Mercurial > repos > bgruening > autodock_vina
diff convert_pdbqt_to_sdf.py @ 9:90ea16534012 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
| author | bgruening |
|---|---|
| date | Tue, 21 Dec 2021 14:18:33 +0000 |
| parents | 7a871df65202 |
| children |
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--- a/convert_pdbqt_to_sdf.py Tue Jul 28 08:13:41 2020 -0400 +++ b/convert_pdbqt_to_sdf.py Tue Dec 21 14:18:33 2021 +0000 @@ -1,40 +1,43 @@ import sys -from openbabel import pybel, openbabel +from openbabel import openbabel, pybel + def main(): - if len(sys.argv) == 3: - process(sys.argv[1], sys.argv[2]) - else: - print("Usage: convert_pdbqt_to_sdf.py <input-pdbqt-file> <output-sdf-file>") - exit(1) + if len(sys.argv) == 3: + process(sys.argv[1], sys.argv[2]) + else: + print("Usage: convert_pdbqt_to_sdf.py <input-pdbqt-file> <output-sdf-file>") + exit(1) + def add_property(mol, prop_name, prop_value): - newData = openbabel.OBPairData() - newData.SetAttribute(prop_name) - newData.SetValue(prop_value) - mol.OBMol.CloneData(newData) + newData = openbabel.OBPairData() + newData.SetAttribute(prop_name) + newData.SetValue(prop_value) + mol.OBMol.CloneData(newData) + def process(input, output): - docked = pybel.readfile('pdbqt', input) - sdf = pybel.Outputfile("sdf", output, overwrite=True) - for mol in docked: - if mol.OBMol.HasData('REMARK'): - remark = mol.OBMol.GetData('REMARK').GetValue() - lines = remark.splitlines() - tokens = lines[0].split() - - # add the score property - add_property(mol, "SCORE", tokens[2]) - # add the first RMSD property - add_property(mol, "RMSD_LB", tokens[3]) - # add the second RMSD property - add_property(mol, "RMSD_UB", tokens[4]) + docked = pybel.readfile("pdbqt", input) + sdf = pybel.Outputfile("sdf", output, overwrite=True) + for mol in docked: + if mol.OBMol.HasData("REMARK"): + remark = mol.OBMol.GetData("REMARK").GetValue() + lines = remark.splitlines() + tokens = lines[0].split() - sdf.write(mol) + # add the score property + add_property(mol, "SCORE", tokens[2]) + # add the first RMSD property + add_property(mol, "RMSD_LB", tokens[3]) + # add the second RMSD property + add_property(mol, "RMSD_UB", tokens[4]) - sdf.close() + sdf.write(mol) + + sdf.close() + if __name__ == "__main__": main() -