add test set files

app.py

@@ -10,16 +10,16 @@ import os
 
 
 def load(value: str):
-    full_pdb_path = '../MolCRAFT/data/test_set/' + value
+    full_pdb_path = './test_set/' + value
     sdf_path = glob.glob(full_pdb_path.rstrip('.pdb') + '*.sdf')
     assert len(sdf_path) == 1
     sdf_path = sdf_path[0]
     return [full_pdb_path, sdf_path]
 
-pdb_files = glob.glob("../MolCRAFT/data/test_set/*/*.pdb")
+pdb_files = glob.glob("./test_set/*/*.pdb")
 pdb_files = [f for f in pdb_files if 'ligand' not in f and 'complex' not in f]
 pdb_files = sorted(pdb_files)
-pdb_files = [f[26:] for f in pdb_files if '../MolCRAFT/data/test_set/' in f and '_tmp.pdb' not in f]
+pdb_files = [f[11:] for f in pdb_files if './test_set/' in f and '_tmp.pdb' not in f]
 pdb_files = [f for f in pdb_files if 'pdb/' not in f]
 
 

test_set/.pqr.log

@@ -0,0 +1,210 @@
+2024-03-03 11:21:47,224 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:21:47,224 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:21:47,224 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:21:47,225 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:21:47,227 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:21:47,334 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:21:56,759 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:21:56,759 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:21:56,759 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:21:56,759 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:21:56,760 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:21:56,865 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:21:58,490 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:21:58,490 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:21:58,491 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:21:58,491 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:21:58,491 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:21:58,555 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:22:17,740 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:22:17,740 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:22:17,741 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:22:17,741 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:22:17,742 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:22:17,846 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:22:36,768 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:22:36,768 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:22:36,768 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:22:36,769 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:22:36,769 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:22:36,873 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:22:37,956 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:22:37,956 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:22:37,956 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:22:37,956 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:22:37,957 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:22:38,043 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:08,448 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:08,448 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:08,448 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:08,448 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:08,449 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:08,553 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:10,106 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:10,106 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:10,106 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:10,106 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:10,107 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:10,198 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:12,100 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:12,100 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:12,100 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:12,100 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:12,101 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:12,177 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:15,482 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:15,482 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:15,482 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:15,482 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:15,483 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:15,539 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:29,231 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:29,231 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:29,231 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:29,231 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:29,232 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:29,335 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:30,156 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:30,156 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:30,156 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:30,156 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:30,157 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:30,214 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:30,715 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:30,715 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:30,715 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:30,715 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:30,716 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:30,807 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:38,719 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:38,720 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:38,720 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:38,720 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:38,721 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:38,824 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:47,801 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:47,801 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:47,801 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:47,801 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:47,801 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:47,861 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:48,483 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:48,483 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:48,483 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:48,483 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:48,484 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:48,581 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:24:50,109 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:24:50,109 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:24:50,110 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:24:50,110 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:24:50,110 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:24:50,170 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:25:00,159 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:25:00,159 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:25:00,159 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:25:00,159 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:25:00,160 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:25:00,230 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:25:38,922 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:25:38,922 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:25:38,922 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:25:38,922 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:25:38,923 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:25:39,026 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:25:51,476 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:25:51,476 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:25:51,476 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:25:51,476 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:25:51,477 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:25:51,578 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:19,646 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:19,646 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:19,646 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:19,646 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:19,647 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:19,703 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:20,379 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:20,379 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:20,379 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:20,379 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:20,379 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:20,429 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:20,890 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:20,890 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:20,890 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:20,890 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:20,891 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:20,943 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:21,585 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:21,585 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:21,585 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:21,585 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:21,586 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:21,637 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:22,087 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:22,087 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:22,087 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:22,087 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:22,087 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:22,138 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:22,906 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:22,906 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:22,906 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:22,906 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:22,906 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:22,956 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:27:24,188 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:27:24,189 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:27:24,189 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:27:24,189 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:27:24,189 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:27:24,283 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-03 11:28:15,118 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-03 11:28:15,118 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-03 11:28:15,118 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-03 11:28:15,118 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-03 11:28:15,119 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-03 11:28:15,169 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-24 22:44:01,247 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-24 22:44:01,247 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 22:44:01,247 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 22:44:01,247 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-24 22:44:01,249 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-24 22:44:01,337 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-24 22:59:08,444 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-24 22:59:08,444 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 22:59:08,444 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 22:59:08,444 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-24 22:59:08,470 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-24 22:59:08,561 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-24 23:06:00,805 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-24 23:06:00,805 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 23:06:00,806 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 23:06:00,806 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-24 23:06:00,808 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-24 23:06:00,896 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-24 23:33:15,137 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-24 23:33:15,137 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 23:33:15,137 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 23:33:15,137 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-24 23:33:15,141 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-24 23:33:15,625 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-25 01:10:37,479 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-25 01:10:37,479 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-25 01:10:37,479 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-25 01:10:37,479 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-25 01:10:37,480 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-25 01:10:37,583 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-25 04:11:38,836 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-25 04:11:38,836 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-25 04:11:38,836 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-25 04:11:38,836 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-25 04:11:38,837 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-25 04:11:38,930 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb
+2024-03-25 06:21:16,202 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2024-03-25 06:21:16,202 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-25 06:21:16,202 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-25 06:21:16,202 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2024-03-25 06:21:16,203 INFO:main.py:763:main_driver:Loading topology files.
+2024-03-25 06:21:16,269 INFO:main.py:765:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/.pdb

test_set/1coy_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:08,848 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:08,848 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:08,848 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:08,848 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:08,848 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:08,950 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/1coy_A_rec.pdb
+2024-03-24 04:40:03,059 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:03,059 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:03,059 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:03,059 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:03,060 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:03,162 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/1coy_A_rec.pdb
+2024-03-24 04:40:29,087 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:29,087 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:29,087 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:29,087 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:29,087 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:29,187 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/1coy_A_rec.pdb

test_set/1fmc_B_rec.log

@@ -0,0 +1,6 @@
+2024-03-24 04:39:12,871 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:12,871 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:12,872 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:12,872 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:12,872 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:12,972 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/1fmc_B_rec.pdb

test_set/2e24_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:02,142 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:02,142 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:02,142 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:02,142 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:02,142 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:02,247 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/2e24_A_rec.pdb
+2024-03-24 04:39:55,969 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:55,969 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:55,969 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:55,969 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:55,969 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:56,046 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/2e24_A_rec.pdb
+2024-03-24 04:40:22,252 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:22,252 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:22,252 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:22,252 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:22,252 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:22,343 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/2e24_A_rec.pdb

test_set/3dzh_A_rec.log

@@ -0,0 +1,24 @@
+2024-03-24 04:38:57,596 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:38:57,596 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:38:57,596 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:38:57,596 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:38:57,596 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:38:57,695 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3dzh_A_rec.pdb
+2024-03-24 04:39:52,105 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:52,105 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:52,105 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:52,105 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:52,105 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:52,171 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3dzh_A_rec.pdb
+2024-03-24 04:40:18,191 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:18,191 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:18,192 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:18,192 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:18,192 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:18,292 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3dzh_A_rec.pdb
+2024-03-24 04:42:24,980 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:42:24,980 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:42:24,980 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:42:24,980 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:42:24,980 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:42:25,085 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3dzh_A_rec.pdb

