Intercaat 3.11

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

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.
2. Qhull is recommended since it is much faster. Qhull can be downloaded from here: http://www.qhull.org/download/.
3. 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 between macromolecules

AUTHORS Steven Grudman [e-mail] Eduardo Fajardo [e-mail] Andras Fiser [e-mail]