rowan-python 3.0.5__py3-none-any.whl → 3.0.6__py3-none-any.whl

rowan/molecule.py

@@ -52,28 +52,36 @@ class Molecule(BaseModel):
         return cls(_stjames=stjames.Molecule.from_smiles(smiles))
 
     @classmethod
-    def from_xyz(cls, xyz_string: str, charge: int = 0, multiplicity: int = 1) -> Self:
+    def from_xyz(
+        cls, xyz_string: str, charge: int | None = None, multiplicity: int | None = None
+    ) -> Self:
         """
-        Create molecule from XYZ string.
+        Create Molecule from XYZ string.
 
-        :param xyz_string: XYZ format string.
-        :param charge: Molecular charge (default 0).
-        :param multiplicity: Spin multiplicity (default 1).
-        :returns: Molecule instance.
+        :param xyz_string: XYZ format string
+        :param charge: charge
+        :param multiplicity: spin multiplicity
+        :returns: Molecule
         """
-        stj = stjames.Molecule.from_xyz(xyz_string)
-        stj = stjames.Molecule(atoms=stj.atoms, charge=charge, multiplicity=multiplicity)
-        return cls(_stjames=stj)
+        return cls(
+            _stjames=stjames.Molecule.from_xyz(
+                xyz_string,
+                charge=charge,
+                multiplicity=multiplicity,
+            )
+        )
 
     @classmethod
-    def from_xyz_file(cls, path: str | Path, charge: int = 0, multiplicity: int = 1) -> Self:
+    def from_xyz_file(
+        cls, path: str | Path, charge: int | None = None, multiplicity: int | None = None
+    ) -> Self:
         """
         Create molecule from XYZ file.
 
-        :param path: Path to XYZ file.
-        :param charge: Molecular charge (default 0).
-        :param multiplicity: Spin multiplicity (default 1).
-        :returns: Molecule instance.
+        :param path: path to XYZ file
+        :param charge: charge
+        :param multiplicity: spin multiplicity
+        :returns: Molecule
         """
         return cls.from_xyz(Path(path).read_text(), charge=charge, multiplicity=multiplicity)
 
@@ -82,8 +90,8 @@ class Molecule(BaseModel):
         """
         Create from stjames.Molecule.
 
-        :param stj: stjames.Molecule instance.
-        :returns: Molecule instance.
+        :param stj: stjames.Molecule
+        :returns: Molecule
         """
         return cls(_stjames=stj)
 

rowan/protein.py

@@ -305,7 +305,7 @@ def list_proteins(
 
 
 def upload_protein(
-    name: str, file_path: Path, project_uuid: str | Project | None = None
+    name: str, file_path: str | Path, project_uuid: str | Project | None = None
 ) -> Protein:
     """
     Uploads a protein from a PDB file to the API.
@@ -315,6 +315,7 @@ def upload_protein(
     :returns: Protein object representing the uploaded protein
     :raises requests.HTTPError: if the request to the API fails
     """
+    file_path = Path(file_path)
     if isinstance(project_uuid, Project):
         project_uuid = project_uuid.uuid
     with api_client() as client:

rowan/workflows/pka.py

@@ -183,8 +183,7 @@ def submit_pka_workflow(
         )
     if method in _PKA_SMILES_METHODS and not initial_smiles:
         raise ValueError(
-            f"{method} requires a SMILES string. "
-            "Provide a SMILES string, not a 3D structure."
+            f"{method} requires a SMILES string. Provide a SMILES string, not a 3D structure."
         )
     if method in _PKA_WATER_ONLY_METHODS and solvent != "water":
         raise ValueError(f"{method} only supports water as solvent.")