test_set/3l3n_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:07,413 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:07,413 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:07,413 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:07,413 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:07,413 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:07,498 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3l3n_A_rec.pdb
+2024-03-24 04:40:01,627 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:01,627 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:01,628 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:01,628 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:01,628 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:01,739 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3l3n_A_rec.pdb
+2024-03-24 04:40:27,729 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:27,729 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:27,729 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:27,729 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:27,729 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:27,811 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3l3n_A_rec.pdb

test_set/3pdh_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:00,819 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:00,819 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:00,820 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:00,820 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:00,820 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:00,888 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3pdh_A_rec.pdb
+2024-03-24 04:39:54,612 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:54,612 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:54,612 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:54,612 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:54,612 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:54,681 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3pdh_A_rec.pdb
+2024-03-24 04:40:20,966 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:20,966 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:20,966 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:20,966 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:20,966 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:21,064 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3pdh_A_rec.pdb

test_set/3tym_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:38:59,533 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:38:59,533 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:38:59,533 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:38:59,533 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:38:59,533 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:38:59,631 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3tym_A_rec.pdb
+2024-03-24 04:39:53,371 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:53,371 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:53,371 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:53,371 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:53,371 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:53,460 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3tym_A_rec.pdb
+2024-03-24 04:40:19,529 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:19,529 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:19,529 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:19,529 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:19,529 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:19,629 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/3tym_A_rec.pdb

test_set/4aua_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:06,024 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:06,024 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:06,024 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:06,024 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:06,025 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:06,130 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4aua_A_rec.pdb
+2024-03-24 04:40:00,171 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:00,172 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:00,172 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:00,172 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:00,172 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:00,277 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4aua_A_rec.pdb
+2024-03-24 04:40:26,413 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:26,413 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:26,413 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:26,413 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:26,413 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:26,499 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4aua_A_rec.pdb

test_set/4rlu_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:04,670 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:04,670 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:04,670 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:04,671 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:04,671 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:04,761 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4rlu_A_rec.pdb
+2024-03-24 04:39:58,822 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:58,822 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:58,822 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:58,822 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:58,822 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:58,922 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4rlu_A_rec.pdb
+2024-03-24 04:40:25,024 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:25,024 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:25,024 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:25,024 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:25,024 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:25,118 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4rlu_A_rec.pdb

test_set/4xli_B_rec.log

@@ -0,0 +1,6 @@
+2024-03-24 04:39:11,442 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:11,442 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:11,442 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:11,443 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:11,443 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:11,512 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/4xli_B_rec.pdb

test_set/5d7n_D_rec.log

@@ -0,0 +1,12 @@
+2024-03-24 04:39:10,165 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:10,165 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:10,165 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:10,165 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:10,166 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:10,255 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/5d7n_D_rec.pdb
+2024-03-24 04:40:04,458 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:04,458 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:04,458 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:04,458 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:04,458 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:04,558 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/5d7n_D_rec.pdb

test_set/5i0b_A_rec.log

@@ -0,0 +1,18 @@
+2024-03-24 04:39:03,478 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:03,479 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:03,479 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:03,479 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:03,479 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:03,550 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/5i0b_A_rec.pdb
+2024-03-24 04:39:57,389 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:39:57,389 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:39:57,389 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:39:57,389 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:39:57,389 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:39:57,487 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/5i0b_A_rec.pdb
+2024-03-24 04:40:23,670 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-24 04:40:23,671 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-24 04:40:23,671 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-24 04:40:23,671 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-24 04:40:23,671 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-24 04:40:23,781 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/5i0b_A_rec.pdb

test_set/8RI2_molec.log

@@ -0,0 +1,60 @@
+2024-03-06 10:53:49,928 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:49,928 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:49,928 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:49,928 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:49,928 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:49,989 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:51,520 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:51,520 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:51,520 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:51,520 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:51,520 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:51,580 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:52,987 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:52,987 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:52,987 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:52,987 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:52,987 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:53,046 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:54,328 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:54,329 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:54,329 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:54,329 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:54,329 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:54,388 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:55,674 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:55,674 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:55,674 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:55,674 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:55,674 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:55,746 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:57,011 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:57,011 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:57,011 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:57,011 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:57,011 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:57,071 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:58,479 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:58,479 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:58,479 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:58,480 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:58,480 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:58,567 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:53:59,884 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:53:59,884 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:53:59,884 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:53:59,884 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:53:59,884 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:53:59,943 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:54:01,220 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:54:01,220 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:54:01,220 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:54:01,220 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:54:01,220 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:54:01,280 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb
+2024-03-06 10:54:02,565 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.2: biomolecular structure conversion software.
+2024-03-06 10:54:02,565 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2024-03-06 10:54:02,565 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2024-03-06 10:54:02,565 INFO:main.py:768:main_driver:Checking and transforming input arguments.
+2024-03-06 10:54:02,565 INFO:main.py:772:main_driver:Loading topology files.
+2024-03-06 10:54:02,625 INFO:main.py:774:main_driver:Loading molecule: /sharefs/share/sbdd_data/test_set/8RI2_molec.pdb

test_set/ABL2_HUMAN_274_551_0/4xli_B_rec.log

@@ -0,0 +1,32 @@
+2023-07-11 15:23:05,131 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2023-07-11 15:23:05,131 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2023-07-11 15:23:05,131 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2023-07-11 15:23:05,131 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2023-07-11 15:23:05,131 INFO:main.py:763:main_driver:Loading topology files.
+2023-07-11 15:23:05,175 INFO:main.py:765:main_driver:Loading molecule: ./data/test_set/ABL2_HUMAN_274_551_0/4xli_B_rec.pdb
+2023-07-11 15:23:05,175 ERROR:pdb.py:2584:read_pdb:Error parsing line: invalid literal for int() with base 10: 'Sel'
+2023-07-11 15:23:05,175 ERROR:pdb.py:2585:read_pdb:<REMARK Selection '(protein and ch... and not water)'>
+2023-07-11 15:23:05,175 ERROR:pdb.py:2586:read_pdb:Truncating remaining errors for record type:REMARK
+2023-07-11 15:23:05,183 WARNING:io.py:467:get_molecule:Warning: data/test_set/ABL2_HUMAN_274_551_0/4xli_B_rec.pdb is a non-standard PDB file.
+
+2023-07-11 15:23:05,183 ERROR:io.py:468:get_molecule:['REMARK']
+2023-07-11 15:23:05,183 INFO:main.py:770:main_driver:Setting up molecule.
+2023-07-11 15:23:05,199 INFO:main.py:408:setup_molecule:Created biomolecule object with 264 residues and 2131 atoms.
+2023-07-11 15:23:05,199 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
+2023-07-11 15:23:05,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY B 295 and GLY B 300!
+2023-07-11 15:23:05,204 INFO:main.py:604:non_trivial:Loading forcefield.
+2023-07-11 15:23:05,211 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
+2023-07-11 15:23:05,213 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue SER B 546
+2023-07-11 15:23:05,214 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue SER B 546
+2023-07-11 15:23:05,214 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
+2023-07-11 15:23:05,215 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue SER B 546
+2023-07-11 15:23:05,216 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue SER B 546 at coordinates 19.876, 3.803, 49.896
+2023-07-11 15:23:05,216 INFO:main.py:623:non_trivial:Updating disulfide bridges.
+2023-07-11 15:23:05,216 INFO:main.py:626:non_trivial:Debumping biomolecule.
+2023-07-11 15:23:05,265 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
+2023-07-11 15:23:05,482 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
+2023-07-11 15:23:05,726 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
+2023-07-11 15:23:06,219 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
+2023-07-11 15:23:06,223 INFO:main.py:713:non_trivial:Regenerating headers.
+2023-07-11 15:23:06,224 INFO:main.py:738:non_trivial:Regenerating PDB lines.
+2023-07-11 15:23:06,242 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.

