rowan-python 2.1.8__tar.gz → 2.1.9__tar.gz

{rowan_python-2.1.8 → rowan_python-2.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.1.8
+Version: 2.1.9
 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-2.1.8 → rowan_python-2.1.9}/pixi.lock

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       - pypi: https://files.pythonhosted.org/packages/ee/49/1377b49de7d0c1ce41292161ea0f721913fa8722c19fb9c1e3aa0367eecb/pytest_cov-7.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/14/1b/a298b06749107c305e1fe0f814c6c74aea7b2f1e10989cb30f544a1b3253/python_dotenv-1.2.1-py3-none-any.whl
@@ -302,7 +302,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/80/46/b06b28b43d70a83cfd35a1ede3b549d2b2bf9547e898bb95aa84e9ed10e8/rdkit-2025.9.1-cp314-cp314-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/d9/0f/90088510d4758e0ee475ae1fc7f96e7bccd0e31f24107567075482b2fe9e/rdkit_stubs-0.8-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/1e/db/4254e3eabe8020b458f1a747140d32277ec7a271daf1d235b70dc0b4e6e3/requests-2.32.5-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/de/03/db1bce591d55fd5f8a08bb02517fa0b5097b2ccabd4ea1ee29aa72b67d96/ruff-0.14.3-py3-none-macosx_11_0_arm64.whl
+      - pypi: https://files.pythonhosted.org/packages/14/bb/1564b000219144bf5eed2359edc94c3590dd49d510751dad26202c18a17d/ruff-0.14.4-py3-none-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e9/44/75a9c9421471a6c4805dbf2356f7c181a29c1879239abab1ea2cc8f38b40/sniffio-1.3.1-py3-none-any.whl
@@ -451,17 +451,17 @@ packages:
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   sha256: 4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6
   requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*'
-- pypi: https://files.pythonhosted.org/packages/42/82/cdeed03bfead45203fb651ed756dfb5266028f5f939e7f06efac4041dad5/coverage-7.11.0-cp314-cp314-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/20/1d/784b87270784b0b88e4beec9d028e8d58f73ae248032579c63ad2ac6f69a/coverage-7.11.3-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: coverage
-  version: 7.11.0
-  sha256: a3d0e2087dba64c86a6b254f43e12d264b636a39e88c5cc0a01a7c71bcfdab7e
+  version: 7.11.3
+  sha256: 9061a3e3c92b27fd8036dafa26f25d95695b6aa2e4514ab16a254f297e664f83
   requires_dist:
   - tomli ; python_full_version <= '3.11' and extra == 'toml'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/80/c0/5b259b029694ce0a5bbc1548834c7ba3db41d3efd3474489d7efce4ceb18/coverage-7.11.0-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/28/76/1079547f9d46f9c7c7d0dad35b6873c98bc5aa721eeabceafabd722cd5e7/coverage-7.11.3-cp314-cp314-macosx_11_0_arm64.whl
   name: coverage
-  version: 7.11.0
-  sha256: c6f31f281012235ad08f9a560976cc2fc9c95c17604ff3ab20120fe480169bca
+  version: 7.11.3
+  sha256: fe3425dc6021f906c6325d3c415e048e7cdb955505a94f1eb774dafc779ba203
   requires_dist:
   - tomli ; python_full_version <= '3.11' and extra == 'toml'
   requires_python: '>=3.10'
@@ -502,13 +502,16 @@ packages:
   - markdown ; extra == 'dev'
   - flake8 ; extra == 'dev'
   - wheel ; extra == 'dev'
-- pypi: https://files.pythonhosted.org/packages/2a/b1/9ff6578d789a89812ff21e4e0f80ffae20a65d5dd84e7a17873fe3b365be/griffe-1.14.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/9c/83/3b1d03d36f224edded98e9affd0467630fc09d766c0e56fb1498cbb04a9b/griffe-1.15.0-py3-none-any.whl
   name: griffe
-  version: 1.14.0
