DRfold/DRfold.sh at main · leeyang/DRfold · GitHub

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#!/bin/bash
INR="$1"                # input.fasta
WDIR=`realpath -s $2`  # working folder
IN=$WDIR/seq.fasta
mkdir -p $WDIR
export PETFOLDBIN="/home/liyangum/projects/RNA/DRfold/bin/PETfold/bin"
PYTHON="python"
export MKL_THREADING_LAYER=GNU
full_path=$(realpath $0)

dir_path=$(dirname $full_path)

if [ ! -s $WDIR/seq_ss.npy ]
then
    echo "Generating ss features"
    $PYTHON $dir_path/scripts/Feature.py $(realpath $INR) $WDIR/seq_ss $IN >>$WDIR/running.log
fi

if [ ! -s $WDIR/geo_1.npy ]
then
    echo "Predicting geo 1/3"
    $PYTHON $dir_path/DeepGeoPotential/config1/predict.py $(realpath $IN)  $WDIR/seq_ss.npy $WDIR/geo_1 >>$WDIR/running.log
fi

if [ ! -s $WDIR/geo_2.npy ]
then
    echo "Predicting geo 2/3"
    $PYTHON $dir_path/DeepGeoPotential/config2/predict.py $(realpath $IN)  $WDIR/seq_ss.npy $WDIR/geo_2 >>$WDIR/running.log
fi

if [ ! -s $WDIR/geo_3.npy ]
then
    echo "Predicting geo 3/3"
    $PYTHON $dir_path/DeepGeoPotential/config3/predict.py $(realpath $IN)  $WDIR/seq_ss.npy $WDIR/geo_3 >>$WDIR/running.log
fi

if [ ! -s $WDIR/geo.npy ]
then
    echo "Combining geo potentials"
    $PYTHON $dir_path/scripts/combine.py $WDIR/geo $WDIR/geo_1.npy $WDIR/geo_2.npy $WDIR/geo_3.npy >>$WDIR/running.log
fi

if [ ! -s $WDIR/e2e_5.npy ]
then
    echo "Predicting e2e "
    $PYTHON $dir_path/DeepE2EPotential/predict.py $(realpath $IN)  $WDIR/seq_ss.npy $WDIR/e2e >>$WDIR/running.log
fi

if [ ! -s $WDIR/DPRcg.pdb ]
then
    echo "Optimizing structure"
    $PYTHON $dir_path/PotentialFold/Fold.py $(realpath $IN) $WDIR/geo.npy $WDIR/DPRcg $WDIR/e2e_0.npy $WDIR/e2e_1.npy $WDIR/e2e_2.npy $WDIR/e2e_3.npy $WDIR/e2e_4.npy $WDIR/e2e_5.npy  >>$WDIR/running.log
fi

if [ ! -s $WDIR/DPR_5.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg_5.pdb $WDIR/DPR_5.pdb 6 >>$WDIR/running.log
fi
if [ ! -s $WDIR/DPR_4.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg_4.pdb $WDIR/DPR_4.pdb 6 >>$WDIR/running.log
fi
if [ ! -s $WDIR/DPR_3.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg_3.pdb $WDIR/DPR_3.pdb 6 >>$WDIR/running.log
fi
if [ ! -s $WDIR/DPR_2.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg_2.pdb $WDIR/DPR_2.pdb 6 >>$WDIR/running.log
fi
if [ ! -s $WDIR/DPR_1.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg_1.pdb $WDIR/DPR_1.pdb 6 >>$WDIR/running.log
fi
if [ ! -s $WDIR/DPR_0.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg_0.pdb $WDIR/DPR_0.pdb 6 >>$WDIR/running.log
fi

if [ ! -s $WDIR/DPRr1.pdb ]
then
    echo "Filling full atoms"
    $dir_path/bin/Arena $WDIR/DPRcg.pdb $WDIR/DPRr1.pdb 6 >>$WDIR/running.log
fi

if [ ! -s $WDIR/DPR.pdb ]
then
    echo "Refinement"
    $PYTHON $dir_path/scripts/refine.py $WDIR/DPRr1.pdb $WDIR/DPR.pdb 0.6 >>$WDIR/running.log
fi