test_set/ABL2_HUMAN_274_551_0/4xli_B_rec_4xli_1n1_lig_tt_min_0.sdf

@@ -0,0 +1,83 @@
+__4xli_B_rec_4xli_1n1_lig_min.pdb
+ OpenBabel10171920533D
+
+ 33 36  0  0  0  0  0  0  0  0999 V2000
+    6.9040    6.2090   22.9690 N   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0620    7.2160   23.3240 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.0420    6.9230   24.2150 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.1490    7.9270   24.6100 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3280    9.4590   23.2720 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4440   10.8410   22.7330 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.3450    9.1990   24.1560 N   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1890    8.4920   22.8640 N   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7840    7.1640   27.0900 N   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7720    7.8870   24.9140 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.0790    6.4100   26.2380 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.0930    7.7020   25.5360 N   0  0  0  0  0  0  0  0  0  0  0  0
+    0.8660    8.2430   26.0740 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1030    6.5250   27.4190 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0360    7.7640   28.2400 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7960    7.8930   29.5640 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2380    9.2530   29.7000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.1350    6.0520   21.6340 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.8200    7.1630   20.8360 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.0440    6.4270   22.2720 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.1170    5.6210   22.4690 N   0  0  0  0  0  0  0  0  0  0  0  0
+    8.1980    7.7170   21.1090 S   0  0  0  0  0  0  0  0  0  0  0  0
+   10.6180    7.9690   19.8410 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.6330    7.3000   19.3290 N   0  0  0  0  0  0  0  0  0  0  0  0
+   10.3670    9.1410   19.5890 O   0  0  0  0  0  0  0  0  0  0  0  0
+   14.1160    9.5230   16.8370 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.4450    9.4520   18.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.6880    8.6800   19.0550 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.0340    8.6060   20.4860 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.5520    7.8960   18.5310 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.2670    8.0590   17.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.0310    8.8590   16.3010 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.8650    7.1590   16.5470 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+  1 20  1  0  0  0  0
+  1  2  1  0  0  0  0
+  2  8  2  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  2  0  0  0  0
+  4  7  1  0  0  0  0
+  4 12  1  0  0  0  0
+  5  6  1  0  0  0  0
+  5  8  1  0  0  0  0
+  5  7  2  0  0  0  0
+  9 13  1  0  0  0  0
+  9 14  1  0  0  0  0
+  9 15  1  0  0  0  0
+ 10 12  1  0  0  0  0
+ 10 13  1  0  0  0  0
+ 11 12  1  0  0  0  0
+ 11 14  1  0  0  0  0
+ 15 16  1  0  0  0  0
+ 16 17  1  0  0  0  0
+ 18 19  2  0  0  0  0
+ 18 21  1  0  0  0  0
+ 19 23  1  0  0  0  0
+ 19 22  1  0  0  0  0
+ 20 22  1  0  0  0  0
+ 20 21  2  0  0  0  0
+ 23 24  1  0  0  0  0
+ 23 25  2  0  0  0  0
+ 24 30  1  0  0  0  0
+ 26 32  2  0  0  0  0
+ 26 27  1  0  0  0  0
+ 27 28  2  0  0  0  0
+ 28 30  1  0  0  0  0
+ 28 29  1  0  0  0  0
+ 30 31  2  0  0  0  0
+ 31 32  1  0  0  0  0
+ 31 33  1  0  0  0  0
+M  END
+>  <COMPND>
+    UNNAMED
+
+>  <AUTHOR>
+    GENERATED BY OPEN BABEL 2.4.90
+
+>  <MASTER>
+        0    0    0    0    0    0    0    0   33    0   33    0
+

test_set/ACE_HUMAN_650_1230_0/3l3n_A_rec.log

@@ -0,0 +1,36 @@
+2023-07-28 20:31:41,722 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2023-07-28 20:31:41,722 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2023-07-28 20:31:41,722 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2023-07-28 20:31:41,722 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2023-07-28 20:31:41,723 INFO:main.py:763:main_driver:Loading topology files.
+2023-07-28 20:31:41,816 INFO:main.py:765:main_driver:Loading molecule: /data/crossdock/test_set/ACE_HUMAN_650_1230_0/3l3n_A_rec.pdb
+2023-07-28 20:31:41,817 ERROR:pdb.py:2584:read_pdb:Error parsing line: invalid literal for int() with base 10: 'Sel'
+2023-07-28 20:31:41,817 ERROR:pdb.py:2585:read_pdb:<REMARK Selection 'protein or ion and not water'>
+2023-07-28 20:31:41,817 ERROR:pdb.py:2586:read_pdb:Truncating remaining errors for record type:REMARK
+2023-07-28 20:31:41,866 WARNING:io.py:467:get_molecule:Warning: /data/crossdock/test_set/ACE_HUMAN_650_1230_0/3l3n_A_rec.pdb is a non-standard PDB file.
+
+2023-07-28 20:31:41,866 ERROR:io.py:468:get_molecule:['REMARK']
+2023-07-28 20:31:41,866 INFO:main.py:770:main_driver:Setting up molecule.
+2023-07-28 20:31:41,912 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for ZN.  Parsing as new residue.
+2023-07-28 20:31:41,912 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for CL.  Parsing as new residue.
+2023-07-28 20:31:41,913 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for CL.  Parsing as new residue.
+2023-07-28 20:31:41,914 INFO:main.py:408:setup_molecule:Created biomolecule object with 578 residues and 4692 atoms.
+2023-07-28 20:31:41,915 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
+2023-07-28 20:31:42,055 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 435 and SER A 439!
+2023-07-28 20:31:42,057 INFO:main.py:604:non_trivial:Loading forcefield.
+2023-07-28 20:31:42,070 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
+2023-07-28 20:31:42,079 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue PRO A 617
+2023-07-28 20:31:42,083 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue PRO A 617
+2023-07-28 20:31:42,083 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
+2023-07-28 20:31:42,088 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue PRO A 617
+2023-07-28 20:31:42,092 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue PRO A 617 at coordinates 1.630, -10.537, 50.625
+2023-07-28 20:31:42,092 INFO:main.py:623:non_trivial:Updating disulfide bridges.
+2023-07-28 20:31:42,095 INFO:main.py:626:non_trivial:Debumping biomolecule.
+2023-07-28 20:31:42,325 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
+2023-07-28 20:31:43,591 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
+2023-07-28 20:31:44,899 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
+2023-07-28 20:31:47,251 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
+2023-07-28 20:31:47,271 INFO:main.py:713:non_trivial:Regenerating headers.
+2023-07-28 20:31:47,275 INFO:main.py:738:non_trivial:Regenerating PDB lines.
+2023-07-28 20:31:47,358 WARNING:main.py:311:print_pqr:Ignoring 856 header lines in output.
+2023-07-28 20:31:47,359 WARNING:main.py:315:print_pqr:Ignoring 3 missing lines in output.

