mol_frag_test.sh

#!/bin/bash

# set -x #DEBUG

# --view --> call mview on .smi files
MVIEW=""
if [ "$1" == "--view" ] || [ "$2" == "--view" ]; then
    MVIEW="1"
fi

# --big --> work on the "big" dataset
BIG=""
if [ "$1" == "--big" ] || [ "$2" == "--big" ]; then
    BIG="1"
fi

if [ "$BIG" == "" ]; then
    # clean
    rm -f data/3.to_frag data/3_frags.txt data/3_frags.smi \
       data/3_genmols.txt data/3_genmols.smi
    # regen
    ./bin/molenc_frag.py -i data/3.smi -o data/3.to_frag
    [ "$MVIEW" == "1" ] && mview data/3.smi &
    ./molenc_frag -im data/3.to_frag -of data/3_frags.txt -s 1234
    ./bin/molenc_frag2smi.py -i data/3_frags.txt -o data/3_frags.smi
    [ "$MVIEW" == "1" ] && mview data/3_frags.smi &
    ./molenc_frag -if data/3_frags.txt -om data/3_genmols.txt -s 1234 -n 20
    ./bin/molenc_mol2smi.py -i data/3_genmols.txt -o data/3_genmols.smi
    cut -f1 data/3_genmols.smi | sort -u > data/3_genmols_uniq.smi
    [ "$MVIEW" == "1" ] && mview data/3_genmols_uniq.smi &
else
    IN=data/chembl_antivirals
    ./bin/molenc_frag.py -i $IN.smi -o $IN.to_frag --draw
    ./molenc_frag -im $IN.to_frag -of $IN.frags -s 1234
    ./bin/molenc_frag2smi.py -i $IN.frags -o $IN.frags.smi
    ./molenc_frag -if $IN.frags -om $IN.mols -s 1234 -n 50
    ./bin/molenc_mol2smi.py -i $IN.mols -o $IN.mols.smi
fi