docking 2020

#grab files:
awk -F "," '{print $1}' CID_60961_compound.csv > ids.csv
while read -r line; do curl https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${line}/record/SDF/\?record_type=3d\&response_type=save\&response_basename=Conformer3D_CID_${line} -o ${line}.sdf; done < ids.csv

#dock them:
#!/bin/bash

for file in *.sdf; do babel $file ${file%sdf}pdbqt; done

mkdir O43148_rez/
for file in *.pdbqt; do ~/bin/qvina-master/bin/qvina-w --receptor /home/vytautas/methyl_transferases_docking/human/O43148/5e8j_A.pdbqt --ligand $file --center_x -2 --center_y -6 --center_z -3 --size_x 20 --size_y 20 --size_z 20 --num_modes 1 --out O43148_rez/${file%.pdbqt}_out.pdbqt; done
cd O43148_rez/
for file in *_out.pdbqt; do echo -n ${file%_out.pdbqt} && echo -n ", " && grep -m 1 "REMARK VINA RESULT" $file | awk '{print $4}'; done > rez.csv
cd ..

mkdir nsp10+nsp14_rez/
for file in *.pdbqt; do ~/bin/qvina-master/bin/qvina-w --receptor /home/vytautas/methyl_transferases_docking/virus/nsp10+nsp14/5c8s.1_nsp10+nsp14_fix.pdbqt --ligand $file --center_x -10 --center_y -38 --center_z -8 --size_x 20 --size_y 20 --size_z 20 --num_modes 1 --out nsp10+nsp14_rez/${file%.pdbqt}_out.pdbqt; done
cd nsp10+nsp14_rez/
for file in *_out.pdbqt; do echo -n ${file%_out.pdbqt} && echo -n ", " && grep -m 1 "REMARK VINA RESULT" $file | awk '{print $4}'; done > rez.csv
cd ..

mkdir Q8N1G2_rez/
for file in *.pdbqt; do ~/bin/qvina-master/bin/qvina-w --receptor /home/vytautas/methyl_transferases_docking/human/Q8N1G2/4n49_fix.pdbqt --ligand $file --center_x 8 --center_y 20 --center_z 17 --size_x 20 --size_y 20 --size_z 20 --num_modes 1 --out Q8N1G2_rez/${file%.pdbqt}_out.pdbqt; done
cd Q8N1G2_rez/
for file in *_out.pdbqt; do echo -n ${file%_out.pdbqt} && echo -n ", " && grep -m 1 "REMARK VINA RESULT" $file | awk '{print $4}'; done > rez.csv
cd ..

mkdir nsp16+nsp10_rez/
for file in *.pdbqt; do ~/bin/qvina-master/bin/qvina-w --receptor /home/vytautas/methyl_transferases_docking/virus/nsp16+nsp10/6w4h_fix.pdbqt --ligand $file --center_x 84 --center_y 15 --center_z 27 --size_x 20 --size_y 20 --size_z 20 --num_modes 1 --out nsp16+nsp10_rez/${file%.pdbqt}_out.pdbqt; done
cd nsp16+nsp10_rez/
for file in *_out.pdbqt; do echo -n ${file%_out.pdbqt} && echo -n ", " && grep -m 1 "REMARK VINA RESULT" $file | awk '{print $4}'; done > rez.csv
cd ..

join -t "," ??????_rez/rez.csv > human_rez.csv
join -t "," nsp1?+nsp1?_rez/rez.csv > virus_rez.csv
join -t "," human_rez.csv virus_rez.csv > docking_rez.csv

#po 100 failu:
#!/bin/bash

for i in {101..129}
do
mkdir $i
for file in $(ls -p *.sdf | grep -v / | tail -100)
do
        mv $file $i
done
done