rowan-python 2.1.8__tar.gz → 2.1.10__tar.gz

{rowan_python-2.1.8 → rowan_python-2.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.8
+Version: 2.1.10
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -11,7 +11,7 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.125
+Requires-Dist: stjames>=0.0.128
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

rowan_python-2.1.10/examples/dcd_download.py

@@ -0,0 +1,10 @@
+from pathlib import Path
+
+import rowan
+
+# rowan.api_key = ""
+
+pose_analysis_md_workflows = rowan.list_workflows(workflow_type="pose_analysis_md", status=2)
+for workflow in pose_analysis_md_workflows:
+    print(workflow.name)
+    workflow.download_dcd_files(replicates=[0], name=workflow.name, path=Path("dcd_files"))

rowan_python-2.1.10/examples/pdb_download.py

@@ -0,0 +1,10 @@
+from pathlib import Path
+
+import rowan
+
+# rowan.api_key = ""
+
+proteins = rowan.list_proteins()
+for protein in proteins:
+    print(protein.name)
+    protein.download_pdb_file(name=protein.name, path=Path("pdb_files"))

{rowan_python-2.1.8 → rowan_python-2.1.10}/pixi.lock

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{rowan_python-2.1.8 → rowan_python-2.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.8"
+version = "2.1.10"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
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+    "stjames>=0.0.128",
     "setuptools",
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{rowan_python-2.1.8 → rowan_python-2.1.10}/rowan/folder.py

@@ -58,6 +58,7 @@ class Folder(BaseModel):
 
         return self
 
+
     def update(
         self,
         name: str | None = None,
@@ -110,6 +111,15 @@ class Folder(BaseModel):
             response = client.delete(f"/folder/{self.uuid}")
             response.raise_for_status()
 
+    def print_folder_tree(self, max_depth: int = 10, show_uuids: bool = False) -> None:
+        """
+        Retrieves a folder tree from the API.
+
+        :param max_depth: The maximum depth of the folder tree.
+        :param show_uuids: Whether to show the UUIDs of the folders.
+        :raises HTTPError: If the API request fails.
+        """
+        print_folder_tree(self.uuid, max_depth, show_uuids)
 
 def retrieve_folder(uuid: str) -> Folder:
     """
@@ -125,19 +135,6 @@ def retrieve_folder(uuid: str) -> Folder:
         return Folder(**response.json())
 
 
-def home_folder() -> Folder:
-    """
-    Retrieves the home folder from the API.
-
-    :return: A Folder object representing the home folder.
-    :raises HTTPError: If the API request fails.
-    """
-    with api_client() as client:
-        response = client.get("/user/me/root_folders")
-        response.raise_for_status()
-        return Folder(**response.json()["user_root"])
-
-
 def list_folders(
     parent_uuid: str | None = None,
     name_contains: str | None = None,
@@ -210,3 +207,22 @@ def create_folder(
         response.raise_for_status()
         folder_data = response.json()
     return Folder(**folder_data)
+
+def print_folder_tree(uuid: str, max_depth: int = 10, show_uuids: bool = False) -> None:
+    """
+    Retrieves a folder tree from the API.
+
+    :param uuid: The UUID of the root of the folder tree.
+    :param max_depth: The maximum depth of the folder tree.
+    :param show_uuids: Whether to show the UUIDs of the folders.
+    :raises HTTPError: If the API request fails.
+    """
+    params: dict[str, Any] = {
+        "max_depth": max_depth,
+        "show_uuids": show_uuids,
+    }
+    with api_client() as client:
+        response = client.get(f"/folder/{uuid}/folder_tree", params=params)
+        response.raise_for_status()
+        folder_data = response.json()
+    print(folder_data)

{rowan_python-2.1.8 → rowan_python-2.1.10}/rowan/protein.py

@@ -114,6 +114,27 @@ class Protein(BaseModel):
             response = client.post(f"/protein/sanitize/{self.uuid}")
             response.raise_for_status()
 
