rdworks 0.45.1__py3-none-any.whl → 0.46.1__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.45.1'
+__version__ = '0.46.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

rdworks/conf.py

@@ -210,7 +210,7 @@ class Conf:
             
             if calculator.lower() == 'xTB'.lower():
                 water = kwargs.get('water', None)
-                result = GFN2xTB(self.rdmol).optimize(water=water)
+                results = GFN2xTB(self.rdmol).optimize(water=water)
                 # SimpleNamespace(
                 #         PE = datadict['total energy'] * hartree2kcalpermol,
                 #         charges = datadict['partial charges'],
@@ -218,8 +218,8 @@ class Conf:
                 #         geometry = rdmol_opt,
                 # )
                 try:
-                    self.rdmol = result.geometry
-                    PE_final = result.PE
+                    self.rdmol = results.geometry
+                    PE_final = results.PE
                     retcode = 0
                 except:
                     retcode = 1
@@ -382,7 +382,14 @@ class Conf:
         if isinstance(calculator, str):
             if calculator.lower() == 'xTB'.lower():
                 water = kwargs.get('water', None)
-                PE = GFN2xTB(self.rdmol).singlepoint(water=water)
+                results = GFN2xTB(self.rdmol).singlepoint(water=water)
+                # SimpleNamespace(
+                #     PE = datadict['total energy'] * hartree2kcalpermol,
+                #     Gsolv = Gsolv, 
+                #     charges = datadict['partial charges'], 
+                #     wbo = Wiberg_bond_orders,
+                #     )
+                PE = results.PE
             
             elif calculator.lower() == 'MMFF94'.lower() or calculator.lower() == 'MMFF'.lower():
                 mp = Chem.rdForceFieldHelpers.MMFFGetMoleculeProperties(self.rdmol, mmffVariant='MMFF94')

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-0.45.1.dist-info → rdworks-0.46.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.45.1
+Version: 0.46.1
 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-0.45.1.dist-info → rdworks-0.46.1.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=4nKRLc9DB8UyBCp6htdSfcZ2pvpi4crr5WGkLpD1Bus,1368
-rdworks/conf.py,sha256=QolIR0iaDwdneFNuLXDNw6z_2rfnGTGsHr8_A-E9alY,33834
+rdworks/__init__.py,sha256=7XXFLbhQnYgT28SFGHOyEYq-nMnUQGq-ZHWrwI7NA20,1368
+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
@@ -66,8 +66,8 @@ 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=GqcseDk_sgmKbmKvDvObjNTk0tvAWYd7ZxjnLq0uVK0,21596
-rdworks-0.45.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.45.1.dist-info/METADATA,sha256=ZkVfFGhi8IdIFpfPOvY3WuzX6WkCZJT1ty193RZxcxo,1967
-rdworks-0.45.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.45.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.45.1.dist-info/RECORD,,
+rdworks-0.46.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.46.1.dist-info/METADATA,sha256=W_HHV2S8tUb7qxhAuZ1v4LNrzGzLzjeXNyurik9DkcY,1967
+rdworks-0.46.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.46.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.46.1.dist-info/RECORD,,