rowan-python 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

rowan/client.py

@@ -3,105 +3,150 @@ from __future__ import annotations
 import cctk
 import httpx
 from typing import Optional
-import numpy as np
 import stjames
 from dataclasses import dataclass, field
 import time
 
 import rowan
 
-API_URL = "https://api.rowansci.com/calculation"
+API_URL = "https://api.rowansci.com"
 
-# cf. /opt/miniconda3/envs/openai/lib/python3.9/site-packages/openai/__init__.py
 
 @dataclass
 class Client:
     blocking: bool = True
     print: bool = True
     ping_interval: int = 5
+    delete_when_finished: bool = False
 
     headers: dict = field(init=False)
 
     def __post_init__(self):
         self.headers = {"X-API-Key": rowan.utils.get_api_key()}
 
+        if not self.blocking and self.delete_when_finished:
+            print("Warning: ``delete_when_finished`` has no effect when ``blocking`` is False. To delete calculations, call ``Client.delete()`` manually.")
+
     def compute(
         self,
-        input_molecule: cctk.Molecule,
+        type: Optional[str] = "calculation",
+        input_mol: Optional[cctk.Molecule] = None,
+        input_smiles: Optional[str] = None,
         name: Optional[str] = None,
-        folder_id: Optional[str] = None,
+        folder_uuid: Optional[str] = None,
+        engine: str = "peregrine",
         **options,
-    ) -> stjames.Calculation | int:
-        atomic_numbers = input_molecule.atomic_numbers.view(np.ndarray)
-        geometry = input_molecule.geometry.view(np.ndarray)
-
-        atoms = list()
-        for i in range(input_molecule.num_atoms()):
-            atoms.append(
-                stjames.Atom(atomic_number=atomic_numbers[i], position=geometry[i])
-            )
-
-        molecule = stjames.Molecule(
-            atoms=atoms,
-            charge=input_molecule.charge,
-            multiplicity=input_molecule.multiplicity,
-        )
-        settings = stjames.Settings(**options)
-        calc = stjames.Calculation(molecules=[molecule], name=name, settings=settings)
+    ) -> dict | str:
+        if (input_mol is None) == (input_smiles is None):
+            raise ValueError("Must specify exactly one of ``input_smiles`` and ``input_mol``!")
+
+        if input_mol is None:
+            input_mol = cctk.Molecule.new_from_smiles(input_smiles)
+
+        molecule = rowan.utils.cctk_to_stjames(input_mol)
 
         with httpx.Client() as client:
-            response = client.post(
-                f"{API_URL}",
-                headers=self.headers,
-                json={
-                    "json_data": calc.model_dump(mode="json"),
-                    "folder_id": folder_id,
-                },
-            )
+            if type == "calculation":
+                settings = stjames.Settings(**options)
+                calc = stjames.Calculation(molecules=[molecule], name=name, engine=engine, settings=settings)
+
+                response = client.post(
+                    f"{API_URL}/calculation",
+                    headers=self.headers,
+                    json={
+                        "json_data": calc.model_dump(mode="json"),
+                        "folder_uuid": folder_uuid,
+                    },
+                )
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.post(
+                    f"{API_URL}/workflow",
+                    headers=self.headers,
+                    json={
+                        "initial_molecule": molecule.model_dump(mode="json"),
+                        "workflow_type": type,
+                        "name": name,
+                        "folder_uuid": folder_uuid,
+                        "workflow_data": options,
+                    },
+                )
+
             response.raise_for_status()
             response_dict = response.json()
-            calc_id = response_dict["id"]
-
-            if self.print:
-                print(f"Calculation {calc_id} submitted")
-
-            if self.blocking:
-                while not response_dict["is_finished"]:
-                    time.sleep(self.ping_interval)
-                    response = client.get(f"{API_URL}/{calc_id}", headers=self.headers)
-                    response_dict = response.json()
-                    if not response.status_code == 200:
-                        raise ValueError(
-                            f"Error {response.status_code}: {response.reason}"
-                        )
-
-                # we finished! get proper schema
-                response = client.get(
-                    f"{API_URL}/{calc_id}/stjames", headers=self.headers
-                )
+            calc_uuid = response_dict["uuid"]
+
+        if self.blocking:
+            while not self.is_finished(calc_uuid, type):
+                time.sleep(self.ping_interval)
+            result = self.get(calc_uuid, type)
+
+            if self.delete_when_finished:
+                self.delete(calc_uuid, type)
+
+            return result
+
+        else:
+            return calc_uuid
+
+    def is_finished(self, calc_uuid: str, type: str = "calculation") -> bool:
+        with httpx.Client() as client:
+            if type == "calculation":
+                response = client.get(f"{API_URL}/calculation/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
                 response_dict = response.json()
+                status = response_dict["status"]
 