test_set/ACE_HUMAN_650_1230_0/3l3n_A_rec_2iux_nxa_lig_tt_docked_2.sdf

@@ -0,0 +1,34 @@
+__3l3n_A_rec_2iux_nxa_lig_docked.pdb
+ OpenBabel10171921053D
+
+  9  8  0  0  1  0  0  0  0  0999 V2000
+  -13.6120   -8.0970   23.1700 N   0  0  0  0  0  0  0  0  0  0  0  0
+  -12.2880   -7.7880   21.1860 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -14.6040   -7.9060   21.1990 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -13.4260   -7.9200   21.8000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -12.3760   -8.1480   24.0250 C   0  0  1  0  0  0  0  0  0  0  0  0
+  -12.7900   -7.3580   25.2550 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -11.7250   -9.4670   24.5120 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -10.6290   -9.2580   25.1680 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -11.9840  -10.7100   24.4300 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+  2  4  2  0  0  0  0
+  3  4  1  0  0  0  0
+  5  7  1  0  0  0  0
+  5  6  1  1  0  0  0
+  7  8  2  0  0  0  0
+  7  9  1  0  0  0  0
+M  END
+>  <MODEL>
+       3
+
+>  <COMPND>
+    UNNAMED
+
+>  <AUTHOR>
+    GENERATED BY OPEN BABEL 2.4.90
+
+>  <MASTER>
+        0    0    0    0    0    0    0    0    9    0    9    0
+

test_set/AK1BA_HUMAN_1_316_0/5liu_X_rec.log

@@ -0,0 +1,82 @@
+2023-07-28 20:45:52,413 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2023-07-28 20:45:52,413 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2023-07-28 20:45:52,413 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2023-07-28 20:45:52,413 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2023-07-28 20:45:52,414 INFO:main.py:763:main_driver:Loading topology files.
+2023-07-28 20:45:52,494 INFO:main.py:765:main_driver:Loading molecule: /data/crossdock/test_set/AK1BA_HUMAN_1_316_0/5liu_X_rec.pdb
+2023-07-28 20:45:52,499 ERROR:pdb.py:2584:read_pdb:Error parsing line: invalid literal for int() with base 10: 'Sel'
+2023-07-28 20:45:52,500 ERROR:pdb.py:2585:read_pdb:<REMARK Selection 'protein or ion and not water'>
+2023-07-28 20:45:52,500 ERROR:pdb.py:2586:read_pdb:Truncating remaining errors for record type:REMARK
+2023-07-28 20:45:52,531 WARNING:io.py:467:get_molecule:Warning: /data/crossdock/test_set/AK1BA_HUMAN_1_316_0/5liu_X_rec.pdb is a non-standard PDB file.
+
+2023-07-28 20:45:52,531 ERROR:io.py:468:get_molecule:['REMARK']
+2023-07-28 20:45:52,531 INFO:main.py:770:main_driver:Setting up molecule.
+2023-07-28 20:45:52,597 INFO:main.py:408:setup_molecule:Created biomolecule object with 302 residues and 2422 atoms.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CA in GLU X 30.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CB in GLU X 30.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CG in GLU X 30.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CD in GLU X 30.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: OE1 in GLU X 30.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: OE2 in GLU X 30.
+2023-07-28 20:45:52,597 WARNING:main.py:424:setup_molecule:Multiple occupancies found in GLU X 30. At least one of the instances is being ignored.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CA in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CB in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CG in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CD1 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CD2 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: NE1 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CE2 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CE3 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CZ2 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CZ3 in TRP X 112.
+2023-07-28 20:45:52,597 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CH2 in TRP X 112.
+2023-07-28 20:45:52,598 WARNING:main.py:424:setup_molecule:Multiple occupancies found in TRP X 112. At least one of the instances is being ignored.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CA in GLN X 114.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CB in GLN X 114.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CG in GLN X 114.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CD in GLN X 114.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: OE1 in GLN X 114.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: NE2 in GLN X 114.
+2023-07-28 20:45:52,598 WARNING:main.py:424:setup_molecule:Multiple occupancies found in GLN X 114. At least one of the instances is being ignored.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: N in SER X 227.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CA in SER X 227.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: C in SER X 227.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: O in SER X 227.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CB in SER X 227.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: OG in SER X 227.
+2023-07-28 20:45:52,598 WARNING:main.py:424:setup_molecule:Multiple occupancies found in SER X 227. At least one of the instances is being ignored.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: N in ASN X 300.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CA in ASN X 300.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: C in ASN X 300.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: O in ASN X 300.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CB in ASN X 300.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: CG in ASN X 300.
+2023-07-28 20:45:52,598 WARNING:main.py:418:setup_molecule:Multiple occupancies found: OD1 in ASN X 300.
+2023-07-28 20:45:52,599 WARNING:main.py:418:setup_molecule:Multiple occupancies found: ND2 in ASN X 300.
+2023-07-28 20:45:52,599 WARNING:main.py:424:setup_molecule:Multiple occupancies found in ASN X 300. At least one of the instances is being ignored.
+2023-07-28 20:45:52,599 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
+2023-07-28 20:45:52,609 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA X 11 and MET X 13!
+2023-07-28 20:45:52,609 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY X 26 and VAL X 28!
+2023-07-28 20:45:52,609 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL X 32 and VAL X 34!
+2023-07-28 20:45:52,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU X 61 and ILE X 63!
+2023-07-28 20:45:52,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU X 65 and ALA X 67!
+2023-07-28 20:45:52,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU X 94 and THR X 96!
+2023-07-28 20:45:52,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU X 97 and ASP X 99!
+2023-07-28 20:45:52,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL X 154 and ALA X 156!
+2023-07-28 20:45:52,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU X 176 and TYR X 178!
+2023-07-28 20:45:52,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER X 202 and GLY X 204!
+2023-07-28 20:45:52,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO X 232 and ILE X 234!
+2023-07-28 20:45:52,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS X 241 and THR X 244!
+2023-07-28 20:45:52,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO X 262 and SER X 264!
+2023-07-28 20:45:52,613 INFO:main.py:604:non_trivial:Loading forcefield.
+2023-07-28 20:45:52,625 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
+2023-07-28 20:45:52,643 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
+2023-07-28 20:45:52,643 INFO:main.py:623:non_trivial:Updating disulfide bridges.
+2023-07-28 20:45:52,644 INFO:main.py:626:non_trivial:Debumping biomolecule.
+2023-07-28 20:45:52,845 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
+2023-07-28 20:45:53,394 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
+2023-07-28 20:45:54,024 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
+2023-07-28 20:45:55,191 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
+2023-07-28 20:45:55,202 INFO:main.py:713:non_trivial:Regenerating headers.
+2023-07-28 20:45:55,204 INFO:main.py:738:non_trivial:Regenerating PDB lines.
+2023-07-28 20:45:55,248 WARNING:main.py:311:print_pqr:Ignoring 392 header lines in output.

