rowan-python 3.2.0__tar.gz → 3.2.2__tar.gz

{rowan_python-3.2.0 → rowan_python-3.2.2}/.envrc

@@ -2,5 +2,5 @@ watch_file pyproject.toml
 watch_file uv.lock
 dotenv_if_exists .env
 
-uv sync --locked
+uv sync --frozen
 source .venv/bin/activate

{rowan_python-3.2.0 → rowan_python-3.2.2}/.github/workflows/build-and-deploy-docs.yml

@@ -1,8 +1,8 @@
 name: Build & Deploy Rowan Python Docs
 
 on:
-  release:
-    types: [published]
+  push:
+    branches: [master]
   workflow_dispatch:
 
 permissions:
@@ -10,17 +10,18 @@ permissions:
 
 jobs:
   build-and-deploy-docs:
+    if: github.repository == 'rowansci/rowan-python' && github.ref == 'refs/heads/master'
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7.0.1
         with:
           fetch-depth: 0
           ref: master
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.1.0
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           enable-cache: true
 
@@ -42,4 +43,7 @@ jobs:
       - name: Deploy with rsync
         run: |
           rsync -avz --delete site/ \
-            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:${{ secrets.DOCS_TARGET_DIR }}
+            ${{ secrets.DOCS_USERNAME }}@${{ secrets.DOCS_IP }}:${{ secrets.DOCS_TARGET_DIR }}/site/
+
+      - name: Verify deployed docs
+        run: curl --fail --silent --show-error --location --retry 5 --retry-delay 5 --retry-all-errors https://docs.rowansci.com/api/python/v3/ -o /dev/null

{rowan_python-3.2.0 → rowan_python-3.2.2}/.github/workflows/publish-skill.yml

@@ -16,7 +16,7 @@ jobs:
     if: github.repository == 'rowansci/rowan-python'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7.0.1
       - name: Zip skill
         run: cd skills && zip -r ../computational-chemistry-and-biology-skill.zip computational-chemistry-and-biology
       - name: Publish/refresh release

{rowan_python-3.2.0 → rowan_python-3.2.2}/.github/workflows/python-publish.yml

@@ -18,16 +18,19 @@ jobs:
     # Enable after configuring the repository environment.
     # environment:
     #   name: pypi
+    # permissions:
+    #   id-token: write
+    #   contents: read
     steps:
       - name: Skip if running with act
         if: ${{ env.ACT == 'true' }}
         run: exit 1
 
       - name: Checkout
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7.0.1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.1.0
+        uses: astral-sh/setup-uv@v10.2.0
 
       - name: Install Python
         run: uv python install

{rowan_python-3.2.0 → rowan_python-3.2.2}/.github/workflows/test.yml

@@ -23,10 +23,10 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7.0.1
 
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v7.6
+        uses: astral-sh/setup-uv@v10.2.0
         with:
           enable-cache: true
 
@@ -38,8 +38,11 @@ jobs:
 
       - name: Check TOML/YAML/whitespace
         run: |
-          uv run prek run --all-files --show-diff-on-failure --color=always \
-            check-toml check-yaml trailing-whitespace end-of-file-fixer
+          uv run -- prek run --all-files --show-diff-on-failure --color=always \
+            check-toml \
+            check-yaml \
+            trailing-whitespace \
+            end-of-file-fixer
 
       - run: uv run rumdl fmt --check --diff .
       - run: uv run rumdl check .
@@ -50,9 +53,3 @@ jobs:
       - run: uv run ty check
 
       - run: uv run pytest --cov --cov-report=xml
-
-      # Enable after configuring Codecov and its repository token.
-      # - name: Upload coverage to Codecov
-      #   uses: codecov/codecov-action@v5
-      #   with:
-      #     token: ${{ secrets.CODECOV_TOKEN }}

rowan_python-3.2.2/.gitignore

@@ -0,0 +1,66 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# Packaging
+build/
+dist/
+*.egg-info/
+
+# Testing and coverage
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+
+# uv
+.venv/
+
+# rumdl
+.rumdl_cache/
+
+# direnv
+.direnv/
+
+# Editors
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Environment
+.env
+.env.*
+.app.json
+
+# Documentation and notebooks
+/site/
+.ipynb_checkpoints/
+
+# Legacy environments
+.pixi/
+
+# Scientific application output
+timer.dat
+psi*.clean
+*.CP
+*.CPC
+*.lprof
+pyscf.chk
+local/
+cyp/
+msa_directory/
+
+# Local notes and machine-specific agent settings
+notes.md
+/.claude/settings.local.json

