Feature_selection_MP/net_features.sh at master · rodriluc/Feature_selection_MP · GitHub

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#!/usr/bin/env bash

#Overall aim: to save feature vectors

# Strip PDB files in correct format
cd PDB_files
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/strip_pdb.py
done
cd ..
# Create individual PDB files for hydrophobic and charged residues
cd PDB_edited
for file in *pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/create_pdb.py
done
cd ..
# Compute side-chain distance map from all PDBs now
cd PDB_edited
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/MD_cmaps.py -top $file -trj $file -fe ${file%.*} -od /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/ -sc_cmap
done
# Get binary contact map Origin pdb
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/MD_cmaps.py -d_in /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/distance_matrix_min_${file%.*}.txt -fe ${file%.*} -od /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/ -bin -coff 0.45
done
cd ..
cd hydrophobic_files
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/MD_cmaps.py -top $file -trj $file -fe ${file%.*} -od /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/ -sc_cmap
done
# Get binary contact map Hydrophobic pdb
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/MD_cmaps.py -d_in /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/distance_matrix_min_${file%.*}.txt -fe ${file%.*} -od /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/ -bin -coff 0.45
done
cd ..
cd charged_files
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/MD_cmaps.py -top $file -trj $file -fe ${file%.*} -od /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/ -sc_cmap
done
# Get binary contact map Charged pdb
for file in *.pdb
do
echo $file
python /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/MD_cmaps.py -d_in /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/distance_matrix_min_${file%.*}.txt -fe ${file%.*} -od /data2/LucieR/Delemotte-summerlab_ERnorm_100ER_4.5A/Results_data/ -bin -coff 0.45
done
cd ..
# Create feature vector
python input_netx.py