fixing handling of error writing to disk

docs/source/CHANGELOG.md

@@ -7,6 +7,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
+## [3.3.0]
+
+### Changed
+
+- `moldrug.utils.__tar_errors__` by `moldrug.utils.tar_errors`.
+- Default value of `moldrug.utils.tar_errors` is `error` instead of `.error`.
+- `moldrug.constraintconf.generate_conformers` outputs warnings and errors to `error` instead of `.error`.
+- `moldrug.fitness.__vinadock` by `moldrug.fitness._vinadock`.
+- `moldrug.fitness._vinadock` outputs warnings and errors to `error` instead of `.error`.
+
+### Fixed
+
+- The use of `moldrug.utils.tar_errors` inside of `moldrug.utils.Local` and `moldrug.utils.GA`.
+- Clean code.
+
 ## [3.2.5] - 2020.12.20
 
 ### Fixed
@@ -279,8 +294,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Minor code cleaning.
 - Better code covered during testing
 
-[unreleased]: https://github.com/ale94mleon/MolDrug/compare/3.2.5...HEAD
-[3.2.4]: https://github.com/ale94mleon/MolDrug/compare/3.2.2...3.2.5
+[unreleased]: https://github.com/ale94mleon/MolDrug/compare/3.3.0...HEAD
+[3.3.0]: https://github.com/ale94mleon/MolDrug/compare/3.2.5...3.3.0
+[3.2.5]: https://github.com/ale94mleon/MolDrug/compare/3.2.2...3.2.5
 [3.2.2]: https://github.com/ale94mleon/MolDrug/compare/3.2.0...3.2.2
 [3.2.0]: https://github.com/ale94mleon/MolDrug/compare/3.1.0...3.2.0
 [3.1.0]: https://github.com/ale94mleon/MolDrug/compare/3.0.3...3.1.0

moldrug/_version.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 # We will use semantic version (major, minor, patch)
-__version_tuple__ = version_tuple = (3, 2, 5)
+__version_tuple__ = version_tuple = (3, 3, 0)
 __version__ = version = '.'.join([str(i) for i in __version_tuple__])

moldrug/constraintconf.py

@@ -127,8 +127,8 @@ def generate_conformers(mol: Chem.rdchem.Mol,
         current directory generate_conformers_error.log with the nature of the Exception.
     """
     # Creating the error directory if needed
-    if not os.path.isdir('.error'):
-        os.makedirs('.error')
+    if not os.path.isdir('error'):
+        os.makedirs('error')
     # if SMILES to be fixed are not given, assume to the MCS
     if ref_smi:
         if not Chem.MolFromSmiles(ref_smi):
@@ -170,8 +170,8 @@ def generate_conformers(mol: Chem.rdchem.Mol,
     except Exception as e:
         print(e)
         cwd = os.getcwd()
-        warnings.warn(f"generate_conformers failed. Check the file {os.path.join(cwd, '.error/generate_conformers_error.pbz2')}")
-        compressed_pickle('.error/generate_conformers_error', e)
+        warnings.warn(f"generate_conformers failed. Check the file {os.path.join(cwd, 'error/generate_conformers_error.pbz2')}")
+        compressed_pickle('error/generate_conformers_error', e)
         mol.RemoveAllConformers()
         return mol
 

moldrug/fitness.py

@@ -238,8 +238,8 @@ def __vinadock(
     constraint_type = constraint_type.lower()
 