{rowan_python-3.2.0 → rowan_python-3.2.2}/.rumdl.toml

@@ -7,6 +7,7 @@ disable = [
 
 exclude = [
     ".git",
+    ".venv",
     "node_modules",
     "vendor",
     "dist",
@@ -17,5 +18,4 @@ respect-gitignore = true
 
 [per-file-ignores]
 # Skill files start with frontmatter, not headings
-".claude/**/*.md" = ["MD041"]
-".agents/**/*.md" = ["MD041"]
+"**/skills/**/*.md" = ["MD041"]

{rowan_python-3.2.0 → rowan_python-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: rowan-python
-Version: 3.2.0
+Version: 3.2.2
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -12,22 +12,19 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.261
+Requires-Dist: stjames>=0.0.281
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
 
 [![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://docs.astral.sh/uv/)
-[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Downloads](https://img.shields.io/pypi/dm/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python/)
 [![License](https://img.shields.io/github/license/rowansci/rowan-python)](LICENSE)
 [![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/rowansci/rowan-python/test.yml?branch=master&logo=github-actions)](https://github.com/rowansci/rowan-python/actions)
-[![Typing: ty](https://img.shields.io/badge/typing-ty-EFC621.svg)](https://github.com/astral-sh/ty)
-<!-- Enable these badges with the corresponding tooling/services.
+[![ty](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ty/main/assets/badge/v0.json)](https://github.com/astral-sh/ty)
 [![Markdown style: rumdl](https://img.shields.io/badge/md%20style-rumdl-000000.svg)](https://rumdl.dev)
-[![Codecov](https://img.shields.io/codecov/c/github/rowansci/rowan-python)](https://codecov.io/gh/rowansci/rowan-python)
--->
 
 The Rowan Python library is the Python SDK for running Rowan computational chemistry workflows
 programmatically. Use it from scripts and applications to submit calculations, monitor workflow

{rowan_python-3.2.0 → rowan_python-3.2.2}/README.md

@@ -2,15 +2,12 @@
 
 [![pypi](https://img.shields.io/pypi/v/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://docs.astral.sh/uv/)
-[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Downloads](https://img.shields.io/pypi/dm/rowan-python.svg)](https://pypi.python.org/pypi/rowan-python/)
 [![License](https://img.shields.io/github/license/rowansci/rowan-python)](LICENSE)
 [![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/rowansci/rowan-python/test.yml?branch=master&logo=github-actions)](https://github.com/rowansci/rowan-python/actions)
-[![Typing: ty](https://img.shields.io/badge/typing-ty-EFC621.svg)](https://github.com/astral-sh/ty)
-<!-- Enable these badges with the corresponding tooling/services.
+[![ty](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ty/main/assets/badge/v0.json)](https://github.com/astral-sh/ty)
 [![Markdown style: rumdl](https://img.shields.io/badge/md%20style-rumdl-000000.svg)](https://rumdl.dev)
-[![Codecov](https://img.shields.io/codecov/c/github/rowansci/rowan-python)](https://codecov.io/gh/rowansci/rowan-python)
--->
 
 The Rowan Python library is the Python SDK for running Rowan computational chemistry workflows
 programmatically. Use it from scripts and applications to submit calculations, monitor workflow

{rowan_python-3.2.0 → rowan_python-3.2.2}/prek.toml

@@ -1,4 +1,6 @@
+# schema https://www.schemastore.org/prek.json
 exclude = '(^\.venv/|^\.pixi/|\.dat$|\.patch$)'
+default_install_hook_types = ["pre-commit", "pre-push"]
 default_stages = ["pre-commit", "pre-push"]
 
