sample PDB and the expected results from running the test commands below:
intercaat -pdb 1cph.pdb -qc B -ic A 
intercaat -pdb 1cph.pdb -qc A,6,7,8,9 -ic B -di no -cc no -sr 1.7 

CONFIGURATION
For ease of use the program is set to run with Python implementation as a default.
To run with qhull, you must set "run_python_version = no" and specify the "qvoronoi_path" and
"qhull_path" path to run the qvoronoi executable in the intercaat_config.ini file.

API
Intercaat can be imported into python using 'from intercaat.intercaatWrapper import intercaat'
The API call will return two dictionaries. The first contains the interface residue, 
residue id and # of interactions. The second contains the query chain, interacting chains, distance and atom classes. 
The command line arguments are accepted as function arguments.
EX: 
from intercaat.intercaatWrapper import intercaat
matches, interactions = intercaat("1cph.pdb", "B", "A")

HELP
The help function for INTERCAAT can be displayed by typing either intercaat or intercaat -h into 
your terminal. After doing so, instructions for how to run this program along with an 
example for each switch will be shown.

OUTPUT
The main output of this program displays every atomic interaction between the query chain 
and the interacting chain(s), the distance between the interacting atoms, and the assigned 
atom classes. The compatibility matrix, if displayed, shows each interface residue in the 
query chain and its corresponding quantity of atomic interactions.

REFERENCE
INTERCAAT: identifying interface residues be-tween macromolecules

AUTHORS
Steven Grudman	steven.grudman@einsteinmed.org
Eduardo Fajardo	eduardo@fiserlab.org
Andras Fiser    andras.fiser@einsteinmed.org