-                if self.print:
-                    print(
-                        f"Calculation {calc_id} completed after {response_dict['elapsed']:.1f} s of CPU time"
-                    )
-                    print(
-                        f"(View the results at labs.rowansci.com/calculations/{calc_id})"
-                    )
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.get(f"{API_URL}/workflow/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                status = response_dict["object_status"]
 
-                return stjames.Calculation.model_validate(response_dict)
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")
+
+        return status in [2, 3, 4]
+
+    def get(self, calc_uuid: str, type: str = "calculation") -> dict:
+        with httpx.Client() as client:
+            if type == "calculation":
+                response = client.get(f"{API_URL}/calculation/{calc_uuid}/stjames", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                return response_dict
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.get(f"{API_URL}/workflow/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+                response_dict = response.json()
+                return response_dict["object_data"]
 
             else:
-                return calc_id
+                raise ValueError(f"Unknown type ``{type}``!")
 
-    def get(self, calc_id: int) -> stjames.Calculation:
+    def stop(self, calc_uuid: str, type: str = "calculation") -> None:
         with httpx.Client() as client:
-            response = client.get(f"{API_URL}/{calc_id}/stjames", headers=self.headers)
-            response.raise_for_status()
-            response_dict = response.json()
-            return stjames.Calculation.model_validate(response_dict)
+            if type == "calculation":
+                response = client.post(f"{API_URL}/calculation/{calc_uuid}/stop", headers=self.headers)
+                response.raise_for_status()
 
-    def stop(self, calc_id: int) -> None:
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.post(f"{API_URL}/workflow/{calc_uuid}/stop", headers=self.headers)
+                response.raise_for_status()
+
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")
+
+    def delete(self, calc_uuid: str, type: str = "calculation") -> None:
         with httpx.Client() as client:
-            response = client.post(f"{API_URL}/{calc_id}/stop", headers=self.headers)
-            response.raise_for_status()
+            if type == "calculation":
+                response = client.delete(f"{API_URL}/calculation/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+
+            elif type in ["pka", "conformers", "tautomers"]:
+                response = client.delete(f"{API_URL}/folder/{calc_uuid}", headers=self.headers)
+                response.raise_for_status()
+
+            else:
+                raise ValueError(f"Unknown type ``{type}``!")

rowan/utils.py

@@ -1,4 +1,7 @@
 import os
+import cctk
+import stjames
+import numpy as np
 
 import rowan
 
@@ -13,3 +16,18 @@ def get_api_key() -> str:
         raise ValueError(
             "No API key provided. You can set your API key using 'rowan.api_key = <API-KEY>', or you can set the environment variable ROWAN_API_KEY=<API-KEY>)."
         )
+
+
+def cctk_to_stjames(molecule: cctk.Molecule) -> stjames.Molecule:
+    atomic_numbers = molecule.atomic_numbers.view(np.ndarray)
+    geometry = molecule.geometry.view(np.ndarray)
+
+    atoms = list()
+    for i in range(molecule.num_atoms()):
+        atoms.append(stjames.Atom(atomic_number=atomic_numbers[i], position=geometry[i]))
+
+    return stjames.Molecule(
+        atoms=atoms,
+        charge=molecule.charge,
+        multiplicity=molecule.multiplicity,
+    )

rowan_python-0.0.3.dist-info/LICENSE

@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) Rowan (https://rowansci.com)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

rowan_python-0.0.3.dist-info/METADATA

@@ -0,0 +1,32 @@
+Metadata-Version: 2.1
+Name: rowan-python
+Version: 0.0.3
+Summary: Rowan Python Library
+Author-email: Corin Wagen <corin@rowansci.com>
+Project-URL: Homepage, https://github.com/rowansci/rowan-client
+Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cctk >=0.2.18
+Requires-Dist: httpx >=0.25
+Requires-Dist: numpy >=1.24
+Requires-Dist: stjames >=0.0.23
+
+# Rowan Python Library
+
+[![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+
+The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
+
+## Documentation
+
+The documentation is available [here](https://docs.rowansci.com/python-api).
+
+
+## Issues
+
+To report issues, please use the "Issues" tab above.
+
+*Corin Wagen, 2023*