 [[repos]]
@@ -6,6 +8,7 @@ repo = "builtin"
 hooks = [
   { id = "check-toml" },
   { id = "check-yaml", args = ["--unsafe"] },
+  { id = "check-merge-conflict" },
   { id = "end-of-file-fixer" },
   { id = "trailing-whitespace" },
 ]
@@ -13,6 +16,14 @@ hooks = [
 [[repos]]
 repo = "local"
 
+[[repos.hooks]]
+id = "uv-lock-check"
+name = "uv lock --check"
+language = "system"
+entry = "uv lock --check"
+files = '^(pyproject\.toml|uv\.lock)$'
+pass_filenames = false
+
 [[repos.hooks]]
 id = "rumdl-fmt"
 name = "rumdl-fmt"
@@ -29,13 +40,12 @@ entry = "uv run rumdl check . --fix"
 types = ["markdown"]
 pass_filenames = false
 
-
 [[repos.hooks]]
 id = "ruff-format"
 name = "ruff-format"
 language = "system"
 entry = "uv run ruff format ."
-types = ["python"]
+types_or = ["python", "pyi"]
 pass_filenames = false
 
 [[repos.hooks]]
@@ -43,7 +53,7 @@ id = "ruff-check"
 name = "ruff-check"
 language = "system"
 entry = "uv run ruff check . --fix"
-types = ["python"]
+types_or = ["python", "pyi"]
 pass_filenames = false
 
 [[repos.hooks]]
@@ -51,15 +61,14 @@ id = "ty"
 name = "ty"
 language = "system"
 entry = "uv run ty check"
-types = ["python"]
+types_or = ["python", "pyi"]
 pass_filenames = false
-stages = ["pre-commit"]
 
 [[repos.hooks]]
 id = "pytest"
-stages = ["pre-push"]
 name = "pytest"
 language = "system"
 entry = "uv run pytest"
-types = ["python"]
+always_run = true
 pass_filenames = false
+stages = ["pre-push"]

{rowan_python-3.2.0 → rowan_python-3.2.2}/pyproject.toml

@@ -1,9 +1,10 @@
 [project]
 name = "rowan-python"
-version = "3.2.0"
+version = "3.2.2"
 description = "Rowan Python Library"
 readme = "README.md"
 license = "MIT"
+license-files = ["LICENSE"]
 requires-python = ">=3.12"
 authors = [
     { name = "Corin Wagen", email = "corin@rowansci.com" },
@@ -11,7 +12,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.261",
+    "stjames>=0.0.281",
     "setuptools",
     "rdkit",
     "nest-asyncio",
@@ -104,6 +105,9 @@ ignore = [
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401", "F403"]
 
+[tool.ruff.lint.flake8-type-checking]
+runtime-evaluated-base-classes = ["pydantic.BaseModel"]
+
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
@@ -139,7 +143,6 @@ packages = ["rowan"]
 [tool.hatch.build.targets.sdist]
 exclude = [
     "/AGENTS.md",
-    "/CLAUDE.md",
     "/.agents",
     "/.claude",
 ]

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/__init__.py

@@ -67,6 +67,7 @@ from stjames.engine_compatibility import (
     METHOD_ENGINES,
     get_supported_corrections,
 )
+from stjames.pdb import ResidueRef
 from stjames.optimization.band_method import NEBSettings
 from stjames.optimization.interpolation import Interpolation
 from stjames.optimization.string_method import FSMSettings, StringMethodSettings

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/folder.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from datetime import datetime
 from typing import TYPE_CHECKING, Any, Self
 
 from pydantic import BaseModel
@@ -8,8 +9,6 @@ from .project import default_project, retrieve_project
 from .utils import api_client, get_project_uuid
 
 if TYPE_CHECKING:
-    from datetime import datetime
-
     from .workflows.base import Workflow
 
 
@@ -65,8 +64,6 @@ class Folder(BaseModel):
         for field_name in self.__class__.model_fields:
             setattr(self, field_name, getattr(updated_folder, field_name))
 
-        self.model_rebuild()
-
         return self
 
     def update(

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/project.py

@@ -197,8 +197,15 @@ def default_project() -> Project:
 
