rowan-python 2.0.2__tar.gz → 2.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {rowan_python-2.0.2 → rowan_python-2.1.0}/LICENSE +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/PKG-INFO +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/conformers.py +1 -1
- rowan_python-2.1.0/examples/data/workflow_example.json +177 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/docking_screen.py +3 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/irc.py +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/macropka.py +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/optimization.py +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/pka.py +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/protein_cofolding.py +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/scan.py +1 -1
- {rowan_python-2.0.2 → rowan_python-2.1.0}/pixi.lock +56 -55
- {rowan_python-2.0.2 → rowan_python-2.1.0}/pyproject.toml +2 -2
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/__init__.py +1 -0
- rowan_python-2.1.0/rowan/project.py +136 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/protein.py +7 -2
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/utils.py +3 -3
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/workflow.py +1 -1
- rowan_python-2.0.2/examples/data/workflow_example.json +0 -190
- {rowan_python-2.0.2 → rowan_python-2.1.0}/.envrc +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/.github/workflows/python-publish.yml +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/.github/workflows/test.yml +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/.gitignore +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/.pre-commit-config.yaml +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/README.md +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/docs/images/deciduous-tree-favicon.png +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/docs/index.md +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/docs/rowan_rdkit.md +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/docs/stylesheets/colors.css +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/PROTAC_solubility.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/basic_calculation_from_json.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/basic_calculation_with_constraint.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/basic_calculation_with_solvent.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/bde.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/cofolding_screen.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/conformer_dependent_redox.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/multistage_opt.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/examples/phenol_pka.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/mkdocs.yml +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/constants.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/folder.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/py.typed +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/rowan_rdkit/__init__.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/rowan_rdkit/chem_utils.py +0 -0
- {rowan_python-2.0.2 → rowan_python-2.1.0}/rowan/user.py +0 -0
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The MIT License
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Copyright (c) Rowan
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Copyright (c) Rowan Scientific Corporation
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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A class representing a project in the Rowan API.
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+
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:ivar uuid: The UUID of the project.
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:ivar name: The name of the project.
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:ivar created_at: The date and time the project was created.
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"""
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uuid: str
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name: str | None = None
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created_at: datetime | None = None
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def __repr__(self) -> str:
|
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return f"<Project name='{self.name}' created_at='{self.created_at}' uuid='{self.uuid}'>"
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def update(
|
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self,
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name: str | None = None,
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) -> Self:
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"""
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Update a project.
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:param name: The new name of the project.
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:return: The updated project object.
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"""
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payload = {
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"name": name if name is not None else self.name,
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}
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with api_client() as client:
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response = client.post(f"/project/{self.uuid}", json=payload)
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response.raise_for_status()
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updated_data = response.json()
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self.name = updated_data.get("name")
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return self
|
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def delete(self) -> None:
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"""
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Delete the project.
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This is a destructive action, it will delete all the folders and
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workflows that are inside this project.
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:raises requests.HTTPError: if the request to the API fails.
|
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+
"""
|
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with api_client() as client:
|
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response = client.delete(f"/project/{self.uuid}")
|
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response.raise_for_status()
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+
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+
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def retrieve_project(uuid: str) -> Project:
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"""
|
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Retrieves a project from the API by UUID. Project UUID can be found in the project's URL.
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|
|
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:param uuid: The UUID of the project to retrieve.
|
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:return: A Project object representing the retrieved project.
|
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:raises HTTPError: If the API request fails.
|
|
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|
+
"""
|
|
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|
+
with api_client() as client:
|
|
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|
+
response = client.get(f"/project/{uuid}")
|
|
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response.raise_for_status()
|
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|
+
return Project(**response.json())
|
|
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|
+
|
|
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+
|
|
76
|
+
def list_projects(
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name_contains: str | None = None,
|
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78
|
+
page: int = 0,
|
|
79
|
+
size: int = 10,
|
|
80
|
+
) -> list[Project]:
|
|
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|
+
"""
|
|
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|
+
Retrieve a list of projects based on the specified criteria.
|
|
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|
+
|
|
84
|
+
:param name_contains: Substring to search for in project names.
|
|
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|
+
:param page: Pagination parameter to specify the page number.
|
|
86
|
+
:param size: Pagination parameter to specify the number of items per page.
|
|
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|
+
:return: A list of Folder objects that match the search criteria.
|
|
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|
+
:raises requests.HTTPError: if the request to the API fails.
|
|
89
|
+
"""
|
|
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|
+
|
|
91
|
+
params: dict[str, Any] = {
|
|
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|
+
"page": page,
|
|
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"size": size,
|
|
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|
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}
|
|
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|
+
|
|
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|
+
if name_contains is not None:
|
|
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|
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params["name_contains"] = name_contains
|
|
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|
+
|
|
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|
+
with api_client() as client:
|
|
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|
+
response = client.get("/project", params=params)
|
|
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|
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response.raise_for_status()
|
|
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|
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items = response.json()
|
|
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|
+
|
|
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|
+
return [Project(**item) for item in items]
|
|
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|
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|
|
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|
|
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|
+
def create_project(
|
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name: str,
|
|
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|
+
) -> Project:
|
|
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|
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"""
|
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Create a new project.