rowan_python-0.0.3.dist-info/RECORD

@@ -0,0 +1,8 @@
+rowan/__init__.py,sha256=0O7Cmo2Io01Uqqx9iL8xcWW0t0YfgwBX7RKxDPXnbVU,61
+rowan/client.py,sha256=m3Zoi3tKtirejRQf1YKCnu6I2KL9OZwgJNhBXKdKwQA,5632
+rowan/utils.py,sha256=AVldYWowm7g1Ffs7JhJY7X85goNuFHvMUel0zXguDrk,932
+rowan_python-0.0.3.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+rowan_python-0.0.3.dist-info/METADATA,sha256=Bvw7gSUtk4F7F6CSU1k3o40IqNvm9gQGVrqbkQ-PaTY,1067
+rowan_python-0.0.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+rowan_python-0.0.3.dist-info/top_level.txt,sha256=0B0BJ1GvTwD5rxpsHctrermP7PVk4SFaQb2syJpGQl8,6
+rowan_python-0.0.3.dist-info/RECORD,,

{rowan_python-0.0.1.dist-info → rowan_python-0.0.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

rowan_python-0.0.1.dist-info/METADATA

@@ -1,78 +0,0 @@
-Metadata-Version: 2.1
-Name: rowan-python
-Version: 0.0.1
-Summary: Rowan Python Library
-Author-email: Corin Wagen <corin@rowansci.com>
-Project-URL: Homepage, https://github.com/rowansci/rowan-client
-Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-Requires-Dist: cctk >=0.2.18
-Requires-Dist: httpx >=0.25
-Requires-Dist: numpy >=1.24
-Requires-Dist: stjames >=0.0.5
-
-# Rowan Python Library
-
-The Rowan Python library provides convenient access to the Rowan API from applications written in the Python language.
-
-## Documentation
-
-The documentation is available [here](https://docs.rowansci.com).
-
-## Installation
-
-To install, run `pip install rowan-python`.
-
-## Usage
-
-Rowan can be run in either blocking (wait until job is complete) or non-blocking (don't wait) modes.
-Both modes require generation of an API key at [labs.rowansci.com](https://labs.rowansci.com/account/api-keys).
-
-For now, molecules are specified through [*cctk*](https://cctk.rtfd.io). Additional ways to specify molecules will be added in the future.
-
-Results are returned as dictionaries in the [*stjames*](https://github.com/rowansci/stjames) format.
-
-### Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client()
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# run calculation remotely and return result
-result = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-print(result)
-```
-
-### Non-Blocking
-```
-import cctk
-import rowan
-
-rowan.api_key = "rowan-sk..."
-client = rowan.Client(blocking=False)
-
-# load molecule by name (cctk can also load in a variety of file formats)
-molecule = cctk.Molecule.new_from_name("cyclobutane")
-
-# start calculation and return id
-calc_id = client.compute(molecule, name="opt cyclobutane", method="b97-3c", tasks=["optimize", "charge"])
-
-# retrieve result (and status)
-result = client.get(calc_id)
-print(result)
-
-# alternately, cancel queued or running calculation
-client.stop(calc_id)
-```
-
-## Issues
-
-To report issues, please use the "Issues" tab above.
-
-*Corin Wagen, 2023*

rowan_python-0.0.1.dist-info/RECORD

@@ -1,7 +0,0 @@
-rowan/__init__.py,sha256=0O7Cmo2Io01Uqqx9iL8xcWW0t0YfgwBX7RKxDPXnbVU,61
-rowan/client.py,sha256=K1EgAl7yuyziX_1L_-5QpBbdtQFeRdZLis19N7i3hbQ,3622
-rowan/utils.py,sha256=_dZVPMBwgp02loVkNesXlJWOIG8zUKM8SlbjZq5R840,421
-rowan_python-0.0.1.dist-info/METADATA,sha256=M7DxYJx42a0_uc-X7nHK6K6KAg_JTflqWVC4PwhsOGI,2228
-rowan_python-0.0.1.dist-info/WHEEL,sha256=Xo9-1PvkuimrydujYJAjF7pCkriuXBpUPEjma1nZyJ0,92
-rowan_python-0.0.1.dist-info/top_level.txt,sha256=0B0BJ1GvTwD5rxpsHctrermP7PVk4SFaQb2syJpGQl8,6
-rowan_python-0.0.1.dist-info/RECORD,,