rdworks 0.46.1__tar.gz → 0.47.1__tar.gz

{rdworks-0.46.1 → rdworks-0.47.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.46.1
+Version: 0.47.1
 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-0.46.1 → rdworks-0.47.1}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.46.1'
+__version__ = '0.47.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.46.1 → rdworks-0.47.1}/src/rdworks/torsion.py

@@ -462,7 +462,7 @@ def create_torsion_fragment(rdmol: Chem.Mol,
 
     # fragmented
     WBO_filtered = False
-    if GFN2xTB().version() is not None:
+    if GFN2xTB.is_ready():
         # filter candidate(s) by Wiberg bond order (WBO) if xTB is available
         jk = tuple(sorted([j, k]))
         wbo_passed_candidates = {}

{rdworks-0.46.1 → rdworks-0.47.1}/src/rdworks/xtb/wrapper.py

@@ -45,42 +45,28 @@ class GFN2xTB:
         resource.setrlimit(resource.RLIMIT_STACK, (resource.RLIM_INFINITY, resource.RLIM_INFINITY))
 
 
-    def version(self) -> str | None:
-        """Check xtb version.
-
-        Returns:
-            str | None: version statement.
-        """
-        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
-        
-        return None
-
-
-    def is_xtb_ready(self, cmd: str = 'xtb') -> bool:
+    @staticmethod
+    def is_xtb_ready() -> bool:
         """Check if xtb is available.
 
         Returns:
             bool: True if `xtb` is available, False otherwise.
         """
-        return shutil.which(cmd) is not None
+        return shutil.which('xtb') is not None
 
 
-    def is_cpx_ready(self, cmd: str = 'cpx') -> bool:
+    @staticmethod
+    def is_cpx_ready() -> bool:
         """Checks if the CPCM-X command-line tool, `cpx`, is accessible in the system.
 
         Returns:
             bool: True if the cpx is found, False otherwise.
         """
-        return shutil.which(cmd) is not None
+        return shutil.which('cpx') is not None
     
 
-    def is_cpcmx_ready(self) -> bool:
+    @staticmethod
+    def is_cpcmx_option_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). 
@@ -89,18 +75,50 @@ class GFN2xTB:
         Returns:
             bool: True if the --cpcmx option is working, False otherwise.
         """
-        cmd = ['xtb', '--cpcmx']
-        proc = subprocess.run(cmd, capture_output=True, text=True)
-        # we are expecting an error because no input file is given
-        assert proc.returncode != 0
-        for line in proc.stdout.split('\n'):
-            line = line.strip()
-            if 'CPCM-X library was not included' in line:
-                return False
+        if GFN2xTB.is_xtb_ready():
+            cmd = ['xtb', '--cpcmx']
+            proc = subprocess.run(cmd, capture_output=True, text=True)
+            # we are expecting an error because no input file is given
+            assert proc.returncode != 0
+            for line in proc.stdout.split('\n'):
+                line = line.strip()
+                if 'CPCM-X library was not included' in line:
+                    return False
         
         return True
 
 
+    @staticmethod
+    def is_ready() -> bool:
+        """Check if `xtb` and `cpx` are accessible and `xtb --cpcmx` are available.
+
+        Returns:
+            bool: True if both `xtb` and `cpx` are accessible, False otherwise.
+        """
+        return all([GFN2xTB.is_xtb_ready(),
+                    GFN2xTB.is_cpx_ready(),
+                    GFN2xTB.is_cpcmx_option_ready()])
+    
+
+    @staticmethod
+    def version() -> str | None:
+        """Check xtb version.
+
+        Returns:
+            str | None: version statement.
+        """
+        if GFN2xTB.is_ready():
+            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
+            
+        return None
+    
+
     def to_xyz(self) -> str:
         """Export to XYZ formatted string.
 
@@ -345,7 +363,7 @@ 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_ready():
+                elif water == 'cpcmx' and self.is_cpcmx_option_ready():
                     options += ['--cpcmx', 'water']
 
             # 'xtbout.json', 'xtbrestart', 'xtbtopo.mol', 'charges', and 'wbo' files will be 

{rdworks-0.46.1 → rdworks-0.47.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.46.1
+Version: 0.47.1
 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-0.46.1 → rdworks-0.47.1}/tests/test_basics.py

@@ -460,7 +460,11 @@ def test_optimize_confs():
 
 def test_xtb_wrapper():
     from rdworks.xtb.wrapper import GFN2xTB
-    assert GFN2xTB().version()
+    assert GFN2xTB.is_xtb_ready() == True
+    assert GFN2xTB.is_cpx_ready() == True
+    assert GFN2xTB.is_cpcmx_option_ready() == True
+    assert GFN2xTB.is_ready() == True
+    assert GFN2xTB.version() is not None
 
 
 def test_torsion_fragment():

{rdworks-0.46.1 → rdworks-0.47.1}/tests/test_xtb.py

@@ -31,11 +31,12 @@ 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)
-
-    print("GFN2xTB.version():", gfn2xtb.version())
+    print("GFN2xTB.is_cpcmx_option_ready()", GFN2xTB.is_cpcmx_option_ready())
+    print("GFN2xTB.version():", GFN2xTB.version())
     print()
 
+    gfn2xtb = GFN2xTB(mol.confs[0].rdmol, ncores=8)
+    
     print("GFN2xTB.singlepoint()")
     outdict = gfn2xtb.singlepoint()
     print(outdict)
@@ -52,7 +53,6 @@ def test_singlepoint():
     print()
 
     print("GFN2xTB.singlepoint(water='cpcmx')")
-    print("GFN2xTB.is_cpcmx_ready()", gfn2xtb.is_cpcmx_ready())
     outdict = gfn2xtb.singlepoint(water='cpcmx')
     print(outdict)
     print()