rowan-python 2.0.3__tar.gz → 2.1.0__tar.gz

{rowan_python-2.0.3 → rowan_python-2.1.0}/LICENSE

@@ -1,6 +1,6 @@
 The MIT License
 
-Copyright (c) Rowan (https://rowansci.com)
+Copyright (c) Rowan Scientific Corporation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{rowan_python-2.0.3 → rowan_python-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.0.3
+Version: 2.1.0
 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-2.0.3 → rowan_python-2.1.0}/examples/conformers.py

@@ -28,4 +28,4 @@ result = rowan.submit_conformer_search_workflow(
     initial_molecule=Molecule.from_smiles("CCOCC"),
 )
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

rowan_python-2.1.0/examples/data/workflow_example.json

@@ -0,0 +1,177 @@
+{
+  "mode": "auto",
+  "engine": "omol25",
+  "messages": [],
+  "settings": {
+    "mode": "rapid",
+    "tasks": [
+      "optimize"
+    ],
+    "method": "omol25_conserving_s",
+    "basis_set": null,
+    "corrections": [],
+    "opt_settings": {
+      "max_steps": 250,
+      "constraints": [],
+      "optimize_cell": false,
+      "energy_threshold": 0.00005,
+      "transition_state": false,
+      "recalc_hess_every": 0,
+      "max_gradient_threshold": 0.005,
+      "rms_gradient_threshold": 0.0035
+    },
+    "scf_settings": {
+      "soscf": "upon_failure",
+      "max_iters": 250
+    },
+    "level_of_theory": "omol25_conserving_s",
+    "compute_settings": {
+      "compute_type_used": null,
+      "requested_compute_type": "cpu"
+    },
+    "solvent_settings": null,
+    "thermochem_settings": {
+      "temperature": 298,
+      "concentration": 0.0408740470708,
+      "scaling_factor": 1,
+      "cutoff_frequency": 100
+    }
+  },
+  "initial_molecule": {
+    "cell": null,
+    "atoms": [
+      {
+        "position": [
+          -1.57521701,
+          0.46946663,
+          0.02709079
+        ],
+        "atomic_number": 6
+      },
+      {
+        "position": [
+          -0.55694222,
+          -0.3145698,
+          -0.78629029
+        ],
+        "atomic_number": 6
+      },
+      {
+        "position": [
+          0.64857101,
+          -0.77828652,
+          0.03187563
+        ],
+        "atomic_number": 6
+      },
+      {
+        "position": [
+          1.50511158,
+          0.36668167,
+          0.55011421
+        ],
+        "atomic_number": 6
+      },
+      {
+        "position": [
+          -1.16251671,
+          1.42010117,
+          0.37728614
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          -1.90971756,
+          -0.10479157,
+          0.89680558
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          -2.45269203,
+          0.69552118,
+          -0.58729768
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          -0.22095177,
+          0.29430816,
+          -1.63370132
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          -1.05225015,
+          -1.19769669,
+          -1.20718455
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          0.31306273,
+          -1.39292336,
+          0.87531072
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          1.27184498,
+          -1.42141593,
+          -0.6008237
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          2.3966558,
+          -0.02720645,
+          1.04864872
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          0.96154654,
+          0.97685605,
+          1.27736127
+        ],
+        "atomic_number": 1
+      },
+      {
+        "position": [
+          1.83349502,
+          1.01395547,
+          -0.26919568
+        ],
+        "atomic_number": 1
+      }
+    ],
+    "charge": 0,
+    "dipole": null,
+    "energy": null,
+    "smiles": "CCCC",
+    "stress": null,
+    "elapsed": null,
+    "gradient": null,
+    "velocities": null,
+    "multiplicity": 1,
+    "homo_lumo_gap": null,
+    "scf_completed": null,
+    "scf_iterations": null,
+    "mulliken_charges": null,
+    "calculation_index": null,
+    "vibrational_modes": null,
+    "zero_point_energy": null,
+    "thermal_energy_corr": null,
+    "thermal_enthalpy_corr": null,
+    "mulliken_spin_densities": null,
+    "thermal_free_energy_corr": null
+  }
+}

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/docking_screen.py

@@ -116,7 +116,9 @@ results = {}
 docking_result_folder = rowan.create_folder(name="Docking results")
 
