rdworks 0.36.2__tar.gz → 0.36.4__tar.gz

{rdworks-0.36.2 → rdworks-0.36.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.2
+Version: 0.36.4
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.36.2 → rdworks-0.36.4}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.36.2'
+__version__ = '0.36.4'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.36.2 → rdworks-0.36.4}/src/rdworks/mol.py

@@ -368,56 +368,62 @@ class Mol:
                 self.confs.append(conf)
         
         elif method.upper() == 'CONFORGE':
-            with tempfile.NamedTemporaryFile(suffix='.sdf', delete=False) as tmpfile:
-                mol = CDPL.Chem.parseSMILES(self.smiles)
-                # create and initialize an instance of the class ConfGen.ConformerGenerator which
-                # will perform the actual conformer ensemble generation work
-                conf_gen = CDPL.ConfGen.ConformerGenerator()
-                conf_gen.settings.timeout = 60 * 1000  # 60 sec.
-                conf_gen.settings.minRMSD = 0.5
-                conf_gen.settings.energyWindow = 20.0 # kcal/mol(?)
-                conf_gen.settings.maxNumOutputConformers = n
-                # dictionary mapping status codes to human readable strings
-                status_to_str = { 
-                    CDPL.ConfGen.ReturnCode.UNINITIALIZED                  : 'uninitialized',
-                    CDPL.ConfGen.ReturnCode.TIMEOUT                        : 'max. processing time exceeded',
-                    CDPL.ConfGen.ReturnCode.ABORTED                        : 'aborted',
-                    CDPL.ConfGen.ReturnCode.FORCEFIELD_SETUP_FAILED        : 'force field setup failed',
-                    CDPL.ConfGen.ReturnCode.FORCEFIELD_MINIMIZATION_FAILED : 'force field structure refinement failed',
-                    CDPL.ConfGen.ReturnCode.FRAGMENT_LIBRARY_NOT_SET       : 'fragment library not available',
-                    CDPL.ConfGen.ReturnCode.FRAGMENT_CONF_GEN_FAILED       : 'fragment conformer generation failed',
-                    CDPL.ConfGen.ReturnCode.FRAGMENT_CONF_GEN_TIMEOUT      : 'fragment conformer generation timeout',
-                    CDPL.ConfGen.ReturnCode.FRAGMENT_ALREADY_PROCESSED     : 'fragment already processed',
-                    CDPL.ConfGen.ReturnCode.TORSION_DRIVING_FAILED         : 'torsion driving failed',
-                    CDPL.ConfGen.ReturnCode.CONF_GEN_FAILED                : 'conformer generation failed',
-                    }
-                writer = CDPL.Chem.MolecularGraphWriter(tmpfile.name, "sdf" )
-                # SB - io.StringIO does not work with Chem.MolecularGraphWriter()
-                # We have to create a temporary file and re-read it for storing individual conformers. 
-                try:
-                    # prepare the molecule for conformer generation
-                    CDPL.ConfGen.prepareForConformerGeneration(mol) 
-                    # generate the conformer ensemble
-                    status = conf_gen.generate(mol)             
-                    # if successful, store the generated conformer ensemble as
-                    # per atom 3D coordinates arrays (= the way conformers are represented in CDPKit)
-                    if status == CDPL.ConfGen.ReturnCode.SUCCESS or status == CDPL.ConfGen.ReturnCode.TOO_MUCH_SYMMETRY:
-                        # TOO_MUCH_SYMMETRY: output ensemble may contain duplicates
-                        conf_gen.setConformers(mol)
-                        writer.write(mol)                            
-                    else:
-                        raise RuntimeError('Error: conformer generation failed: %s' % status_to_str[status])
-                except Exception as e:
-                    raise RuntimeError('Error: conformer generation failed: %s' % str(e))
+            mol = CDPL.Chem.parseSMILES(self.smiles)
+            # create and initialize an instance of the class ConfGen.ConformerGenerator which
+            # will perform the actual conformer ensemble generation work
+            conf_gen = CDPL.ConfGen.ConformerGenerator()
+            conf_gen.settings.timeout = 60 * 1000  # 60 sec.
+            conf_gen.settings.minRMSD = 0.5
+            conf_gen.settings.energyWindow = 20.0 # kcal/mol(?)
+            conf_gen.settings.maxNumOutputConformers = n
+            # dictionary mapping status codes to human readable strings
+            status_to_str = { 
+                CDPL.ConfGen.ReturnCode.UNINITIALIZED                  : 'uninitialized',
+                CDPL.ConfGen.ReturnCode.TIMEOUT                        : 'max. processing time exceeded',
+                CDPL.ConfGen.ReturnCode.ABORTED                        : 'aborted',
+                CDPL.ConfGen.ReturnCode.FORCEFIELD_SETUP_FAILED        : 'force field setup failed',
+                CDPL.ConfGen.ReturnCode.FORCEFIELD_MINIMIZATION_FAILED : 'force field structure refinement failed',
+                CDPL.ConfGen.ReturnCode.FRAGMENT_LIBRARY_NOT_SET       : 'fragment library not available',
+                CDPL.ConfGen.ReturnCode.FRAGMENT_CONF_GEN_FAILED       : 'fragment conformer generation failed',
+                CDPL.ConfGen.ReturnCode.FRAGMENT_CONF_GEN_TIMEOUT      : 'fragment conformer generation timeout',
+                CDPL.ConfGen.ReturnCode.FRAGMENT_ALREADY_PROCESSED     : 'fragment already processed',
+                CDPL.ConfGen.ReturnCode.TORSION_DRIVING_FAILED         : 'torsion driving failed',
+                CDPL.ConfGen.ReturnCode.CONF_GEN_FAILED                : 'conformer generation failed',
+                }
+            
+            # We have to create a temporary file and re-read it for storing individual conformers.
+            tmp_dir = os.environ.get('TMPDIR', '/tmp')
+            tmp_name = next(tempfile._get_candidate_names()) + '.sdf'
+            tmp_filename = os.path.join(tmp_dir, tmp_name)
+            
+            writer = CDPL.Chem.MolecularGraphWriter(tmp_filename, "sdf" )
+            # SB - io.StringIO does not work with Chem.MolecularGraphWriter()            
+             
+            try:
+                # prepare the molecule for conformer generation
+                CDPL.ConfGen.prepareForConformerGeneration(mol) 
+                # generate the conformer ensemble
+                status = conf_gen.generate(mol)             
+                # if successful, store the generated conformer ensemble as
+                # per atom 3D coordinates arrays (= the way conformers are represented in CDPKit)
+                if status == CDPL.ConfGen.ReturnCode.SUCCESS or status == CDPL.ConfGen.ReturnCode.TOO_MUCH_SYMMETRY:
+                    # TOO_MUCH_SYMMETRY: output ensemble may contain duplicates
+                    conf_gen.setConformers(mol)
+                    writer.write(mol)  
+                    writer.close()                          
+                else:
+                    raise RuntimeError('Error: conformer generation failed: %s' % status_to_str[status])
+            except Exception as e:
+                raise RuntimeError('Error: conformer generation failed: %s' % str(e))
             
