rdworks 0.36.2__tar.gz → 0.36.3__tar.gz

{rdworks-0.36.2 → rdworks-0.36.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.2
+Version: 0.36.3
 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-0.36.3}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.36.2'
+__version__ = '0.36.3'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.36.2 → rdworks-0.36.3}/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:

{rdworks-0.36.2 → rdworks-0.36.3}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.2
+Version: 0.36.3
 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>