test_set/AK1BA_HUMAN_1_316_0/5liu_X_rec_4gq0_qap_lig_tt_min_0.sdf

@@ -0,0 +1,57 @@
+__5liu_X_rec_4gq0_qap_lig_min.pdb
+ OpenBabel10171920543D
+
+ 21 22  0  0  0  0  0  0  0  0999 V2000
+  -17.3270   36.1010    4.3310 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -17.3680   36.5290    5.5900 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -16.2000   31.4000    3.7270 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -14.2680   32.0810    1.8610 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -16.4710   35.0580    3.7650 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -16.7400   33.6910    4.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -15.4270   35.3750    2.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -15.9800   32.7150    3.4180 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -14.9560   33.0470    2.5280 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -14.6760   34.3960    2.2920 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -18.5500   38.5760    5.3540 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -18.3020   37.5910    6.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -18.8710   37.3750    7.2140 O   0  0  0  0  0  0  0  0  0  0  0  0
+  -19.9670   38.2480    7.6050 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -21.0550   37.4250    8.2900 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -22.2630   37.1330    7.4270 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -22.1590   36.3400    6.2940 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -23.5100   37.6440    7.7530 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -23.2680   36.0630    5.5120 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -24.6210   37.3670    6.9700 C   0  0  0  0  0  0  0  0  0  0  0  0
+  -24.5000   36.5760    5.8510 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  5  1  0  0  0  0
+  1  2  2  0  0  0  0
+  2 12  1  0  0  0  0
+  3  8  1  0  0  0  0
+  4  9  1  0  0  0  0
+  5  7  2  0  0  0  0
+  5  6  1  0  0  0  0
+  6  8  2  0  0  0  0
+  7 10  1  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  2  0  0  0  0
+ 11 12  2  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 14  1  0  0  0  0
+ 14 15  1  0  0  0  0
+ 15 16  1  0  0  0  0
+ 16 17  2  0  0  0  0
+ 16 18  1  0  0  0  0
+ 17 19  1  0  0  0  0
+ 18 20  2  0  0  0  0
+ 19 21  2  0  0  0  0
+ 20 21  1  0  0  0  0
+M  END
+>  <COMPND>
+    UNNAMED
+
+>  <AUTHOR>
+    GENERATED BY OPEN BABEL 2.4.90
+
+>  <MASTER>
+        0    0    0    0    0    0    0    0   21    0   21    0
+

test_set/AKT1_HUMAN_1_137_0/3o96_A_rec.log

@@ -0,0 +1,36 @@
+2023-07-28 21:45:50,872 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2023-07-28 21:45:50,872 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2023-07-28 21:45:50,872 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2023-07-28 21:45:50,872 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2023-07-28 21:45:50,873 INFO:main.py:763:main_driver:Loading topology files.
+2023-07-28 21:45:51,016 INFO:main.py:765:main_driver:Loading molecule: /data/crossdock/test_set/AKT1_HUMAN_1_137_0/3o96_A_rec.pdb
+2023-07-28 21:45:51,017 ERROR:pdb.py:2584:read_pdb:Error parsing line: invalid literal for int() with base 10: 'Sel'
+2023-07-28 21:45:51,017 ERROR:pdb.py:2585:read_pdb:<REMARK Selection 'protein or ion and not water'>
+2023-07-28 21:45:51,017 ERROR:pdb.py:2586:read_pdb:Truncating remaining errors for record type:REMARK
+2023-07-28 21:45:51,053 WARNING:io.py:467:get_molecule:Warning: /data/crossdock/test_set/AKT1_HUMAN_1_137_0/3o96_A_rec.pdb is a non-standard PDB file.
+
+2023-07-28 21:45:51,053 ERROR:io.py:468:get_molecule:['REMARK']
+2023-07-28 21:45:51,053 INFO:main.py:770:main_driver:Setting up molecule.
+2023-07-28 21:45:51,080 INFO:main.py:408:setup_molecule:Created biomolecule object with 367 residues and 3031 atoms.
+2023-07-28 21:45:51,081 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
+2023-07-28 21:45:51,092 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 45 and GLU A 49!
+2023-07-28 21:45:51,092 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 88 and THR A 92!
+2023-07-28 21:45:51,093 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 113 and VAL A 145!
+2023-07-28 21:45:51,093 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 188 and ASN A 199!
+2023-07-28 21:45:51,094 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 298 and PRO A 313!
+2023-07-28 21:45:51,096 INFO:main.py:604:non_trivial:Loading forcefield.
+2023-07-28 21:45:51,107 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
+2023-07-28 21:45:51,112 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue VAL A 429
+2023-07-28 21:45:51,115 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue VAL A 429
+2023-07-28 21:45:51,115 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
+2023-07-28 21:45:51,117 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue VAL A 429
+2023-07-28 21:45:51,119 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue VAL A 429 at coordinates 37.370, 63.648, -3.293
+2023-07-28 21:45:51,119 INFO:main.py:623:non_trivial:Updating disulfide bridges.
+2023-07-28 21:45:51,120 INFO:main.py:626:non_trivial:Debumping biomolecule.
+2023-07-28 21:45:51,266 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
+2023-07-28 21:45:52,010 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
+2023-07-28 21:45:52,768 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
+2023-07-28 21:45:54,083 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
+2023-07-28 21:45:54,110 INFO:main.py:713:non_trivial:Regenerating headers.
+2023-07-28 21:45:54,123 INFO:main.py:738:non_trivial:Regenerating PDB lines.
+2023-07-28 21:45:54,233 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.

