rdworks 0.49.1__tar.gz → 0.50.1__tar.gz

{rdworks-0.49.1 → rdworks-0.50.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.49.1
+Version: 0.50.1
 Summary: Routine 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-0.49.1 → rdworks-0.50.1}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.49.1'
+__version__ = '0.50.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.49.1 → rdworks-0.50.1}/src/rdworks/xtb/wrapper.py

@@ -59,6 +59,43 @@ class GFN2xTB:
         return shutil.which('xtb') is not None
 
 
+    @staticmethod
+    def is_optimize_ready() -> bool:
+        try:
+            h2o = [
+                '$coord',
+                ' 0.00000000000000      0.00000000000000     -0.73578586109551      o',
+                ' 1.44183152868459      0.00000000000000      0.36789293054775      h',
+                '-1.44183152868459      0.00000000000000      0.36789293054775      h',
+                '$end',
+            ]
+
+            with tempfile.TemporaryDirectory() as temp_dir:
+                test_geometry = os.path.join(temp_dir, 'coord')
+                with open(test_geometry, 'w') as f:
+                    f.write('\n'.join(h2o))
+                proc = subprocess.run(['xtb', test_geometry, '--opt'], 
+                                      capture_output=True, 
+                                      text=True)
+                assert proc.returncode == 0
+
+            return True
+
+        except:
+            print("""                          
+Conda installed xTB has the Fortran runtime error in geometry optimization. 
+Please install xtb using the compiled binary:
+                    
+$ wget https://github.com/grimme-lab/xtb/releases/download/v6.7.1/xtb-6.7.1-linux-x86_64.tar.xz
+$ tar -xf xtb-6.7.1-linux-x86_64.tar.xz
+$ cp -r xtb-dist/bin/*      /usr/local/bin/
+$ cp -r xtb-dist/lib/*      /usr/local/lib/
+$ cp -r xtb-dist/include/*  /usr/local/include/
+$ cp -r xtb-dist/share      /usr/local/ """)
+            
+            return False
+
+
     @staticmethod
     def is_cpx_ready() -> bool:
         """Checks if the CPCM-X command-line tool, `cpx`, is accessible in the system.
@@ -70,7 +107,7 @@ class GFN2xTB:
     
 
     @staticmethod
-    def is_cpcmx_option_ready() -> bool:
+    def is_cpcmx_ready() -> bool:
         """Checks if xtb works with the `--cpcmx` option.
 
         xtb distributed by the conda does not include CPCM-X function (as of June 17, 2025). 
@@ -101,7 +138,8 @@ class GFN2xTB:
         """
         return all([GFN2xTB.is_xtb_ready(),
                     GFN2xTB.is_cpx_ready(),
-                    GFN2xTB.is_cpcmx_option_ready()])
+                    GFN2xTB.is_cpcmx_ready(),
+                    GFN2xTB.is_optimize_ready()])
     
 
     @staticmethod
@@ -115,10 +153,9 @@ class GFN2xTB:
             cmd = ['xtb', '--version']
             proc = subprocess.run(cmd, capture_output=True, text=True)
             assert proc.returncode == 0, "GFN2xTB() Error: xtb not available"
-            for line in proc.stdout.split('\n'):
-                line = line.strip()
-                if 'version' in line:
-                    return line
+            match = re.search('xtb\s+version\s+(?P<version>[\d.]+)', proc.stdout)
+            if match:
+                return match.group('version')
             
         return None
     
@@ -362,7 +399,7 @@ class GFN2xTB:
                 elif water == 'alpb':
                     options += ['--alpb', 'water']
                     # it does not provide Gsolv contribution to the total energy
-                elif water == 'cpcmx' and self.is_cpcmx_option_ready():
+                elif water == 'cpcmx' and self.is_cpcmx_ready():
                     options += ['--cpcmx', 'water']
 
             if verbose:

{rdworks-0.49.1 → rdworks-0.50.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.49.1
+Version: 0.50.1
 Summary: Routine 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-0.49.1 → rdworks-0.50.1}/tests/test_xtb.py

@@ -27,7 +27,7 @@ def test_xtb_wrapper():
     from rdworks.xtb.wrapper import GFN2xTB
     assert GFN2xTB.is_xtb_ready() == True
     assert GFN2xTB.is_cpx_ready() == True
-    assert GFN2xTB.is_cpcmx_option_ready() == True
+    assert GFN2xTB.is_cpcmx_ready() == True
     assert GFN2xTB.is_ready() == True
     assert GFN2xTB.version() is not None
 
@@ -38,7 +38,7 @@ def test_singlepoint():
     print("number of conformers=", mol.count())
     print("number of atoms=", mol.confs[0].natoms)
 
-    gfn2xtb = GFN2xTB(mol.confs[0].rdmol, ncores=8)
+    gfn2xtb = GFN2xTB(mol.confs[0].rdmol)
 
     print("GFN2xTB.singlepoint()")
     outdict = gfn2xtb.singlepoint()
@@ -65,7 +65,7 @@ def test_optimize():
     mol = testmol.copy()
     print("number of conformers=", mol.count())
     print("GFN2xTB.optimize()")
-    outdict = GFN2xTB(mol.confs[0].rdmol, ncores=8).optimize(verbose=True)
+    outdict = GFN2xTB(mol.confs[0].rdmol).optimize(verbose=True)
     print(outdict)
     print()
 
@@ -92,7 +92,7 @@ def test_state_generate():
         mol = mol.optimize_confs(calculator='MMFF94', verbose=True)
         mol = mol.drop_confs(similar=True, similar_rmsd=0.3, verbose=True)
         mol = mol.sort_confs(calculator='xTB', verbose=True)
-        mol = mol.drop_confs(k=10, window=10.0, verbose=True) # enforcing both conditions
+        mol = mol.drop_confs(k=10, window=15.0, verbose=True) # enforcing both conditions
         _PE = []
         for conf in mol.confs:
             conf = conf.optimize(calculator='xTB', verbose=True)
@@ -154,7 +154,7 @@ def test_state_generate():
 
 
 if __name__ == '__main__':
-    # test_xtb_wrapper()
-    # test_singlepoint()
-    # test_optimize()
+    test_xtb_wrapper()
+    test_singlepoint()
+    test_optimize()
     test_state_generate()