-  sha256: 0e9d52832cccf0f7188cfe585ba962d2674b241c01916d780925df34873bceb0
+  version: 1.15.0
+  sha256: 6f6762661949411031f5fcda9593f586e6ce8340f0ba88921a0f2ef7a81eb9a3
   requires_dist:
   - colorama>=0.4
-  requires_python: '>=3.9'
+  - pip>=24.0 ; extra == 'pypi'
+  - platformdirs>=4.2 ; extra == 'pypi'
+  - wheel>=0.42 ; extra == 'pypi'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/78/e3/94b2e39d841a1c07b586903177d3ee802c8ae87567449a541d14028eb657/griffe_pydantic-1.1.8-py3-none-any.whl
   name: griffe-pydantic
   version: 1.1.8
@@ -695,19 +698,18 @@ packages:
   - markupsafe>=2.0
   - babel>=2.7 ; extra == 'i18n'
   requires_python: '>=3.7'
-- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1aa0949_4.conda
-  sha256: 96b6900ca0489d9e5d0318a6b49f8eff43fd85fef6e07cb0c25344ee94cd7a3a
-  md5: c94ab6ff54ba5172cf1c58267005670f
+- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1aa0949_5.conda
+  sha256: dab1fbf65abb05d3f2ee49dff90d60eeb2e02039fcb561343c7cea5dea523585
+  md5: 511ed8935448c1875776b60ad3daf3a1
   depends:
   - __glibc >=2.17,<3.0.a0
   - zstd >=1.5.7,<1.6.0a0
   constrains:
   - binutils_impl_linux-64 2.44
   license: GPL-3.0-only
-  license_family: GPL
   purls: []
-  size: 742501
-  timestamp: 1761335175964
+  size: 741516
+  timestamp: 1762674665675
 - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda
   sha256: da2080da8f0288b95dd86765c801c6e166c4619b910b11f9a8446fb852438dc2
   md5: 4211416ecba1866fab0c6470986c22d6
@@ -1056,16 +1058,16 @@ packages:
   - mkdocstrings-python-legacy>=0.2.1 ; extra == 'python-legacy'
   - mkdocstrings-python>=1.16.2 ; extra == 'python'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/d5/8f/ce008599d9adebf33ed144e7736914385e8537f5fc686fdb7cceb8c22431/mkdocstrings_python-1.18.2-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/98/5c/2597cef67b6947b15c47f8dba967a0baf19fbdfdc86f6e4a8ba7af8b581a/mkdocstrings_python-1.19.0-py3-none-any.whl
   name: mkdocstrings-python
-  version: 1.18.2
-  sha256: 944fe6deb8f08f33fa936d538233c4036e9f53e840994f6146e8e94eb71b600d
+  version: 1.19.0
+  sha256: 395c1032af8f005234170575cc0c5d4d20980846623b623b35594281be4a3059
   requires_dist:
   - mkdocstrings>=0.30
   - mkdocs-autorefs>=1.4
   - griffe>=1.13
   - typing-extensions>=4.0 ; python_full_version < '3.11'
-  requires_python: '>=3.9'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/a4/8e/469e5a4a2f5855992e425f3cb33804cc07bf18d48f2db061aec61ce50270/more_itertools-10.8.0-py3-none-any.whl
   name: more-itertools
   version: 10.8.0
@@ -1294,17 +1296,17 @@ packages:
   - pytest-benchmark ; extra == 'testing'
   - coverage ; extra == 'testing'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/5b/a5/987a405322d78a73b66e39e4a90e4ef156fd7141bf71df987e50717c321b/pre_commit-4.3.0-py2.py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/27/11/574fe7d13acf30bfd0a8dd7fa1647040f2b8064f13f43e8c963b1e65093b/pre_commit-4.4.0-py2.py3-none-any.whl
   name: pre-commit
-  version: 4.3.0
-  sha256: 2b0747ad7e6e967169136edffee14c16e148a778a54e4f967921aa1ebf2308d8
+  version: 4.4.0
+  sha256: b35ea52957cbf83dcc5d8ee636cbead8624e3a15fbfa61a370e42158ac8a5813
   requires_dist:
   - cfgv>=2.0.0
   - identify>=1.0.0
   - nodeenv>=0.11.1
   - pyyaml>=5.1
   - virtualenv>=20.10.0
-  requires_python: '>=3.9'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/84/03/0d3ce49e2505ae70cf43bc5bb3033955d2fc9f932163e84dc0779cc47f48/prompt_toolkit-3.0.52-py3-none-any.whl