|
|
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|
|
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:param name: The name of the project.
|
|
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|
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:return: The newly created project.
|
|
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|
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"""
|
|
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+
data = {
|
|
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|
+
"name": name,
|
|
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|
+
}
|
|
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|
+
with api_client() as client:
|
|
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|
+
response = client.post("/project", json=data)
|
|
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|
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response.raise_for_status()
|
|
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|
+
project_data = response.json()
|
|
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|
+
return Project(**project_data)
|
|
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|
+
|
|
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|
+
|
|
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|
+
def default_project() -> Project:
|
|
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|
+
"""
|
|
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|
+
Retrieves the default project from the API.
|
|
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|
+
|
|
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|
+
:return: A Project object representing the default project.
|
|
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|
+
:raises HTTPError: If the API request fails.
|
|
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|
+
"""
|
|
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|
+
with api_client() as client:
|
|
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|
+
response = client.get("/user/me/default_project")
|
|
135
|
+
response.raise_for_status()
|
|
136
|
+
return Project(**response.json())
|
|
@@ -189,12 +189,13 @@ def upload_protein(name: str, file_path: Path) -> Protein:
|
|
|
189
189
|
return Protein(**final_response.json())
|
|
190
190
|
|
|
191
191
|
|
|
192
|
-
def create_protein_from_pdb_id(name: str, code: str) -> Protein:
|
|
192
|
+
def create_protein_from_pdb_id(name: str, code: str, project_uuid: str) -> Protein:
|
|
193
193
|
"""
|
|
194
194
|
Creates a protein from a PDB ID.
|
|
195
195
|
|
|
196
196
|
:param name: The name of the protein to create
|
|
197
197
|
:param code: The PDB ID of the protein to create
|
|
198
|
+
:param project_uuid: The UUID of the project to create the protein in
|
|
198
199
|
:return: A Protein object representing the created protein
|
|
199
200
|
:raises requests.HTTPError: if the request to the API fails
|
|
200
201
|
"""
|
|
@@ -207,7 +208,11 @@ def create_protein_from_pdb_id(name: str, code: str) -> Protein:
|
|
|
207
208
|
protein_data = conversion_response.json()
|
|
208
209
|
|
|
209
210
|
# Step 2: Use the converted data to create the final protein object.
|
|
210
|
-
creation_payload = {
|
|
211
|
+
creation_payload = {
|
|
212
|
+
"name": name,
|
|
213
|
+
"protein_data": protein_data,
|
|
214
|
+
"project_uuid": project_uuid,
|
|
215
|
+
}
|
|
211
216
|
final_response = client.post("/protein", json=creation_payload)
|
|
212
217
|
final_response.raise_for_status()
|
|
213
218
|
|
|
@@ -19,10 +19,10 @@ def get_api_key() -> str:
|
|
|
19
19
|
|
|
20
20
|
:return: The API key.
|
|
21
21
|
"""
|
|
22
|
-
if (
|
|
23
|
-
return api_key
|
|
24
|
-
elif hasattr(rowan, "api_key"):
|
|
22
|
+
if hasattr(rowan, "api_key") and rowan.api_key:
|
|
25
23
|
return rowan.api_key
|
|
24
|
+
elif (api_key := os.environ.get("ROWAN_API_KEY")) is not None:
|
|
25
|
+
return api_key
|
|
26
26
|
|
|
27
27
|
raise ValueError(
|
|
28
28
|
"No API key provided. You can set your API key using 'rowan.api_key = <API-KEY>',"
|
|
@@ -52,7 +52,7 @@ class Workflow(BaseModel):
|
|
|
52
52
|
starred: bool
|
|
53
53
|
public: bool
|
|
54
54
|
workflow_type: str = Field(alias="object_type")
|
|
55
|
-
data: dict[str, Any] = Field(default=
|
|
55
|
+
data: dict[str, Any] | None = Field(default=None, alias="object_data")
|
|
56
56
|
email_when_complete: bool
|
|
57
57
|
max_credits: int | None = None
|
|
58
58
|
elapsed: float | None = None
|
|
@@ -1,190 +0,0 @@
|
|
|
1
|
-
{
|
|
2
|
-
"mode": "auto",
|
|
3
|
-
"engine": "xtb",
|
|
4
|
-
"messages": [],
|
|
5
|
-
"settings": {
|
|
6
|
-
"mode": "rapid",
|
|
7
|
-
"tasks": [
|
|
8
|
-
"optimize"
|
|
9
|
-
],
|
|
10
|
-
"method": "gfn2_xtb",
|
|
11
|
-
"basis_set": null,
|
|
12
|
-
"corrections": [],
|
|
13
|
-
"opt_settings": {
|
|
14
|
-
"max_steps": 250,
|
|
15
|
-
"constraints": [
|
|
16
|
-
{
|
|
17
|
-
"atoms": [
|
|
18
|
-
4,
|
|
19
|
-
3,
|
|
20
|
-
2,
|
|
21
|
-
1
|
|
22
|
-
],
|
|
23
|
-
"value": 0,
|
|
24
|
-
"constraint_type": "dihedral"
|
|
25
|
-
}
|
|
26
|
-
],
|
|
27
|
-
"optimize_cell": false,
|
|
28
|
-
"energy_threshold": 0.00005,
|
|
29
|
-
"transition_state": false,
|
|
30
|
-
"recalc_hess_every": 0,
|
|
31
|
-
"max_gradient_threshold": 0.005,
|
|
32
|
-
"rms_gradient_threshold": 0.0035
|
|
33
|
-
},
|
|
34
|
-
"scf_settings": {
|
|
35
|
-
"soscf": false,
|
|
36
|
-
"max_iters": 250
|
|
37
|
-
},
|
|
38
|
-
"level_of_theory": "gfn2_xtb",
|
|
39
|
-
"compute_settings": {
|
|
40
|
-
"compute_type_used": null,
|
|
41
|
-
"requested_compute_type": "cpu"
|
|
42
|
-
},
|
|
43
|
-
"solvent_settings": null,
|
|
44
|
-
"thermochem_settings": {
|
|
45
|
-
"temperature": 298,
|
|
46
|
-
"concentration": 0.0408740470708,
|
|
47
|
-
"scaling_factor": 1,
|
|
48
|
-
"cutoff_frequency": 100
|
|
49
|
-
}
|
|
50
|
-
},
|
|
51
|
-
"calculation_uuid": "54027970-5efb-42df-8125-c8984d8ca7eb",
|
|
52
|
-
"initial_molecule": {
|
|
53
|
-
"cell": null,
|
|
54
|
-
"atoms": [
|
|
55
|
-
{
|
|
56
|
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"position": [
|
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|
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-1.57731622,
|
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|
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0.46259034,
|
|
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|
-
0.02288227
|
|
60
|
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],
|
|
61
|
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"atomic_number": 6
|
|
62
|
-
},
|
|
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|
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{
|
|
64
|
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"position": [
|
|
65
|
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-0.55246934,
|
|
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|
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-0.31349805,
|
|
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|
-
-0.78986664
|
|
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|
-
],
|
|
69
|
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"atomic_number": 6
|
|
70
|
-
},
|
|
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|
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{
|
|
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|
-
"position": [
|
|
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|
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0.65178196,
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|
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|
|
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|
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0.03104792
|
|