     Raises:
         httpx.HTTPStatusError: API request fails
+        ValueError: user has no default project in the API key's organization
     """
     with api_client() as client:
         response = client.get("/user/me/default_project")
         response.raise_for_status()
-        return Project(**response.json())
+        project = response.json()
+    if project is None:
+        raise ValueError(
+            "You have no default project in this organization. "
+            "Set a default project, or pass a folder or project."
+        )
+    return Project(**project)

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/protein.py

@@ -1,4 +1,3 @@
-import time
 import warnings
 from datetime import datetime
 from pathlib import Path
@@ -22,7 +21,6 @@ class Protein(BaseModel):
         created_at: creation date of the protein
         used_in_workflow: whether the protein is used in a workflow
         ancestor_uuid: UUID of the ancestor protein
-        sanitized: whether the protein is sanitized
         name: name of the protein
         data: data of the protein
         public: whether the protein is public
@@ -32,7 +30,6 @@ class Protein(BaseModel):
     created_at: datetime | None = None
     used_in_workflow: bool | None = None
     ancestor_uuid: str | None = None
-    sanitized: int | None = None
     name: str | None = None
     data: dict | None = None
     public: bool | None = None
@@ -188,7 +185,6 @@ class Protein(BaseModel):
         self.data = protein_data.get("data")
         self.public = protein_data.get("public")
         self.pocket = protein_data.get("pocket")
-        self.sanitized = protein_data.get("sanitized")
         self.used_in_workflow = protein_data.get("used_in_workflow")
         self._workflow_uuid = workflow_uuid
         return self
@@ -241,118 +237,6 @@ class Protein(BaseModel):
             response = client.delete(f"/protein/{self.uuid}")
             response.raise_for_status()
 
