rdworks 0.36.1__py3-none-any.whl → 0.36.2__py3-none-any.whl

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/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.dist-info → rdworks-0.36.2.dist-info}/METADATA

@@ -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.dist-info → rdworks-0.36.2.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=XNynPKNPZU13ohhw1sU4JkJOn4FIf6aQXMLqCDGE0OU,1368
+rdworks/__init__.py,sha256=IQYmK2AVX7BA--tFniboPkU1P1f3KlwhLFIUmnYtaUQ,1368
 rdworks/conf.py,sha256=hi8qqcEhDMfiGAj10I7Pl65svVNeV-ihjM7lRKX7OaM,22284
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=5oIjMRpkX792RIpEEE2Ir96icfFaN_h21mSihhfQPAw,6713
 rdworks/matchedseries.py,sha256=A3ON4CUpQV159mu9VqgNiJ8uoQ9ePOry9d3ra4NCAgc,10377
-rdworks/mol.py,sha256=5ZaBIpCnKIqxbIZM0IAJ2uG5fEIlZotw1Lb2QT_IXe0,71145
+rdworks/mol.py,sha256=lF5b_AIueYCfHWgrrnxbcZOFtSPe6dO4oOcovJ3GWhA,71338
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
 rdworks/readin.py,sha256=0bnVcZcAmSLqc6zu1mYcv0LdBv2agQfOpKGwpSRL9VE,11742
@@ -65,8 +65,8 @@ rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0X
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdworks/xtb/wrapper.py,sha256=I0nW89vlJZ5Za5pCjIpjsEOFbTm7HpeNGiPgssheWn8,11350
-rdworks-0.36.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.36.1.dist-info/METADATA,sha256=12x3_XSJPwhUcidBwjWyNRTBV7dbWouucI-KzDrw_ac,1183
-rdworks-0.36.1.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-rdworks-0.36.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.36.1.dist-info/RECORD,,
+rdworks-0.36.2.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.36.2.dist-info/METADATA,sha256=GRcE_cV1nVX4j60RB1Cm_Y69Ad_y3HrZgOwnNau177Y,1183
+rdworks-0.36.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.36.2.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.36.2.dist-info/RECORD,,

{rdworks-0.36.1.dist-info → rdworks-0.36.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any