     # Creating the error directory if needed
-    if not os.path.isdir('.error'):
-        os.makedirs('.error')
+    if not os.path.isdir('error'):
+        os.makedirs('error')
     # Creating the working directory if needed
     if not os.path.exists(wd):
         os.makedirs(wd)
@@ -297,7 +297,7 @@ def __vinadock(
                 # Make a copy to the vina command string and add the out (is needed) and ligand options
                 cmd_vina_str_tmp = cmd_vina_str[:]
                 cmd_vina_str_tmp += f" --ligand {os.path.join(wd, f'{Individual.idx}_conf_{conf.GetId()}.pdbqt')}"
-                
+
                 if constraint_type == 'local_only':
                     cmd_vina_str_tmp += f" --out {os.path.join(wd, f'{Individual.idx}_conf_{conf.GetId()}_out.pdbqt')}"
                 try:
@@ -318,7 +318,7 @@ def __vinadock(
                         'boxcenter': boxcenter,
                         'boxsize': boxsize,
                     }
-                    utils.compressed_pickle(f'.error/idx_{Individual.idx}_conf_{conf.GetId()}_error', error)
+                    utils.compressed_pickle(f'error/idx_{Individual.idx}_conf_{conf.GetId()}_error', error)
                     warnings.warn(f"\nVina failed! Check: idx_{Individual.idx}_conf_{conf.GetId()}_error.pbz2 file in error.\n")
                     vina_score_pdbqt = (np.inf, preparator.write_pdbqt_string())
                     return vina_score_pdbqt
@@ -365,7 +365,7 @@ def __vinadock(
                 'boxcenter': boxcenter,
                 'boxsize': boxsize,
             }
-            utils.compressed_pickle(f'.error/{Individual.idx}_error', error)
+            utils.compressed_pickle(f'error/{Individual.idx}_error', error)
             warnings.warn(f"\nVina failed! Check: {Individual.idx}_error.pbz2 file in error.\n")
 
             vina_score_pdbqt = (np.inf, 'VinaFailed')

moldrug/utils.py

@@ -467,7 +467,7 @@ def import_sascorer():
     """
     # In order to import sascorer from RDConfig.RDContribDir
     from rdkit.Chem import RDConfig
-    import os, importlib.util as importlib_util
+    import importlib.util as importlib_util
     spec=importlib_util.spec_from_file_location('sascorer', os.path.join(RDConfig.RDContribDir, 'SA_Score', 'sascorer.py'))
     sascorer = importlib_util.module_from_spec(spec)
     spec.loader.exec_module(sascorer)
@@ -826,7 +826,7 @@ def make_sdf(individuals:List[Individual], sdf_name = 'out'):
                     print(f"{individual} does not have a valid pdbqt: {individual.pdbqt}.")
         print(f"File {sdf_name}.sdf was createad!")
 
-def __make_kwargs_copy__(costfunc, costfunc_kwargs,):
+def _make_kwargs_copy(costfunc, costfunc_kwargs,):
     """Make a copy of the self.costfunc_kwargs.
     It creates a temporal directory.
 
@@ -841,13 +841,15 @@ def __make_kwargs_copy__(costfunc, costfunc_kwargs,):
         kwargs_copy['wd'] = costfunc_jobs_tmp_dir.name
     return kwargs_copy, costfunc_jobs_tmp_dir
 
-def __tar_errors__(error_path:str = '.error'):
-    """Clena of errors the working directory
+def tar_errors(error_path:str = 'error'):
+    """Clean errors in the working directory.
+    Convert to error.tar.gz the error_path
+    and delete the directory.
 
     Parameters
     ----------
     error_path : str
-        Where the error are storged.
+        Where the errors are storged.
     """
     if os.path.isdir(error_path):
         if os.listdir(error_path):
@@ -946,7 +948,7 @@ def __call__(self, njobs:int = 1, pick:int = None):
         # Creating the arguments
         args_list = []
         # Make a copy of the self.costfunc_kwargs
-        kwargs_copy, costfunc_jobs_tmp_dir = __make_kwargs_copy__(self.costfunc, self.costfunc_kwargs)
+        kwargs_copy, costfunc_jobs_tmp_dir = _make_kwargs_copy(self.costfunc, self.costfunc_kwargs)
 
         for individual in self.pop:
             args_list.append((individual, kwargs_copy))
@@ -959,7 +961,7 @@ def __call__(self, njobs:int = 1, pick:int = None):
         # Clean directory
         costfunc_jobs_tmp_dir.cleanup()
         # Tar errors
-        __tar_errors__('error')
+        tar_errors('error')
 
