sdf2pdbconverter.sh

sdf2pdbconverter.sh

#!/bin/bash

# sdf2pdb converter, created by HS Na (dlwlrma@pusan.ac.kr)
# This script scans the file in the format [cid]_2d.sdf or [cid]_3d.sdf in the directory where the script ran and converts it to a pdb file via molconvert.

# scanning and parsing sdf file.
for sdf_file in *_[23]d.sdf; do
    if [ -f "$sdf_file" ]; then
        filename=$(basename "$sdf_file" .sdf)
        cid=${filename%_*}
        dimension=${filename##*_}
        
        # generate output file name.
        pdb_file="${cid}_${dimension}.pdb"
        
        echo ">>> Converting $sdf_file to $pdb_file"
        
        # Converting SDF to PDB using molconvert.
        molconvert -3 pdb "$sdf_file" -o "$pdb_file"
        
        # check converting status.
        if [ $? -eq 0 ]; then
            echo ">>> Conversion successful: $pdb_file"
        else
            echo ">>> Error converting $sdf_file"
        fi
    fi
done

echo ">>> All conversions completed."