{rowan_python-3.0.5.dist-info → rowan_python-3.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.5
+Version: 3.0.6
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues

{rowan_python-3.0.5.dist-info → rowan_python-3.0.6.dist-info}/RECORD

@@ -3,9 +3,9 @@ rowan/calculation.py,sha256=lZZ52DxPsuJWCTzFZXjhauHK6dV0KCUwzoxtmoxSY48,3442
 rowan/config.py,sha256=3cVKHUNzkIPnN2bvx7l5sia7Zc5poXS8lKOJlowXyLA,21088
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
 rowan/folder.py,sha256=NkimVeHho9nwRXeS87U1tivEVL-1gL2Vqfz1fJ6XpNQ,9222
-rowan/molecule.py,sha256=MppZLHUAHzLCaIZtAbr2tpEULt5yRUR1B5npgFISCbE,10030
+rowan/molecule.py,sha256=KQJhbNF2vmR8okBduXVqG7qG3LXbABLKHanpNhA-0TY,10003
 rowan/project.py,sha256=Wy3VvhwIMIumAZD2s7hPk8jj4bAPHMDNvsqU23RRqFo,4598
-rowan/protein.py,sha256=Ma2tBFF52Rb-ME5vZy5M5juMlmphQVQRL0Q1EBvBeZg,14761
+rowan/protein.py,sha256=jyOM6g5eQH6KO8Eq07AiYBv2vZsGfbNOdtNOb2NWHFc,14799
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/types.py,sha256=rCAnUlCsemyBK9Bbus0pL-THoqNqJIQHaMoDferIfFU,471
 rowan/user.py,sha256=Tnwz1-u_92ACt1xATQegtMj3FcosFsAG4m-4YuAkiyg,5955
@@ -35,7 +35,7 @@ rowan/workflows/membrane_permeability.py,sha256=oIDmB8qF_K_Kesv7o_FiljAk4dpptEeO
 rowan/workflows/msa.py,sha256=V3B1SyWPR8MT306hh9W-T9JTpi_E-XgAIeF9yRQZ7tI,5075
 rowan/workflows/multistage_optimization.py,sha256=HFVx8mnHxG97pDYyL6eOhNGmESqTxaKNgUdwrFpFUJ0,6456
 rowan/workflows/nmr.py,sha256=hergJdsiawKj7iV-jHxDOS03n_EnZcaCIt_ZTl34-JY,5183
-rowan/workflows/pka.py,sha256=YAnFq1zyJO3j9rfYCYyrl-C_o8uaFTpCqoldqiP7o1k,8349
+rowan/workflows/pka.py,sha256=Gh-rMrqZyHbpIpX2LaEiBzlqE4paIE58paSkHEQCoEU,8334
 rowan/workflows/pose_analysis_md.py,sha256=UvotLhWv0_VAkKteZboOutDry7l-Zt1K6_SBx3EXqgM,9530
 rowan/workflows/protein_binder_design.py,sha256=J-9NSbRLdHb6JQRhY_vq43HlHCDCiQqrkOZUCAF-2dk,8604
 rowan/workflows/protein_cofolding.py,sha256=1R29XjAVjWHyelGG-mylP2GIamZbLCQKaaaFsCAnYgI,13012
@@ -49,7 +49,7 @@ rowan/workflows/solvent_dependent_conformers.py,sha256=ovvnhCE4xlkpdhccLHEq7oBJR
 rowan/workflows/spin_states.py,sha256=GZgBJPO6_ds9el4b7wbigIZ5213Z9DwXhokczJ5NDhs,7122
 rowan/workflows/strain.py,sha256=r0tlZoUlAslAiF7dPTpa9WlQFUAKyVjZ19zASjSS8Hs,6339
 rowan/workflows/tautomer_search.py,sha256=aqwXoj0ffWsb5gbvzfz_bpx5ifIfR_K07fbdWhU62Ko,5820
-rowan_python-3.0.5.dist-info/METADATA,sha256=0wZHFNgNRDm1DwrdDVJJh1Xu05Xm8A31whsYlwCSVWM,1600
-rowan_python-3.0.5.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
-rowan_python-3.0.5.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.0.5.dist-info/RECORD,,
+rowan_python-3.0.6.dist-info/METADATA,sha256=8c_sKx6JPCz0nVzsM_rX7N3bBjHz8_DxM58wZSFwLcs,1600
+rowan_python-3.0.6.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+rowan_python-3.0.6.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.0.6.dist-info/RECORD,,