-            # tmpfile is automatically closed here
+            # tmpfile is automatically closed here but kept, as delete=False was set
             
-            with Chem.SDMolSupplier(tmpfile.name, sanitize=True, removeHs=False) as sdf:
+            with Chem.SDMolSupplier(tmp_filename, sanitize=True, removeHs=False) as sdf:
                 self.confs = [ Conf(m) for m in sdf if m is not None ]
             
             # tmpfile is not deleted here because delete=False
             # we should remove the file when it is no longer needed
-            os.remove(tmpfile.name)
+            os.remove(tmp_filename)
 
         # energy evaluations for ranking
         for conf in self.confs:
@@ -996,6 +1002,7 @@ class Mol:
 
         if torsion_key is None:
             torsion_atoms_indices = self.torsion_atoms()
+            # {0: (5, 4, 3, 1)}
         else:
             torsion_atoms_indices = {torsion_key: self.torsion_atoms()[torsion_key]}
 

{rdworks-0.36.2 → rdworks-0.36.4}/src/rdworks/torsion.py

@@ -453,10 +453,14 @@ def create_torsion_fragment(rdmol: Chem.Mol,
 
     candidates = find_bonds_to_prune(rdmol, torsion_indices)
     
+    if not candidates:
+        # no fragmentation
+        return rdmol, torsion_indices
+    
     if GFN2xTB().version() is not None:
+        # filter candidate(s) by Wiberg bond order (WBO) if xTB is available
         jk = tuple(sorted([j, k]))
         wbo_passed_candidates = {}
-        # filter candidate(s) by Wiberg bond order (WBO)
         parent = GFN2xTB(rdmol).singlepoint()
         assert hasattr(parent, 'wbo'), "create_torsion_fragment() Error: no wbo for parent"
         for bond_idx, (p, q) in candidates.items():
@@ -470,6 +474,7 @@ def create_torsion_fragment(rdmol: Chem.Mol,
                 wbo_passed_candidates[bond_idx] = (p, q)
         frag_multi_breaks = create_fragment_on_bonds(rdmol, wbo_passed_candidates) 
     else:
+        # skip WBO filtering
         frag_multi_breaks = create_fragment_on_bonds(rdmol, candidates)
 
     frag_ijkl = get_fragment_idx(rdmol, (i, j, k, l), frag_multi_breaks)

{rdworks-0.36.2 → rdworks-0.36.4}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.2
+Version: 0.36.4
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.36.2 → rdworks-0.36.4}/tests/test_basics.py

@@ -469,12 +469,20 @@ def test_torsion_fragment():
               name="atorvastatin").make_confs(n=1)
     ta = mol.torsion_atoms()
     assert len(ta) == 12
-    # ta[6] = (8, 9, 10, 18, _rot, _fix)
-    # _rot and _fix are not used
-    frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, (8, 9, 10, 18, None, None))
+    # {0: (0, 1, 3, 7),  1: (3, 4, 32, 33),  2: (4, 5, 26, 27),  3: (7, 6, 19, 20),
+    # 4: (3, 7, 8, 9),  5: (7, 8, 9, 10),   6: (8, 9, 10, 18),   7: (18, 10, 11, 12),
+    # 8: (10, 11, 12, 17),  9: (17, 12, 13, 14),   10: (12, 13, 14, 15),   11: (36, 35, 34, 32)}
+    frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, ta[6])
     assert frag_ijkl == (5, 6, 7, 12)
 
 
+    mol2 = Mol(molecule='CC(=O)Nc1ccc(O)cc1', name='acetaminophen.3').make_confs(n=1)
+    ta2 = mol2.torsion_atoms()
+    # {0: (5, 4, 3, 1)}
+    assert len(ta2) == 1
+    frag, frag_ijkl = create_torsion_fragment(mol2.confs[0].rdmol, ta2[0])
+
+
 def test_torsion_energies():
     libr = MolLibr(torsion_dataset_smiles, torsion_dataset_names)
     with open(workdir / 'test_torsion_energies.html', 'w') as f: