This is a simple script to use plip to batch analysis of interactions between proteins and ligands that are results of smina (vina) docking.
Note that you should change the directory settings in the script, you can also change the process number in the script.
The script can combine the ligands and receptors automatically, just prepare the receptor directory and results directory.
plip
openbabel
how to obtain plip:
docker pull pharmai/plip:latestYour work directory should look like this:
.
├── analysis.sh
├── dock2interaction_profile.md
├── receptor
│ ├── receptor1
│ │ ├── A0A1D8AVC9.pdb
│ │ ├── A0A1D8AVC9_addH.pdbqt
│ │ └── A0A1D8AVC9_fix.pdb
│ └── receptor2
│ ├── A0A1J5S7S8.pdb
│ ├── A0A1J5S7S8_addH.pdb
│ ├── A0A1J5S7S8_addH.pdbqt
│ └── A0A1J5S7S8_fix.pdb
└── results
├── receptor1_ligand1
│ ├── receptor1_ligand1.pdbqt
│ ├── receptor1_ligand1_01.pdbqt
│ ├── receptor1_ligand1_02.pdbqt
│ ├── receptor1_ligand1_03.pdbqt
│ ├── receptor1_ligand1_04.pdbqt
│ ├── receptor1_ligand1_05.pdbqt
│ ├── receptor1_ligand1_06.pdbqt
│ ├── receptor1_ligand1_07.pdbqt
│ ├── receptor1_ligand1_08.pdbqt
│ ├── receptor1_ligand1_09.pdbqt
│ ├── receptor1_ligand1_10.pdbqt
│ ├── receptor1_ligand1_11.pdbqt
│ ├── receptor1_ligand1_12.pdbqt
│ ├── receptor1_ligand1_13.pdbqt
│ ├── receptor1_ligand1_14.pdbqt
│ ├── receptor1_ligand1_15.pdbqt
│ ├── receptor1_ligand1_16.pdbqt
│ ├── receptor1_ligand1_17.pdbqt
│ ├── receptor1_ligand1_18.pdbqt
│ ├── receptor1_ligand1_19.pdbqt
│ ├── receptor1_ligand1_20.pdbqt
│ ├── receptor1_ligand1_21.pdbqt
│ ├── receptor1_ligand1_22.pdbqt
│ ├── receptor1_ligand1_23.pdbqt
│ ├── receptor1_ligand1_24.pdbqt
│ ├── receptor1_ligand1_25.pdbqt
│ ├── receptor1_ligand1_26.pdbqt
│ ├── receptor1_ligand1_27.pdbqt
│ ├── receptor1_ligand1_28.pdbqt
│ ├── receptor1_ligand1_29.pdbqt
│ ├── receptor1_ligand1_30.pdbqt
│ ├── receptor1_ligand1_31.pdbqt
│ ├── receptor1_ligand1_32.pdbqt
│ ├── receptor1_ligand1_33.pdbqt
│ ├── receptor1_ligand1_34.pdbqt
│ ├── receptor1_ligand1_35.pdbqt
│ ├── receptor1_ligand1_36.pdbqt
│ ├── receptor1_ligand1_37.pdbqt
│ ├── receptor1_ligand1_38.pdbqt
│ ├── receptor1_ligand1_39.pdbqt
│ └── receptor1_ligand1_40.pdbqt
└── receptor2_ligand1
├── receptor1_ligand11.pdbqt
├── receptor1_ligand1_01.pdbqt
├── receptor1_ligand1_02.pdbqt
├── receptor1_ligand1_03.pdbqt
├── receptor1_ligand1_04.pdbqt
├── receptor1_ligand1_05.pdbqt
├── receptor1_ligand1_06.pdbqt
├── receptor1_ligand1_07.pdbqt
├── receptor1_ligand1_08.pdbqt
├── receptor1_ligand1_09.pdbqt
├── receptor1_ligand1_10.pdbqt
├── receptor1_ligand1_11.pdbqt
├── receptor1_ligand1_12.pdbqt
├── receptor1_ligand1_13.pdbqt
├── receptor1_ligand1_14.pdbqt
├── receptor1_ligand1_15.pdbqt
├── receptor1_ligand1_16.pdbqt
├── receptor1_ligand1_17.pdbqt
├── receptor1_ligand1_18.pdbqt
├── receptor1_ligand1_19.pdbqt
├── receptor1_ligand1_20.pdbqt
├── receptor1_ligand1_21.pdbqt
├── receptor1_ligand1_22.pdbqt
├── receptor1_ligand1_23.pdbqt
├── receptor1_ligand1_24.pdbqt
├── receptor1_ligand1_25.pdbqt
├── receptor1_ligand1_26.pdbqt
├── receptor1_ligand1_27.pdbqt
├── receptor1_ligand1_28.pdbqt
├── receptor1_ligand1_29.pdbqt
├── receptor1_ligand1_30.pdbqt
├── receptor1_ligand1_31.pdbqt
├── receptor1_ligand1_32.pdbqt
├── receptor1_ligand1_33.pdbqt
├── receptor1_ligand1_34.pdbqt
├── receptor1_ligand1_35.pdbqt
├── receptor1_ligand1_36.pdbqt
├── receptor1_ligand1_37.pdbqt
├── receptor1_ligand1_38.pdbqt
├── receptor1_ligand1_39.pdbqt
└── receptor1_ligand1_40.pdbqt
6 directories, 91 filesone command to run analysis:
bash analysis.sh