test_set/AKT1_HUMAN_1_137_0/3o96_A_rec_3o96_iqo_lig_tt_docked_2.sdf

@@ -0,0 +1,108 @@
+__3o96_A_rec_3o96_iqo_lig_docked.pdb
+ OpenBabel10171920423D
+
+ 42 49  0  0  0  0  0  0  0  0999 V2000
+   33.4590   43.8370   16.3950 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.0730   44.5540   17.0660 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.0110   45.4630   17.2280 C   0  0  0  0  0  0  0  0  0  0  0  0
+   33.7280   45.1020   16.8930 C   0  0  0  0  0  0  0  0  0  0  0  0
+   34.5130   42.9030   16.2270 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.8190   43.2660   16.5650 C   0  0  0  0  0  0  0  0  0  0  0  0
+   38.2730   45.7450   16.4940 C   0  0  0  0  0  0  0  0  0  0  0  0
+   39.6260   44.6050   20.2660 C   0  0  0  0  0  0  0  0  0  0  0  0
+   39.5190   46.1040   16.8850 N   0  0  0  0  0  0  0  0  0  0  0  0
+   37.4080   44.9440   17.4210 C   0  0  0  0  0  0  0  0  0  0  0  0
+   37.8800   44.5880   18.6380 N   0  0  0  0  0  0  0  0  0  0  0  0
+   39.1320   44.9690   18.9930 C   0  0  0  0  0  0  0  0  0  0  0  0
+   40.9170   45.0040   20.6410 C   0  0  0  0  0  0  0  0  0  0  0  0
+   41.7010   45.7250   19.8120 C   0  0  0  0  0  0  0  0  0  0  0  0
+   41.2430   46.1060   18.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
+   39.9540   45.7300   18.1160 C   0  0  0  0  0  0  0  0  0  0  0  0
+   42.8270   45.4240   21.5700 C   0  0  0  0  0  0  0  0  0  0  0  0
+   41.6530   44.8070   21.7920 N   0  0  0  0  0  0  0  0  0  0  0  0
+   42.9390   46.0160   20.3730 N   0  0  0  0  0  0  0  0  0  0  0  0
+   37.8020   46.1800   15.1410 C   0  0  0  0  0  0  0  0  0  0  0  0
+   37.7730   45.2220   14.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
+   37.3250   45.6230   12.7590 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.9030   46.9650   12.5340 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.9260   47.9270   13.6160 C   0  0  0  0  0  0  0  0  0  0  0  0
+   37.3710   47.5360   14.9100 C   0  0  0  0  0  0  0  0  0  0  0  0
+   32.0350   43.4630   16.0140 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.5320   41.1510   18.6880 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.0820   42.0130   16.3950 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.5840   42.6320   18.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.9480   41.5000   19.1690 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.4950   40.8570   17.2000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   31.4680   42.3740   16.8360 N   0  0  0  0  0  0  0  0  0  0  0  0
+   27.6000   40.3220   20.0960 C   0  0  0  0  0  0  0  0  0  0  0  0
+   26.0160   39.1260   21.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
+   25.1240   40.2520   21.4640 C   0  0  0  0  0  0  0  0  0  0  0  0
+   25.4940   41.4300   20.7590 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.2660   38.8410   19.8280 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.2770   38.2590   20.6160 N   0  0  0  0  0  0  0  0  0  0  0  0
+   27.2570   39.2140   20.7570 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.8450   40.1340   19.5010 N   0  0  0  0  0  0  0  0  0  0  0  0
+   26.7420   41.4690   20.0670 C   0  0  0  0  0  0  0  0  0  0  0  0
+   30.3260   38.3090   19.4800 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1 26  1  0  0  0  0
+  1  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+  2  3  2  0  0  0  0
+  2  6  1  0  0  0  0
+  2 10  1  0  0  0  0
+  3  4  1  0  0  0  0
+  5  6  2  0  0  0  0
+  7 20  1  0  0  0  0
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+  7 10  1  0  0  0  0
+  8 12  2  0  0  0  0
+  8 13  1  0  0  0  0
+  9 16  1  0  0  0  0
+ 10 11  2  0  0  0  0
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+ 12 16  1  0  0  0  0
+ 13 14  2  0  0  0  0
+ 13 18  1  0  0  0  0
+ 14 15  1  0  0  0  0
+ 14 19  1  0  0  0  0
+ 15 16  2  0  0  0  0
+ 17 19  2  0  0  0  0
+ 17 18  1  0  0  0  0
+ 20 25  2  0  0  0  0
+ 20 21  1  0  0  0  0
+ 21 22  2  0  0  0  0
+ 22 23  1  0  0  0  0
+ 23 24  2  0  0  0  0
+ 24 25  1  0  0  0  0
+ 26 32  1  0  0  0  0
+ 27 31  1  0  0  0  0
+ 27 30  1  0  0  0  0
+ 27 40  1  0  0  0  0
+ 28 32  1  0  0  0  0
+ 28 31  1  0  0  0  0
+ 29 32  1  0  0  0  0
+ 29 30  1  0  0  0  0
+ 33 40  1  0  0  0  0
+ 33 41  2  0  0  0  0
+ 33 39  1  0  0  0  0
+ 34 39  2  0  0  0  0
+ 34 35  1  0  0  0  0
+ 35 36  2  0  0  0  0
+ 36 41  1  0  0  0  0
+ 37 40  1  0  0  0  0
+ 37 42  2  0  0  0  0
+ 37 38  1  0  0  0  0
+ 38 39  1  0  0  0  0
+M  END
+>  <MODEL>
+       3
+
+>  <COMPND>
+    UNNAMED
+
+>  <AUTHOR>
+    GENERATED BY OPEN BABEL 2.4.90
+
+>  <MASTER>
+        0    0    0    0    0    0    0    0   42    0   42    0
+

test_set/AROE_THET8_1_263_0/2cy0_A_rec.log

@@ -0,0 +1,31 @@
+2023-07-28 20:03:59,013 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2023-07-28 20:03:59,014 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2023-07-28 20:03:59,014 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2023-07-28 20:03:59,014 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2023-07-28 20:03:59,015 INFO:main.py:763:main_driver:Loading topology files.
+2023-07-28 20:03:59,100 INFO:main.py:765:main_driver:Loading molecule: /data/crossdock/test_set/AROE_THET8_1_263_0/2cy0_A_rec.pdb
+2023-07-28 20:03:59,101 ERROR:pdb.py:2584:read_pdb:Error parsing line: invalid literal for int() with base 10: 'Sel'
+2023-07-28 20:03:59,101 ERROR:pdb.py:2585:read_pdb:<REMARK Selection 'protein or ion and not water'>
+2023-07-28 20:03:59,101 ERROR:pdb.py:2586:read_pdb:Truncating remaining errors for record type:REMARK
+2023-07-28 20:03:59,133 WARNING:io.py:467:get_molecule:Warning: /data/crossdock/test_set/AROE_THET8_1_263_0/2cy0_A_rec.pdb is a non-standard PDB file.
+
+2023-07-28 20:03:59,133 ERROR:io.py:468:get_molecule:['REMARK']
+2023-07-28 20:03:59,133 INFO:main.py:770:main_driver:Setting up molecule.
+2023-07-28 20:03:59,162 INFO:main.py:408:setup_molecule:Created biomolecule object with 525 residues and 3994 atoms.
+2023-07-28 20:03:59,163 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
+2023-07-28 20:03:59,178 INFO:main.py:604:non_trivial:Loading forcefield.
+2023-07-28 20:03:59,186 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
+2023-07-28 20:03:59,191 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue GLY A 262
+2023-07-28 20:03:59,194 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue GLY A 262
+2023-07-28 20:03:59,196 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
+2023-07-28 20:03:59,197 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue GLY A 262
+2023-07-28 20:03:59,200 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue GLY A 262 at coordinates 40.613, 26.907, 17.026
+2023-07-28 20:03:59,201 INFO:main.py:623:non_trivial:Updating disulfide bridges.
+2023-07-28 20:03:59,201 INFO:main.py:626:non_trivial:Debumping biomolecule.
+2023-07-28 20:03:59,339 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
+2023-07-28 20:04:00,012 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
+2023-07-28 20:04:00,938 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
+2023-07-28 20:04:01,944 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
+2023-07-28 20:04:01,962 INFO:main.py:713:non_trivial:Regenerating headers.
+2023-07-28 20:04:01,965 INFO:main.py:738:non_trivial:Regenerating PDB lines.
+2023-07-28 20:04:02,060 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.