 
-protein = rowan.create_protein_from_pdb_id("CDK2", "1HCK")
+protein = rowan.create_protein_from_pdb_id(
+    "CDK2", "1HCK", project_uuid=rowan.default_project().uuid
+)
 
 protein.sanitize()
 time.sleep(60)

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/irc.py

@@ -21,4 +21,4 @@ H     1.26740151   0.88347299   0.53620841
     preopt=False,
 )
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/macropka.py

@@ -10,4 +10,4 @@ result = rowan.submit_macropka_workflow(
 )
 
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/optimization.py

@@ -18,4 +18,4 @@ result = rowan.submit_basic_calculation_workflow(
     name="Water Optimization",
 )
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/pka.py

@@ -19,4 +19,4 @@ result = rowan.submit_pka_workflow(
     name="Pyridine pKa",
 )
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/protein_cofolding.py

@@ -14,4 +14,4 @@ result = rowan.submit_protein_cofolding_workflow(
     name="Torcetrapib Cofolding",
 )
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.0.3 → rowan_python-2.1.0}/examples/scan.py

@@ -25,4 +25,4 @@ result = rowan.submit_scan_workflow(
     calculation_engine="xtb",
 )
 
-print(result)
+print(result.wait_for_result().fetch_latest(in_place=True))

{rowan_python-2.0.3 → rowan_python-2.1.0}/pixi.lock

@@ -137,7 +137,7 @@ environments:
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+      - pypi: https://files.pythonhosted.org/packages/d7/4b/d1048082a7c9af83c0a426880a7bbebb517b3646a6e57f43315421c672b6/griffe-1.12.0-py3-none-any.whl
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       - pypi: ./
@@ -504,10 +504,10 @@ packages:
   - markdown ; extra == 'dev'
   - flake8 ; extra == 'dev'
   - wheel ; extra == 'dev'
-- pypi: https://files.pythonhosted.org/packages/e6/a3/451ffd422ce143758a39c0290aaa7c9727ecc2bcc19debd7a8f3c6075ce9/griffe-1.11.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/d7/4b/d1048082a7c9af83c0a426880a7bbebb517b3646a6e57f43315421c672b6/griffe-1.12.0-py3-none-any.whl
   name: griffe
-  version: 1.11.1
-  sha256: 5799cf7c513e4b928cfc6107ee6c4bc4a92e001f07022d97fd8dee2f612b6064
+  version: 1.12.0
+  sha256: 634cf7bf93ab7d12003f3704043e8e530637fc3d40c67a2a052e57d2fcde173a
   requires_dist:
   - colorama>=0.4
   requires_python: '>=3.9'
@@ -1494,8 +1494,8 @@ packages:
   requires_python: '>=3.8'
 - pypi: ./
   name: rowan-python
-  version: 2.0.3
-  sha256: 3d9cab3000e381372c852d88802cc8d55a03c24ed2cdc423a2b81b79aee5d9dd
+  version: 2.1.0
+  sha256: c8838a78320174b0b9f997ab09b77e7c3b08a6f64e39f1aaad16c22921535ee6
   requires_dist:
   - httpx
   - stjames>=0.0.83
@@ -1673,15 +1673,16 @@ packages:
   - pysocks>=1.5.6,!=1.5.7,<2.0 ; extra == 'socks'
   - zstandard>=0.18.0 ; extra == 'zstd'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/ca/ff/ded57ac5ff40a09e6e198550bab075d780941e0b0f83cbeabd087c59383a/virtualenv-20.33.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/76/06/04c8e804f813cf972e3262f3f8584c232de64f0cde9f703b46cf53a45090/virtualenv-20.34.0-py3-none-any.whl
   name: virtualenv
-  version: 20.33.1
-  sha256: 07c19bc66c11acab6a5958b815cbcee30891cd1c2ccf53785a28651a0d8d8a67
+  version: 20.34.0
+  sha256: 341f5afa7eee943e4984a9207c025feedd768baff6753cd660c857ceb3e36026
   requires_dist:
   - distlib>=0.3.7,<1
   - filelock>=3.12.2,<4
   - importlib-metadata>=6.6 ; python_full_version < '3.8'
   - platformdirs>=3.9.1,<5
+  - typing-extensions>=4.13.2 ; python_full_version < '3.11'
   - furo>=2023.7.26 ; extra == 'docs'
   - proselint>=0.13 ; extra == 'docs'
   - sphinx>=7.1.2,!=7.3 ; extra == 'docs'