-    def sanitize(self, poll_interval: float = 10.0, timeout: float = 300.0) -> None:
-        """Sanitizes a protein and waits for the process to complete.
-
-        Protein sanitization runs asynchronously on the server. This method
-        submits the request then polls until sanitization succeeds, fails, or
-        times out.
-
-        Args:
-            poll_interval: seconds between status checks (default 10)
-            timeout: maximum seconds to wait before raising (default 300)
-
-        Raises:
-            RuntimeError: sanitization fails, is stopped, or times out
-            httpx.HTTPStatusError: any API request fails
-        """
-        with api_client() as client:
-            response = client.post(f"/protein/sanitize/{self.uuid}")
-            response.raise_for_status()
-
-        deadline = time.monotonic() + timeout
-        while time.monotonic() < deadline:
-            time.sleep(poll_interval)
-            self.refresh()
-            match self.sanitized:
-                case 2:  # success
-                    return
-                case 3:  # failed
-                    raise RuntimeError(
-                        f"Protein sanitization failed for {self.uuid}. "
-                        "Check the protein in the Rowan UI for details."
-                    )
-                case 4:  # stopped
-                    raise RuntimeError(f"Protein sanitization was stopped for {self.uuid}.")
-                case _:  # 1 (in progress) or None: keep polling
-                    pass
-
-        raise RuntimeError(f"Protein sanitization timed out after {timeout:.0f}s for {self.uuid}.")
-
-    def prepare(
-        self,
-        find_missing_residues: bool = True,
-        add_missing_atoms: bool = True,
-        remove_heterogens: bool = True,
-        keep_waters: bool = False,
-        remove_hydrogens: bool = False,
-        remove_invalid_hydrogens: bool = False,
-        add_hydrogens: bool = True,
-        add_hydrogen_ph: float = 7.0,
-        optimize_hydrogens: bool = True,
-        poll_interval: float = 10.0,
-        timeout: float = 300.0,
-    ) -> None:
-        """Quickly prepare a protein in place using PDBFixer and OpenMM.
-
-        Runs PDBFixer to fix nonstandard residues, add missing atoms/hydrogens,
-        and optionally optimizes hydrogen positions with OpenMM. This is the fast
-        preparation option and typically finishes in about a minute or less. Use
-        `submit_protein_preparation_workflow` for the full protein preparation workflow,
-        which can take around ten minutes but includes Boltz-2 missing-structure modeling,
-        terminal capping, selectable protonation methods, and retained non-polymers.
-
-        Args:
-            find_missing_residues: identify and model missing residues
-            add_missing_atoms: add missing heavy atoms to residues
-            remove_heterogens: remove ligands, salts, and other heterogens
-            keep_waters: preserve water molecules when removing heterogens
-            remove_hydrogens: remove all existing hydrogens before adding new ones
-            remove_invalid_hydrogens: remove hydrogens not matching the forcefield template
-            add_hydrogens: add missing hydrogen atoms
-            add_hydrogen_ph: pH used to determine protonation states when adding hydrogens
-            optimize_hydrogens: optimize hydrogen positions with OpenMM energy minimization
-            poll_interval: seconds between status checks (default 10)
-            timeout: maximum seconds to wait before raising (default 300)
-
-        Raises:
-            RuntimeError: preparation fails, is stopped, or times out
-            httpx.HTTPStatusError: any API request fails
-        """
-        params = {
-            "find_missing_residues": find_missing_residues,
-            "add_missing_atoms": add_missing_atoms,
-            "remove_heterogens": remove_heterogens,
-            "keep_waters": keep_waters,
-            "remove_hydrogens": remove_hydrogens,
-            "remove_invalid_hydrogens": remove_invalid_hydrogens,
-            "add_hydrogens": add_hydrogens,
-            "add_hydrogen_ph": add_hydrogen_ph,
-            "optimize_hydrogens": optimize_hydrogens,
-        }
-        with api_client() as client:
-            response = client.post(f"/protein/prepare/{self.uuid}", params=params)
-            response.raise_for_status()
-
-        deadline = time.monotonic() + timeout
-        while time.monotonic() < deadline:
-            time.sleep(poll_interval)
-            self.refresh()
-            match self.sanitized:
-                case 2:
-                    return
-                case 3:
-                    raise RuntimeError(
-                        f"Protein preparation failed for {self.uuid}. "
-                        "Check the protein in the Rowan UI for details."
-                    )
-                case 4:
-                    raise RuntimeError(f"Protein preparation was stopped for {self.uuid}.")
-                case _:
-                    pass
-
-        raise RuntimeError(f"Protein preparation timed out after {timeout:.0f}s for {self.uuid}.")
-
     def validate_protein_forcefield(self, exclude_residues: list[str | int] | None = None) -> None:
         """Validate that this protein can be parameterized with the MD forcefield.
 

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/workflows/binding_affinity.py

@@ -82,7 +82,8 @@ def submit_binding_affinity_workflow(
     input modes are supported:
 
     **Mode 1 – holo protein:** protein already contains the bound ligand. Pass
-    `ligand_residue_name` to identify which residue is the ligand vs. the receptor.
+    `ligand_residue_name` to identify which residue is the ligand vs. the receptor,
+    and exactly one entry in `ligand_smiles` describing that bound ligand.
     Do not pass `ligand_structures`.
 
     **Mode 2 – apo protein + external poses:** protein has no bound ligand. Pass
@@ -101,13 +102,15 @@ def submit_binding_affinity_workflow(
         protein: protein structure. Can be input as a UUID or a Protein object. Required
             unless `protein_sequences` is set (mode 3)
         ligand_residue_name: residue name identifying the ligand in a holo protein PDB
-            (mode 1 only)
+            (mode 1 only); requires exactly one matching `ligand_smiles` entry
         ligand_structures: external ligand poses to score, already in the protein's
             coordinate frame. Must have 3D coordinates (mode 2 only)
         protein_sequences: protein sequences to score against, in place of `protein`
             (mode 3, NESSO only)
-        ligand_smiles: ligand SMILES to score, in place of `ligand_residue_name`/
-            `ligand_structures` (mode 3, NESSO only)
+        ligand_smiles: exactly one SMILES describing the bound ligand with
+            `ligand_residue_name` (mode 1, all methods), or ligand SMILES to score without
+            structural ligand inputs (mode 3, NESSO only). Not accepted with
+            `ligand_structures`
         binding_affinity_settings: settings controlling how binding affinity is
             computed: `SinglePointEnergySettings` (SQM), `GninaAffinitySettings`,
             `AEVPLIGAffinitySettings`, or `NessoAffinitySettings`. Defaults to
@@ -150,9 +153,15 @@ def submit_binding_affinity_workflow(
         binding_affinity_settings=binding_affinity_settings or SinglePointEnergySettings(),
     )
 