test_set/AROE_THET8_1_263_0/2cy0_A_rec_2d5c_skm_lig_tt_min_0.sdf

@@ -0,0 +1,38 @@
+__2cy0_A_rec_2d5c_skm_lig_min.pdb
+ OpenBabel10171921233D
+
+ 12 12  0  0  1  0  0  0  0  0999 V2000
+   24.3790   13.0730   18.1040 O   0  0  0  0  0  0  0  0  0  0  0  0
+   25.3920   13.8240   18.7890 C   0  0  1  0  0  0  0  0  0  0  0  0
+   25.2100   13.6610   20.3230 C   0  0  2  0  0  0  0  0  0  0  0  0
+   23.9140   14.1280   20.6900 O   0  0  0  0  0  0  0  0  0  0  0  0
+   26.2830   14.4630   21.1050 C   0  0  0  0  0  0  0  0  0  0  0  0
+   27.6640   14.4160   20.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
+   27.8870   13.9180   19.2300 C   0  0  0  0  0  0  0  0  0  0  0  0
+   26.8040   13.3300   18.3510 C   0  0  1  0  0  0  0  0  0  0  0  0
+   26.8620   11.8980   18.4530 O   0  0  0  0  0  0  0  0  0  0  0  0
+   28.8120   14.9580   21.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.6750   15.1980   22.5400 O   0  0  0  0  0  0  0  0  0  0  0  0
+   29.8830   15.1850   20.6750 O   0  0  0  0  0  0  0  0  0  0  0  0
+  2  1  1  6  0  0  0
+  2  8  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  1  1  0  0  0
+  3  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  6 10  1  0  0  0  0
+  7  8  1  0  0  0  0
+  8  9  1  1  0  0  0
+ 10 12  2  0  0  0  0
+ 10 11  1  0  0  0  0
+M  END
+>  <COMPND>
+    UNNAMED
+
+>  <AUTHOR>
+    GENERATED BY OPEN BABEL 2.4.90
+
+>  <MASTER>
+        0    0    0    0    0    0    0    0   12    0   12    0
+

