README

InterLig is a software for the sequence-order alignment and Virtual Screening of small molecules.

Installation

To compile InterLig just clone this repo and run the command:

make

A binary named InterLig will be generated in the cloned folder.

Usage

To run the binary in the folder where it is installed:

./InterLig -mol2 target.mol2 database.mol2 <options>

### Main options: ###

-mol2  : Compare a mol2 file with a mol2 database (multiple molecules in the database)
         (./InterLig -mol2 target.mol2 database.mol2)

### Other options: ###

-d0           : d0 parameter in the Levitt-Gerstein score (default: 0.5)
-dW           : weight of sequence similarity (e.g. BLOSUM62) in the optimization procedure (default: 0.5)
-eps          : weight of structural similarity in the optimization procedure (default: 0.5)
-nullP        : percentage of ignored atoms in the smaller molecule (default: 0)
-v            : verbose output
-anneal <int> : number of annealing rounds (default: 1)
-seed <int>   : seed for the stochastic process (random number generation)
-ch <int>     : Markov chain length multiplier (default: 10)
-matrix <path>: optional path to the atom similarity matrix (e.g. MOL2)
-super <path> : calculate optimal superposition between two aligned molecules
                (outputs to <path>)
-h            : print this help

Usage examples

If we want to run on mol2 files with d0 = 0.4 and eps = 0.75:

./InterLig -mol2 examples/target.mol2 examples/database.mol2 -d0 0.4 -eps 0.75

The database file here is always the second file following the mol2 flag.