rdworks 0.45.2__py3-none-any.whl → 0.47.1__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.45.2'
+__version__ = '0.47.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

rdworks/mol.py

@@ -445,6 +445,7 @@ class Mol:
                        calculator: str | Callable = 'MMFF94', 
                        fmax: float = 0.05, 
                        max_iter: int = 1000,
+                       **kwargs
                        ) -> Self:
         """Optimizes 3D geometry of conformers.
 
@@ -469,12 +470,12 @@ class Mol:
         Returns:
             Self: modified self.
         """
-        self.confs = [ conf.optimize(calculator, fmax, max_iter) for conf in self.confs ]
+        self.confs = [ conf.optimize(calculator, fmax, max_iter, **kwargs) for conf in self.confs ]
 
         return self
 
 
-    def sort_confs(self, calculator: str | Callable | None = None) -> Self:
+    def sort_confs(self, calculator: str | Callable | None = None, **kwargs) -> Self:
         """Sorts by `E_tot(kcal/mol)` or `E_tot(eV)` and sets `E_rel(kcal/mol)`. 
 
         Args:
@@ -501,7 +502,7 @@ class Mol:
         if calculator is not None:
             # re-calculate potential energies
             for conf in self.confs:
-                PE = conf.potential_energy(calculator=calculator) # sets `E_tot(kcal/mol)`
+                PE = conf.potential_energy(calculator=calculator, **kwargs) # sets `E_tot(kcal/mol)`
 
         if all(['E_tot(kcal/mol)' in conf.props for conf in self.confs]):
             sort_by = 'E_tot(kcal/mol)'

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/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-0.45.2.dist-info → rdworks-0.47.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.45.2
+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-0.45.2.dist-info → rdworks-0.47.1.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=SK_EU8Z7TY12w-fszqAQN03x6MydoGabg98zBOetlLI,1368
+rdworks/__init__.py,sha256=CkKXxGhqvK8jzCxjOXnj2IOOvdHKpHE6ekjM5ZECSUw,1368
 rdworks/conf.py,sha256=iQLb3Qg3pjGiiMVMJ5-d57BC1id3zxEhEGlhhrLrA_c,34162
 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=JC1IHM6mw9uap_uV3i5d6ZAnZqA1kcyOnvwB6lgH4xA,68070
+rdworks/mol.py,sha256=e62DYV8XeqLL1mBydbS881pSUfJjaeHxalG64CIant8,68133
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
 rdworks/readin.py,sha256=0bnVcZcAmSLqc6zu1mYcv0LdBv2agQfOpKGwpSRL9VE,11742
@@ -14,7 +14,7 @@ rdworks/std.py,sha256=qOVS_lGogueLKh4rsbrsYIMR0c7z_xh6BqLEzD4X9sE,7938
 rdworks/stereoisomers.py,sha256=g8hhPI-mbYX-MzbF1uAqo5fDZOCNiKYjxI-kLBGdGgg,4980
 rdworks/tautomers.py,sha256=gtZHZJ-aJbryhBdljHbfjx7xhVW3u_OzdYPtwPail54,610
 rdworks/testdata.py,sha256=TmbNPA-ju6nTBt_Yts4EJUFmL9Cd6DCVXrDF42QLlHw,1732
-rdworks/torsion.py,sha256=7xlOUYXmBSkjPuNxGXNF-F3G9XWO2ER15xGOY0ejpcc,18801
+rdworks/torsion.py,sha256=UUaYOvNS89SlLFauYiAboUqysy32EN0_Gktc4xxuDQI,18788
 rdworks/units.py,sha256=nljKPHcr6IWoAp0CkL7y1gSNDd6a07NeVfxXwSMuHQM,365
 rdworks/utils.py,sha256=d2Sio8WTlGPsmBOHIYDCMWg_7X4rTWjJQAqzd7ywo2A,14191
 rdworks/xml.py,sha256=aaMhwVRGvt1VzasaKDnkYnZ4kp2cIgvGb1CsmMgwQ_c,10704
@@ -65,9 +65,9 @@ rdworks/predefined/misc/reactive-part-2.xml,sha256=0vNTMwWrrQmxBpbgbyRHx8sVs83cq
 rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0Xu51j3JnIapRYo4,3094
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rdworks/xtb/wrapper.py,sha256=GqcseDk_sgmKbmKvDvObjNTk0tvAWYd7ZxjnLq0uVK0,21596
-rdworks-0.45.2.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.45.2.dist-info/METADATA,sha256=DfyxepI-h3XBWrwQzzCLVQWBXs-mc5snQ4LIKbGzW4w,1967
-rdworks-0.45.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.45.2.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.45.2.dist-info/RECORD,,
+rdworks/xtb/wrapper.py,sha256=NQgkdRKN5YEtv_UPYKWDijzMEs5v2kFrhUWHqiro7bE,22174
+rdworks-0.47.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.47.1.dist-info/METADATA,sha256=w8BCgsWZ6AqzjSjZL1z4ker0-mwca09u5XiBsXa0ycw,1967
+rdworks-0.47.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.47.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.47.1.dist-info/RECORD,,