https://github.com/unixjunkie/interlig
mirror of https://bitbucket.org/clami66/interlig
https://github.com/unixjunkie/interlig
Last synced: about 1 year ago
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mirror of https://bitbucket.org/clami66/interlig
- Host: GitHub
- URL: https://github.com/unixjunkie/interlig
- Owner: UnixJunkie
- License: other
- Created: 2019-04-19T01:43:22.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2019-04-19T01:43:39.000Z (about 7 years ago)
- Last Synced: 2025-01-31T09:31:30.500Z (over 1 year ago)
- Language: C++
- Homepage: http://wallnerlab.org/interlig
- Size: 994 KB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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
### 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 : number of annealing rounds (default: 1)
-seed : seed for the stochastic process (random number generation)
-ch : Markov chain length multiplier (default: 10)
-matrix : optional path to the atom similarity matrix (e.g. MOL2)
-super : calculate optimal superposition between two aligned molecules
(outputs to )
-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.