rdworks 0.36.1__tar.gz → 0.36.2__tar.gz

{rdworks-0.36.1 → rdworks-0.36.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.1
+Version: 0.36.2
 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-0.36.1 → rdworks-0.36.2}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.36.1'
+__version__ = '0.36.2'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.36.1 → rdworks-0.36.2}/src/rdworks/mol.py

@@ -3,6 +3,7 @@ import itertools
 import json
 import logging
 import tempfile
+import os
 
 from io import StringIO, BytesIO
 from pathlib import Path
@@ -367,7 +368,7 @@ class Mol:
                 self.confs.append(conf)
         
         elif method.upper() == 'CONFORGE':
-            with tempfile.NamedTemporaryFile() as tmpfile:
+            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
@@ -390,7 +391,7 @@ class Mol:
                     CDPL.ConfGen.ReturnCode.TORSION_DRIVING_FAILED         : 'torsion driving failed',
                     CDPL.ConfGen.ReturnCode.CONF_GEN_FAILED                : 'conformer generation failed',
                     }
-                writer = CDPL.Chem.MolecularGraphWriter( f"{tmpfile.name}.sdf", "sdf" )
+                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:
@@ -403,15 +404,20 @@ class Mol:
                     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)
-                        with Chem.SDMolSupplier(f"{tmpfile.name}.sdf", sanitize=True, removeHs=False) as sdf:
-                            self.confs = [ Conf(m) for m in sdf if m is not None ]                            
+                        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))
-            # tmpfile is automatically closed and deleted here
-
+            
+            # tmpfile is automatically closed here
+            
+            with Chem.SDMolSupplier(tmpfile.name, 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)
 
         # energy evaluations for ranking
         for conf in self.confs:

{rdworks-0.36.1 → rdworks-0.36.2}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.1
+Version: 0.36.2
 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>