Mercurial > repos > bgruening > autodock_vina

comparison convert_pdbqt_to_sdf.py @ 9:90ea16534012 draft default tip

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"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
comparison
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8:7a871df65202 9:90ea16534012
1 import sys 1 import sys
2 2
3 from openbabel import pybel, openbabel 3 from openbabel import openbabel, pybel
4
4 5
5 def main(): 6 def main():
6 if len(sys.argv) == 3: 7 if len(sys.argv) == 3:
7 process(sys.argv[1], sys.argv[2]) 8 process(sys.argv[1], sys.argv[2])
8 else: 9 else:
9 print("Usage: convert_pdbqt_to_sdf.py <input-pdbqt-file> <output-sdf-file>") 10 print("Usage: convert_pdbqt_to_sdf.py <input-pdbqt-file> <output-sdf-file>")
10 exit(1) 11 exit(1)
12
11 13
12 def add_property(mol, prop_name, prop_value): 14 def add_property(mol, prop_name, prop_value):
13 newData = openbabel.OBPairData() 15 newData = openbabel.OBPairData()
14 newData.SetAttribute(prop_name) 16 newData.SetAttribute(prop_name)
15 newData.SetValue(prop_value) 17 newData.SetValue(prop_value)
16 mol.OBMol.CloneData(newData) 18 mol.OBMol.CloneData(newData)
19
17 20
18 def process(input, output): 21 def process(input, output):
19 docked = pybel.readfile('pdbqt', input) 22 docked = pybel.readfile("pdbqt", input)
20 sdf = pybel.Outputfile("sdf", output, overwrite=True) 23 sdf = pybel.Outputfile("sdf", output, overwrite=True)
21 for mol in docked: 24 for mol in docked:
22 if mol.OBMol.HasData('REMARK'): 25 if mol.OBMol.HasData("REMARK"):
23 remark = mol.OBMol.GetData('REMARK').GetValue() 26 remark = mol.OBMol.GetData("REMARK").GetValue()
24 lines = remark.splitlines() 27 lines = remark.splitlines()
25 tokens = lines[0].split() 28 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 29
34 sdf.write(mol) 30 # add the score property
31 add_property(mol, "SCORE", tokens[2])
32 # add the first RMSD property
33 add_property(mol, "RMSD_LB", tokens[3])
34 # add the second RMSD property
35 add_property(mol, "RMSD_UB", tokens[4])
35 36
36 sdf.close() 37 sdf.write(mol)
38
39 sdf.close()
40
37 41
38 if __name__ == "__main__": 42 if __name__ == "__main__":
39 main() 43 main()
40