+    workflow_data = workflow.model_dump(serialize_as_any=True, mode="json")
+    if isinstance(workflow.binding_affinity_settings, SinglePointEnergySettings):
+        workflow_data["binding_affinity_settings"]["truncation_radius"] = (
+            workflow.binding_affinity_settings.truncation_radius
+        )
+
     data = {
         "workflow_type": "binding_affinity",
-        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
+        "workflow_data": workflow_data,
         "name": name,
         "folder_uuid": folder_uuid,
         "max_credits": max_credits,

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/workflows/protein_md.py

@@ -142,13 +142,14 @@ def submit_protein_md_workflow(
     nonbonded_cutoff: float = 8.0,
     ionic_strength_M: float = 0.0,
     water_buffer: float = 8.0,
+    frame_save_interval_ps: float = 10.0,
     save_solvent: bool = False,
     num_solvent_to_save: int | None = None,
     small_molecules: dict[str | int, str | None] | None = None,
     binder: Binder | None = None,
     protein_restraint_cutoff: float | None = None,
     protein_restraint_constant: float = 100,
-    analysis_interval_ps: float | None = None,
+    analysis_interval_ps: float | None = 100,
     clustering: KMeansClusteringSettings | GreedyClusteringSettings | None = None,
     validate_forcefield: bool = True,
     name: str = "Protein MD Workflow",
@@ -178,6 +179,8 @@ def submit_protein_md_workflow(
         nonbonded_cutoff: nonbonded cutoff for particle-mesh Ewald, in A
         ionic_strength_M: ionic strength of the solution, in M (molar)
         water_buffer: amount of water to add around the protein, in A
+        frame_save_interval_ps: how often to save a frame to the trajectory, in ps; must be
+            an integer multiple of timestep_fs
         save_solvent: whether solvent should be saved
         num_solvent_to_save: keep this many solvent molecules nearest the binder, or all if None;
             only meaningful when save_solvent is True and a binder is present
@@ -191,8 +194,8 @@ def submit_protein_md_workflow(
         protein_restraint_cutoff: cutoff distance from the binder past which Cα atoms are
             harmonically restrained, in Å; None disables restraints
         protein_restraint_constant: force constant for Cα backbone restraints, in kcal/mol/Ų
-        analysis_interval_ps: interval at which to compute per-frame SASA and polar SASA, in ps.
-            None disables those analyses
+        analysis_interval_ps: interval at which to compute per-frame SASA and polar SASA
+            (default 100), in ps. None disables those analyses
         clustering: how to cluster trajectory frames. None disables clustering; pass a
             KMeansClusteringSettings (num_clusters) or GreedyClusteringSettings (cutoff_angstrom)
         validate_forcefield: validate the protein forcefield
@@ -246,6 +249,7 @@ def submit_protein_md_workflow(
         nonbonded_cutoff=nonbonded_cutoff,
         ionic_strength_M=ionic_strength_M,
         water_buffer=water_buffer,
+        frame_save_interval_ps=frame_save_interval_ps,
         save_solvent=save_solvent,
         num_solvent_to_save=num_solvent_to_save,
         small_molecules=small_molecules,

{rowan_python-3.2.0 → rowan_python-3.2.2}/rowan/workflows/protein_preparation.py

@@ -75,7 +75,7 @@ def submit_protein_preparation_workflow(
     """Submit a protein-preparation workflow to the API.
 
     Full protein preparation can take around ten minutes, depending on the structure and
-    settings. For a faster PDBFixer/OpenMM-only path, use `Protein.prepare()`.
+    settings.
 
     Args:
         protein: protein to prepare, as a UUID or Protein object