+    def download_pdb_file(self, path: Path | None = None, name: str | None = None) -> None:
+        """
+        Downloads the PDB file for a protein
+
+        :param path: Directory to save the file to (defaults to current directory)
+        :param name: Optional custom name for the file (defaults to protein name)
+        :raises requests.HTTPError: if the request to the API fails
+        """
+        if path is None:
+            path = Path.cwd()
+
+        path.mkdir(parents=True, exist_ok=True)
+
+        with api_client() as client:
+            response = client.get(f"/protein/{self.uuid}/get_pdb_file")
+            response.raise_for_status()
+
+        file_path = path / f"{name or self.name}.pdb"
+        with open(file_path, "wb") as f:
+            f.write(response.content)
+
 
 def retrieve_protein(uuid: str) -> Protein:
     """

{rowan_python-2.1.8 → rowan_python-2.1.10}/rowan/workflow.py

@@ -240,6 +240,35 @@ class Workflow(BaseModel):
         with open(path / f"{self.name}-msa.tar.gz", "wb") as f:
             f.write(response.content)
 
+    def download_dcd_files(self, replicates: list[int],
+                           name: str | None = None, path: Path | None = None) -> None:
+        """
+        Downloads DCD trajectory files for specified replicates
+
+        :param replicates: List of replicate indices to download
+        :param name: Optional custom name for the tar.gz file (defaults to workflow name)
+        :param path: Directory to save the file to (defaults to current directory)
+        :raises ValueError: if workflow is not a pose analysis MD workflow
+        :raises requests.HTTPError: if the request to the API fails
+        """
+        if self.workflow_type != "pose_analysis_md":
+            raise ValueError("This workflow is not a pose analysis molecular dynamics workflow.")
+
+        if path is None:
+            path = Path.cwd()
+
+        path.mkdir(parents=True, exist_ok=True)
+
+        with api_client() as client:
+            response = client.post(
+                f"/trajectory/{self.uuid}/trajectory_dcds", json=replicates
+            )
+            response.raise_for_status()
+
+        file_path = path / f"{name or self.name}.tar.gz"
+        with open(file_path, "wb") as f:
+            f.write(response.content)
+
 
 def submit_workflow(
     workflow_type: stjames.WORKFLOW_NAME,
@@ -379,6 +408,33 @@ def retrieve_workflow(uuid: str) -> Workflow:
         return Workflow(**response.json())
 
 
+def retrieve_workflows(uuids: list[str]) -> list[Workflow]:
+    """
+    Retrieves a list of workflows from the API.
+
+    :param uuids: The UUIDs of the workflows to retrieve.
+    :return: A list of Workflow objects representing the retrieved workflows.
+    :raises HTTPError: If the API request fails.
+    """
+    with api_client() as client:
+        response = client.post("/workflow/batch_retrieve", json={"uuids": uuids})
+        response.raise_for_status()
+        return [Workflow(**workflow_data) for workflow_data in response.json()]
+
+def batch_poll_status(uuids: list[str]) -> list[Workflow]:
+    """
+    Polls the status of a list of workflows.
+
+    :param uuids: The UUIDs of the workflows to poll.
+    :return: A dictionary of statuses and the count of workflows in that status.
+    :raises HTTPError: If the API request fails.
+    """
+    with api_client() as client:
+        response = client.post("/workflow/batch_status", json={"uuids": uuids})
+        response.raise_for_status()
+        return response.json()
+
+
 def retrieve_calculation_molecules(
     uuid: str, return_frequencies: bool = False
 ) -> list[dict[str, Any]]:
@@ -1520,7 +1576,16 @@ def submit_msa_workflow(
     max_credits: int | None = None,
 ) -> Workflow:
     """
-    Submits an MSA workflow to the API.
+    Submits a multiple sequence alignment (MSA) workflow to the API.
+
+    :param initial_protein_sequences: List of protein sequences to align, as ProteinSequence objects
+    sor strings.
+    :param output_formats: List of output formats for the resulting MSA files.
+    :param name: The name to assign to the workflow.
+    :param folder_uuid: UUID of the folder where the workflow will be stored.
+    :param max_credits: The maximum number of credits to use for the workflow.
+    :return: A Workflow object representing the submitted MSA workflow.
+    :raises HTTPError: If the API request fails.
     """
     workflow = stjames.MSAWorkflow(
         initial_protein_sequences=initial_protein_sequences,