{rowan_python-2.0.3 → rowan_python-2.1.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.0.3"
+version = "2.1.0"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.9"

{rowan_python-2.0.3 → rowan_python-2.1.0}/rowan/__init__.py

@@ -3,6 +3,7 @@ from . import constants
 
 from .folder import *
 from .workflow import *
+from .project import *
 from .protein import *
 from .user import *
 from .utils import *

rowan_python-2.1.0/rowan/project.py

@@ -0,0 +1,136 @@
+from datetime import datetime
+from typing import Any, Self
+
+from pydantic import BaseModel
+
+from .utils import api_client
+
+
+class Project(BaseModel):
+    """
+    A class representing a project in the Rowan API.
+
+    :ivar uuid: The UUID of the project.
+    :ivar name: The name of the project.
+    :ivar created_at: The date and time the project was created.
+    """
+
+    uuid: str
+    name: str | None = None
+    created_at: datetime | None = None
+
+    def __repr__(self) -> str:
+        return f"<Project name='{self.name}' created_at='{self.created_at}' uuid='{self.uuid}'>"
+
+    def update(
+        self,
+        name: str | None = None,
+    ) -> Self:
+        """
+        Update a project.
+
+        :param name: The new name of the project.
+
+        :return: The updated project object.
+        """
+        payload = {
+            "name": name if name is not None else self.name,
+        }
+
+        with api_client() as client:
+            response = client.post(f"/project/{self.uuid}", json=payload)
+            response.raise_for_status()
+            updated_data = response.json()
+
+        self.name = updated_data.get("name")
+        return self
+
+    def delete(self) -> None:
+        """
+        Delete the project.
+
+        This is a destructive action, it will delete all the folders and
+        workflows that are inside this project.
+
+        :raises requests.HTTPError: if the request to the API fails.
+        """
+        with api_client() as client:
+            response = client.delete(f"/project/{self.uuid}")
+            response.raise_for_status()
+
+
+def retrieve_project(uuid: str) -> Project:
+    """
+    Retrieves a project from the API by UUID. Project UUID can be found in the project's URL.
+
+    :param uuid: The UUID of the project to retrieve.
+    :return: A Project object representing the retrieved project.
+    :raises HTTPError: If the API request fails.
+    """
+    with api_client() as client:
+        response = client.get(f"/project/{uuid}")
+        response.raise_for_status()
+        return Project(**response.json())
+
+
+def list_projects(
+    name_contains: str | None = None,
+    page: int = 0,
+    size: int = 10,
+) -> list[Project]:
+    """
+    Retrieve a list of projects based on the specified criteria.
+
+    :param name_contains: Substring to search for in project names.
+    :param page: Pagination parameter to specify the page number.
+    :param size: Pagination parameter to specify the number of items per page.
+    :return: A list of Folder objects that match the search criteria.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+
+    params: dict[str, Any] = {
+        "page": page,
+        "size": size,
+    }
+
+    if name_contains is not None:
+        params["name_contains"] = name_contains
+
+    with api_client() as client:
+        response = client.get("/project", params=params)
+        response.raise_for_status()
+        items = response.json()
+
+    return [Project(**item) for item in items]
+
+
+def create_project(
+    name: str,
+) -> Project:
+    """
+    Create a new project.
+
+    :param name: The name of the project.
+    :return: The newly created project.
+    """
+    data = {
+        "name": name,
+    }
+    with api_client() as client:
+        response = client.post("/project", json=data)
+        response.raise_for_status()
+        project_data = response.json()
+    return Project(**project_data)
+
+
+def default_project() -> Project:
+    """
+    Retrieves the default project from the API.
+
+    :return: A Project object representing the default project.
+    :raises HTTPError: If the API request fails.
+    """
+    with api_client() as client:
+        response = client.get("/user/me/default_project")
+        response.raise_for_status()
+        return Project(**response.json())

{rowan_python-2.0.3 → rowan_python-2.1.0}/rowan/protein.py

@@ -189,12 +189,13 @@ def upload_protein(name: str, file_path: Path) -> Protein:
         return Protein(**final_response.json())
 
 
-def create_protein_from_pdb_id(name: str, code: str) -> Protein:
+def create_protein_from_pdb_id(name: str, code: str, project_uuid: str) -> Protein:
     """
     Creates a protein from a PDB ID.
 