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|
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],
|
|
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|
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"atomic_number": 6
|
|
78
|
-
},
|
|
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|
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{
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|
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|
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"position": [
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|
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|
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0.37070813,
|
|
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|
-
0.55769072
|
|
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|
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],
|
|
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|
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"atomic_number": 6
|
|
86
|
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},
|
|
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|
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{
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|
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|
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"position": [
|
|
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|
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-1.17009891,
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|
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|
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|
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|
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|
|
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|
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],
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|
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|
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|
|
94
|
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},
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|
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{
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-
"position": [
|
|
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|
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|
|
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|
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],
|
|
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|
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|
|
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|
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},
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|
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{
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|
|
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|
|
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|
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],
|
|
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|
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|
|
110
|
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},
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|
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{
|
|
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|
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|
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|
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},
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{
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},
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{
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},
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{
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1.28031633,
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],
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|
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|
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|
|
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|
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},
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|
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{
|
|
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|
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|
|
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|
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|
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|
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],
|
|
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|
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|
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|
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},
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|
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{
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|
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|
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|
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0.95227634,
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|
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|
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|
|
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|
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],
|
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|
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|
|
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|
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},
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|
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{
|
|
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|
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"position": [
|
|
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|
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|
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|
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|
|
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|
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],
|
|
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|
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|
|
166
|
-
}
|
|
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|
-
],
|
|
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|
-
"charge": 0,
|
|
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|
-
"dipole": null,
|
|
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|
-
"energy": null,
|
|
171
|
-
"smiles": "CCCC",
|
|
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|
-
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|
|
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|
-
"elapsed": null,
|
|
174
|
-
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|
|
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|
-
"velocities": null,
|
|
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|
-
"multiplicity": 1,
|
|
177
|
-
"homo_lumo_gap": null,
|
|
178
|
-
"scf_completed": null,
|
|
179
|
-
"scf_iterations": null,
|
|
180
|
-
"mulliken_charges": null,
|
|
181
|
-
"calculation_index": null,
|
|
182
|
-
"vibrational_modes": null,
|
|
183
|
-
"zero_point_energy": null,
|
|
184
|
-
"thermal_energy_corr": null,
|
|
185
|
-
"thermal_enthalpy_corr": null,
|
|
186
|
-
"mulliken_spin_densities": null,
|
|
187
|
-
"thermal_free_energy_corr": null
|
|
188
|
-
}
|
|
189
|
-
}
|
|
190
|
-
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|