Mercurial > repos > bgruening > autodock_vina
comparison convert_pdbqt_to_sdf.py @ 6:0ae768a0e5c0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
| author | bgruening |
|---|---|
| date | Wed, 19 Jun 2019 06:43:41 -0400 |
| parents | |
| children | 7a871df65202 |
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| 5:c410ffcabf9d | 6:0ae768a0e5c0 |
|---|---|
| 1 import pybel, openbabel | |
| 2 import sys | |
| 3 | |
| 4 | |
| 5 def main(): | |
| 6 if len(sys.argv) == 3: | |
| 7 process(sys.argv[1], sys.argv[2]) | |
| 8 else: | |
| 9 print("Usage: convert_pdbqt_to_sdf.py <input-pdbqt-file> <output-sdf-file>") | |
| 10 exit(1) | |
| 11 | |
| 12 def add_property(mol, prop_name, prop_value): | |
| 13 newData = openbabel.OBPairData() | |
| 14 newData.SetAttribute(prop_name) | |
| 15 newData.SetValue(prop_value) | |
| 16 mol.OBMol.CloneData(newData) | |
| 17 | |
| 18 def process(input, output): | |
| 19 docked = pybel.readfile('pdbqt', input) | |
| 20 sdf = pybel.Outputfile("sdf", output, overwrite=True) | |
| 21 for mol in docked: | |
| 22 if mol.OBMol.HasData('REMARK'): | |
| 23 remark = mol.OBMol.GetData('REMARK').GetValue() | |
| 24 lines = remark.splitlines() | |
| 25 tokens = lines[0].split() | |
| 26 | |
| 27 # add the score property | |
| 28 add_property(mol, "SCORE", tokens[2]) | |
| 29 # add the first RMSD property | |
| 30 add_property(mol, "RMSD_LB", tokens[3]) | |
| 31 # add the second RMSD property | |
| 32 add_property(mol, "RMSD_UB", tokens[4]) | |
| 33 | |
| 34 sdf.write(mol) | |
| 35 | |
| 36 sdf.close() | |
| 37 | |
| 38 if __name__ == "__main__": | |
| 39 main() | |
| 40 |