test_set/ATS5_HUMAN_262_480_0/3hy9_B_rec.log

@@ -0,0 +1,108 @@
+2023-07-28 21:04:37,190 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
+2023-07-28 21:04:37,190 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
+2023-07-28 21:04:37,190 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+2023-07-28 21:04:37,190 INFO:main.py:759:main_driver:Checking and transforming input arguments.
+2023-07-28 21:04:37,191 INFO:main.py:763:main_driver:Loading topology files.
+2023-07-28 21:04:37,252 INFO:main.py:765:main_driver:Loading molecule: /data/crossdock/test_set/ATS5_HUMAN_262_480_0/3hy9_B_rec.pdb
+2023-07-28 21:04:37,253 ERROR:pdb.py:2584:read_pdb:Error parsing line: invalid literal for int() with base 10: 'Sel'
+2023-07-28 21:04:37,253 ERROR:pdb.py:2585:read_pdb:<REMARK Selection '(protein and ch... and not water)'>
+2023-07-28 21:04:37,253 ERROR:pdb.py:2586:read_pdb:Truncating remaining errors for record type:REMARK
+2023-07-28 21:04:37,260 WARNING:io.py:467:get_molecule:Warning: /data/crossdock/test_set/ATS5_HUMAN_262_480_0/3hy9_B_rec.pdb is a non-standard PDB file.
+
+2023-07-28 21:04:37,260 ERROR:io.py:468:get_molecule:['REMARK']
+2023-07-28 21:04:37,260 INFO:main.py:770:main_driver:Setting up molecule.
+2023-07-28 21:04:37,281 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for ZN.  Parsing as new residue.
+2023-07-28 21:04:37,281 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for CA.  Parsing as new residue.
+2023-07-28 21:04:37,281 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for CA.  Parsing as new residue.
+2023-07-28 21:04:37,281 WARNING:biomolecule.py:992:create_residue:Unable to find amino or nucleic acid definition for CA.  Parsing as new residue.
+2023-07-28 21:04:37,282 INFO:main.py:408:setup_molecule:Created biomolecule object with 224 residues and 1686 atoms.
+2023-07-28 21:04:37,282 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
+2023-07-28 21:04:37,289 INFO:main.py:604:non_trivial:Loading forcefield.
+2023-07-28 21:04:37,297 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
+2023-07-28 21:04:37,299 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OG in residue SER B 262
+2023-07-28 21:04:37,299 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG1 in residue ILE B 263
+2023-07-28 21:04:37,299 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG2 in residue ILE B 263
+2023-07-28 21:04:37,299 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD1 in residue ILE B 263
+2023-07-28 21:04:37,299 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OG in residue SER B 264
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue ASP B 323
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD1 in residue ASP B 323
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD2 in residue ASP B 323
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue LYS B 324
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD in residue LYS B 324
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CE in residue LYS B 324
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom NZ in residue LYS B 324
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue ASP B 325
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD1 in residue ASP B 325
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD2 in residue ASP B 325
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue LYS B 326
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD in residue LYS B 326
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CE in residue LYS B 326
+2023-07-28 21:04:37,300 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom NZ in residue LYS B 326
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OG in residue SER B 262
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG1 in residue ILE B 263
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG2 in residue ILE B 263
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD1 in residue ILE B 263
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OG in residue SER B 264
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue ASP B 323
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD1 in residue ASP B 323
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD2 in residue ASP B 323
+2023-07-28 21:04:37,301 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue LYS B 324
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD in residue LYS B 324
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CE in residue LYS B 324
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom NZ in residue LYS B 324
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue ASP B 325
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD1 in residue ASP B 325
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD2 in residue ASP B 325
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue LYS B 326
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD in residue LYS B 326
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CE in residue LYS B 326
+2023-07-28 21:04:37,302 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom NZ in residue LYS B 326
+2023-07-28 21:04:37,303 INFO:main.py:618:non_trivial:Attempting to repair 19 missing atoms in biomolecule.
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OG in residue SER B 262
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG1 in residue ILE B 263
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG2 in residue ILE B 263
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD1 in residue ILE B 263
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OG in residue SER B 264
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue ASP B 323
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD1 in residue ASP B 323
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD2 in residue ASP B 323
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue LYS B 324
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD in residue LYS B 324
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CE in residue LYS B 324
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom NZ in residue LYS B 324
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue ASP B 325
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD1 in residue ASP B 325
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OD2 in residue ASP B 325
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CG in residue LYS B 326
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CD in residue LYS B 326
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom CE in residue LYS B 326
+2023-07-28 21:04:37,303 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom NZ in residue LYS B 326
+2023-07-28 21:04:37,304 INFO:biomolecule.py:1077:repair_heavy:Added atom OG to residue SER B 262 at coordinates 18.892, 38.428, 54.947
+2023-07-28 21:04:37,305 INFO:biomolecule.py:1077:repair_heavy:Added atom CG1 to residue ILE B 263 at coordinates 16.865, 39.320, 48.689
+2023-07-28 21:04:37,305 INFO:biomolecule.py:1077:repair_heavy:Added atom CG2 to residue ILE B 263 at coordinates 16.188, 37.170, 47.621
+2023-07-28 21:04:37,305 INFO:biomolecule.py:1077:repair_heavy:Added atom CD1 to residue ILE B 263 at coordinates 17.165, 40.173, 47.491
+2023-07-28 21:04:37,305 INFO:biomolecule.py:1077:repair_heavy:Added atom OG to residue SER B 264 at coordinates 21.282, 33.940, 50.604
+2023-07-28 21:04:37,306 INFO:biomolecule.py:1077:repair_heavy:Added atom CG to residue ASP B 323 at coordinates -1.719, -4.789, 58.505
+2023-07-28 21:04:37,306 INFO:biomolecule.py:1077:repair_heavy:Added atom OD1 to residue ASP B 323 at coordinates -1.486, -5.791, 57.797
+2023-07-28 21:04:37,306 INFO:biomolecule.py:1077:repair_heavy:Added atom OD2 to residue ASP B 323 at coordinates -1.075, -4.523, 59.535
+2023-07-28 21:04:37,306 INFO:biomolecule.py:1077:repair_heavy:Added atom CG to residue LYS B 324 at coordinates -6.682, -2.701, 59.945
+2023-07-28 21:04:37,306 INFO:biomolecule.py:1077:repair_heavy:Added atom CD to residue LYS B 324 at coordinates -6.503, -1.694, 61.063
+2023-07-28 21:04:37,307 INFO:biomolecule.py:1077:repair_heavy:Added atom CE to residue LYS B 324 at coordinates -6.256, -2.343, 62.402
+2023-07-28 21:04:37,307 INFO:biomolecule.py:1077:repair_heavy:Added atom NZ to residue LYS B 324 at coordinates -6.088, -1.319, 63.463
+2023-07-28 21:04:37,307 INFO:biomolecule.py:1077:repair_heavy:Added atom CG to residue ASP B 325 at coordinates -10.242, -1.212, 54.843
+2023-07-28 21:04:37,307 INFO:biomolecule.py:1077:repair_heavy:Added atom OD1 to residue ASP B 325 at coordinates -10.565, -2.333, 55.282
+2023-07-28 21:04:37,307 INFO:biomolecule.py:1077:repair_heavy:Added atom OD2 to residue ASP B 325 at coordinates -10.906, -0.182, 55.052
+2023-07-28 21:04:37,308 INFO:biomolecule.py:1077:repair_heavy:Added atom CG to residue LYS B 326 at coordinates -4.329, -4.711, 51.709
+2023-07-28 21:04:37,308 INFO:biomolecule.py:1077:repair_heavy:Added atom CD to residue LYS B 326 at coordinates -4.115, -5.541, 50.454
+2023-07-28 21:04:37,308 INFO:biomolecule.py:1077:repair_heavy:Added atom CE to residue LYS B 326 at coordinates -4.069, -7.025, 50.742
+2023-07-28 21:04:37,308 INFO:biomolecule.py:1077:repair_heavy:Added atom NZ to residue LYS B 326 at coordinates -3.859, -7.794, 49.489
+2023-07-28 21:04:37,309 INFO:main.py:623:non_trivial:Updating disulfide bridges.
+2023-07-28 21:04:37,310 INFO:main.py:626:non_trivial:Debumping biomolecule.
+2023-07-28 21:04:37,362 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
+2023-07-28 21:04:37,603 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
+2023-07-28 21:04:37,889 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
+2023-07-28 21:04:38,354 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
+2023-07-28 21:04:38,359 INFO:main.py:713:non_trivial:Regenerating headers.
+2023-07-28 21:04:38,360 INFO:main.py:738:non_trivial:Regenerating PDB lines.
+2023-07-28 21:04:38,378 WARNING:main.py:311:print_pqr:Ignoring 887 header lines in output.
+2023-07-28 21:04:38,378 WARNING:main.py:315:print_pqr:Ignoring 4 missing lines in output.

test_set/ATS5_HUMAN_262_480_0/3hy9_B_rec_3hyg_099_lig_tt_min_0.sdf

@@ -0,0 +1,70 @@
+__3hy9_B_rec_3hyg_099_lig_min.pdb
+ OpenBabel10171921493D
+
+ 27 29  0  0  1  0  0  0  0  0999 V2000
+   12.0420    9.1430   34.3820 C   0  0  2  0  0  0  0  0  0  0  0  0
+   12.2510    7.8280   33.6990 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8770    7.9150   32.4880 N   0  0  0  0  0  0  0  0  0  0  0  0
+   11.8850    6.7710   34.1920 O   0  0  0  0  0  0  0  0  0  0  0  0
+   13.8210    5.9110   28.3060 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.8880    7.4370   29.6100 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8470    6.7460   30.3050 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8660    6.6000   27.5890 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.9100    7.3590   28.2310 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.7210    5.3350   30.6370 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.7940    5.9880   29.6800 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3390    5.9750   31.9690 C   0  0  2  0  0  0  0  0  0  0  0  0
+   13.0040    6.6750   31.7720 C   0  0  1  0  0  0  0  0  0  0  0  0
+   15.3000    6.9510   32.3700 O   0  0  0  0  0  0  0  0  0  0  0  0
+   12.4480    8.9820   35.8300 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.4460    8.8960   37.3070 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.5030    9.9720   36.7380 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.6200   10.0640   35.2450 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.9200   10.3700   35.5610 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.7520    9.2200   37.6200 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.8720    9.3170   36.1280 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.6410   11.1240   34.6650 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.5620    9.4730   34.2700 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.3590   10.9130   34.6140 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.2900   11.1010   35.4420 N   0  0  0  0  0  0  0  0  0  0  0  0
+    9.2110   12.3800   36.0160 O   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0690   11.8150   34.2050 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1 23  1  1  0  0  0
+  1 15  1  0  0  0  0
+  2  3  1  0  0  0  0
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+M  END
+>  <COMPND>
+    UNNAMED
+
+>  <AUTHOR>
+    GENERATED BY OPEN BABEL 2.4.90
+
+>  <MASTER>
+        0    0    0    0    0    0    0    0   27    0   27    0
+