     :param name: The name of the protein to create
     :param code: The PDB ID of the protein to create
+    :param project_uuid: The UUID of the project to create the protein in
     :return: A Protein object representing the created protein
     :raises requests.HTTPError: if the request to the API fails
     """
@@ -207,7 +208,11 @@ def create_protein_from_pdb_id(name: str, code: str) -> Protein:
         protein_data = conversion_response.json()
 
         # Step 2: Use the converted data to create the final protein object.
-        creation_payload = {"name": name, "protein_data": protein_data, "ancestor_uuid": None}
+        creation_payload = {
+            "name": name,
+            "protein_data": protein_data,
+            "project_uuid": project_uuid,
+        }
         final_response = client.post("/protein", json=creation_payload)
         final_response.raise_for_status()
 

rowan_python-2.0.3/examples/data/workflow_example.json

@@ -1,190 +0,0 @@
-{
-    "mode": "auto",
-    "engine": "xtb",
-    "messages": [],
-    "settings": {
-      "mode": "rapid",
-      "tasks": [
-        "optimize"
-      ],
-      "method": "gfn2_xtb",
-      "basis_set": null,
-      "corrections": [],
-      "opt_settings": {
-        "max_steps": 250,
-        "constraints": [
-          {
-            "atoms": [
-              4,
-              3,
-              2,
-              1
-            ],
-            "value": 0,
-            "constraint_type": "dihedral"
-          }
-        ],
-        "optimize_cell": false,
-        "energy_threshold": 0.00005,
-        "transition_state": false,
-        "recalc_hess_every": 0,
-        "max_gradient_threshold": 0.005,
-        "rms_gradient_threshold": 0.0035
-      },
-      "scf_settings": {
-        "soscf": false,
-        "max_iters": 250
-      },
-      "level_of_theory": "gfn2_xtb",
-      "compute_settings": {
-        "compute_type_used": null,
-        "requested_compute_type": "cpu"
-      },
-      "solvent_settings": null,
-      "thermochem_settings": {
-        "temperature": 298,
-        "concentration": 0.0408740470708,
-        "scaling_factor": 1,
-        "cutoff_frequency": 100
-      }
-    },
-    "calculation_uuid": "54027970-5efb-42df-8125-c8984d8ca7eb",
-    "initial_molecule": {
-      "cell": null,
-      "atoms": [
-        {
-          "position": [
-            -1.57731622,
-            0.46259034,
-            0.02288227
-          ],
-          "atomic_number": 6
-        },
-        {
-          "position": [
-            -0.55246934,
-            -0.31349805,
-            -0.78986664
-          ],
-          "atomic_number": 6
-        },
-        {
-          "position": [
-            0.65178196,
-            -0.77563238,
-            0.03104792
-          ],
-          "atomic_number": 6
-        },
-        {
-          "position": [
-            1.5013315,
-            0.37070813,
-            0.55769072
-          ],
-          "atomic_number": 6
-        },
-        {
-          "position": [
-            -1.17009891,
-            1.41344062,
-            0.37886292
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            -1.91277475,
-            -0.11690438,
-            0.88874548
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            -2.45332233,
-            0.68757176,
-            -0.59399069
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            -0.21575239,
-            0.30052639,
-            -1.63326648
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            -1.04230601,
-            -1.19688302,
-            -1.21658189
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            0.31558706,
-            -1.39539838,
-            0.87044712
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            1.28031633,
-            -1.41330121,
-            -0.60197473
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            2.39258685,
-            -0.02154188,
-            1.05803044
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            0.95227634,
-            0.97534316,
-            1.28543953
-          ],
-          "atomic_number": 1
-        },
-        {
-          "position": [
-            1.83015992,
-            1.0229789,
-            -0.25746596
-          ],
-          "atomic_number": 1
-        }
-      ],
-      "charge": 0,
-      "dipole": null,
-      "energy": null,
-      "smiles": "CCCC",
-      "stress": null,
-      "elapsed": null,
-      "gradient": null,
-      "velocities": null,
-      "multiplicity": 1,
-      "homo_lumo_gap": null,
-      "scf_completed": null,
-      "scf_iterations": null,
-      "mulliken_charges": null,
-      "calculation_index": null,
-      "vibrational_modes": null,
-      "zero_point_energy": null,
-      "thermal_energy_corr": null,
-      "thermal_enthalpy_corr": null,
-      "mulliken_spin_densities": null,
-      "thermal_free_energy_corr": null
-    }
-  }
-