         # Printing how long was the simulation
         print(f"Finished at {datetime.datetime.now().strftime('%c')}.\n")
@@ -1231,7 +1233,7 @@ def __call__(self, njobs:int = 1):
             args_list = []
             # Make a copy of the self.costfunc_kwargs
                     # Make a copy of the self.costfunc_kwargs
-            kwargs_copy, costfunc_jobs_tmp_dir = __make_kwargs_copy__(self.costfunc, self.costfunc_kwargs)
+            kwargs_copy, costfunc_jobs_tmp_dir = _make_kwargs_copy(self.costfunc, self.costfunc_kwargs)
 
             for individual in self.pop:
                 args_list.append((individual, kwargs_copy))
@@ -1254,7 +1256,7 @@ def __call__(self, njobs:int = 1):
 
             # Clean directory
             costfunc_jobs_tmp_dir.cleanup()
-            
+
             # Adding generation information
             for individual in self.pop:
                 individual.genID = self.NumGens
@@ -1323,7 +1325,7 @@ def __call__(self, njobs:int = 1):
                 # Creating the arguments
                 args_list = []
                 # Make a copy of the self.costfunc_kwargs
-                kwargs_copy, costfunc_jobs_tmp_dir = __make_kwargs_copy__(self.costfunc, self.costfunc_kwargs)
+                kwargs_copy, costfunc_jobs_tmp_dir = _make_kwargs_copy(self.costfunc, self.costfunc_kwargs)
 
                 NumbOfSawIndividuals = len(self.SawIndividuals)
                 for (i, individual) in enumerate(popc):
@@ -1348,6 +1350,7 @@ def __call__(self, njobs:int = 1):
                             f"=========Parellel=========:\n {e1}\n"\
                             f"==========Serial==========:\n {e2}"
                             )
+
                 # Clean directory
                 costfunc_jobs_tmp_dir.cleanup()
 
@@ -1397,7 +1400,7 @@ def __call__(self, njobs:int = 1):
         print(f"\n{50*'=+'}\n")
 
         # Tar errors
-        __tar_errors__('error')
+        tar_errors('error')
 
         # Printing how long was the simulation
         print(f"Total time ({self.maxiter} generations): {time.time() - ts:>5.2f} (s).\nFinished at {datetime.datetime.now().strftime('%c')}.\n")

tests/test_moldrug.py

@@ -247,7 +247,7 @@ def test_fitness_module():
         boxcenter = boxes.r_x0161['A']['boxcenter'], boxsize = boxes.r_x0161['A']['boxsize'],)
 
     # Clean
-    utils.__tar_errors__()
+    utils.tar_errors()
     os.remove('error.tar.gz')
 
 def test_home():
@@ -346,20 +346,20 @@ def test_constraintconf():
         out = os.path.join(tmp_path.name, 'conf.sdf')
     )
     # Clean
-    utils.__tar_errors__()
+    utils.tar_errors()
 
 def test_generate_conformers():
     from moldrug.constraintconf import generate_conformers
     from rdkit.Chem import AllChem
     ref = Chem.MolFromSmiles('O=S(=O)(Nc1ccc(Cl)cc1)c1ccsc1C(O)O')
     mol = Chem.MolFromSmiles('CN(C)S(=O)(=O)c1cc(NS(=O)(=O)c2ccsc2C(O)O)ccc1Cl')
 
-    AllChem.EmbedMolecule(ref) 
+    AllChem.EmbedMolecule(ref)
     AllChem.MMFFOptimizeMolecule(ref)
     generate_conformers(Chem.RemoveHs(mol), Chem.RemoveHs(ref), 50)
 
     # Clean
-    utils.__tar_errors__()
+    utils.tar_errors()
 
 
 if __name__ == '__main__':