run_ProFOLD.sh

#!/bin/bash

if [ $# != 2 ]; then
    echo "Usage $0 <MSA> <output_dir>"
    exit 1
fi

BINROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
aln=$1
outdir=$(readlink -f $2)
_filename=$(basename -- "$aln")
target="${_filename%.*}"
fasta=$outdir/$target.fasta

mkdir -p $outdir
echo ">$target" > $fasta
head -1 $aln >> $fasta

echo "Predict distance--------------------------------------------------------"
$BINROOT/distance_prediction/run_inference.py \
    -m $BINROOT/distance_prediction/model \
    -i $aln \
    -o $outdir/$target.npz
feat=$outdir/$target.npz
if [ ! -e $feat ]; then
    echo "Predict distance failed... Stop"
    exit 1
fi

echo "Generate structure by gradient decent-----------------------------------"
$BINROOT/folding/run_builder.py \
    -i $fasta \
    -f $feat \
    -o $outdir \
    --n_workers 24 \
    --n_structs 20 \
    --n_iter 100

echo "Full-atom relax---------------------------------------------------------"
$BINROOT/folding/run_relax.py \
    -s $fasta \
    -f $feat \
    -i $outdir/final \
    -o $outdir/relax \
    --n_workers 24

echo "Ranking decoy-----------------------------------------------------------"
ls $outdir/relax/*.pdb | while read LINE; do
    echo $LINE $(grep "^pose" $LINE | awk '{print $NF}')
done | sort -k 2 -n > $outdir/rank.txt