   name: prompt-toolkit
   version: 3.0.52
@@ -1364,15 +1366,15 @@ packages:
   - pyyaml
   - pygments>=2.19.1 ; extra == 'extra'
   requires_python: '>=3.9'
-- pypi: https://files.pythonhosted.org/packages/a8/a4/20da314d277121d6534b3a980b29035dcd51e6744bd79075a6ce8fa4eb8d/pytest-8.4.2-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/72/99/cafef234114a3b6d9f3aaed0723b437c40c57bdb7b3e4c3a575bc4890052/pytest-9.0.0-py3-none-any.whl
   name: pytest
-  version: 8.4.2
-  sha256: 872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79
+  version: 9.0.0
+  sha256: e5ccdf10b0bac554970ee88fc1a4ad0ee5d221f8ef22321f9b7e4584e19d7f96
   requires_dist:
   - colorama>=0.4 ; sys_platform == 'win32'
   - exceptiongroup>=1 ; python_full_version < '3.11'
-  - iniconfig>=1
-  - packaging>=20
+  - iniconfig>=1.0.1
+  - packaging>=22
   - pluggy>=1.5,<2
   - pygments>=2.7.2
   - tomli>=1 ; python_full_version < '3.11'
@@ -1383,7 +1385,7 @@ packages:
   - requests ; extra == 'dev'
   - setuptools ; extra == 'dev'
   - xmlschema ; extra == 'dev'
-  requires_python: '>=3.9'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/ee/49/1377b49de7d0c1ce41292161ea0f721913fa8722c19fb9c1e3aa0367eecb/pytest_cov-7.0.0-py3-none-any.whl
   name: pytest-cov
   version: 7.0.0
@@ -1545,8 +1547,8 @@ packages:
   requires_python: '>=3.9'
 - pypi: ./
   name: rowan-python
-  version: 2.1.8
-  sha256: b93aff367817220116208b6e6ec6813669f6acd37d75977b1ba8b6ed6add45da
+  version: 2.1.9
+  sha256: d6fdbc61eb40000173e38b026fee19b4401a08485c97b04700cb10b451356300
   requires_dist:
   - httpx
   - stjames>=0.0.125
@@ -1555,15 +1557,15 @@ packages:
   - nest-asyncio
   requires_python: '>=3.11'
   editable: true
-- pypi: https://files.pythonhosted.org/packages/a7/e7/138b883f0dfe4ad5b76b58bf4ae675f4d2176ac2b24bdd81b4d966b28c61/ruff-0.14.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://files.pythonhosted.org/packages/14/bb/1564b000219144bf5eed2359edc94c3590dd49d510751dad26202c18a17d/ruff-0.14.4-py3-none-macosx_11_0_arm64.whl
   name: ruff
-  version: 0.14.3
-  sha256: 0e2f8a0bbcffcfd895df39c9a4ecd59bb80dca03dc43f7fb63e647ed176b741e
+  version: 0.14.4
+  sha256: 9358d490ec030f1b51d048a7fd6ead418ed0826daf6149e95e30aa67c168af33
   requires_python: '>=3.7'
-- pypi: https://files.pythonhosted.org/packages/de/03/db1bce591d55fd5f8a08bb02517fa0b5097b2ccabd4ea1ee29aa72b67d96/ruff-0.14.3-py3-none-macosx_11_0_arm64.whl
+- pypi: https://files.pythonhosted.org/packages/ee/79/6ad4dda2cfd55e41ac9ed6d73ef9ab9475b1eef69f3a85957210c74ba12c/ruff-0.14.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: ruff
-  version: 0.14.3
-  sha256: 71ff6edca490c308f083156938c0c1a66907151263c4abdcb588602c6e696a14
+  version: 0.14.4
+  sha256: 456daa2fa1021bc86ca857f43fe29d5d8b3f0e55e9f90c58c317c1dcc2afc7b5
   requires_python: '>=3.7'
 - pypi: https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl
   name: setuptools

{rowan_python-2.1.8 → rowan_python-2.1.9}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "2.1.8"
+version = "2.1.9"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.11"

{rowan_python-2.1.8 → rowan_python-2.1.9}/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-2.1.9}/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,
@@ -1520,7 +1549,16 @@ 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,