rowan-python 3.1.10__tar.gz → 3.1.12__tar.gz

{rowan_python-3.1.10 → rowan_python-3.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.10
+Version: 3.1.12
 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-3.1.12/docs/api/api-keys.md

@@ -0,0 +1,24 @@
+# API Keys
+
+::: rowan.api_keys
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: rowan.utils
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - api_credentials
+        - get_api_key

rowan_python-3.1.12/docs/api/calculation.md

@@ -0,0 +1,11 @@
+# Calculation
+
+::: rowan.calculation
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/api/folder.md

@@ -0,0 +1,11 @@
+# Folder
+
+::: rowan.folder
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/api/molecule.md

@@ -0,0 +1,67 @@
+# Molecule
+
+::: rowan.molecule
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: rowan.utils
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - smiles_to_stjames
+
+::: stjames.atom
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: stjames.molecule
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - VibrationalMode
+
+::: stjames.periodic_cell
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: stjames.periodic_properties
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - BandStructure

rowan_python-3.1.12/docs/api/project.md

@@ -0,0 +1,23 @@
+# Project
+
+::: rowan.project
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: rowan.utils
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - get_project_uuid

rowan_python-3.1.12/docs/api/protein.md

@@ -0,0 +1,23 @@
+# Protein
+
+::: rowan.protein
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: stjames.protein
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - ProteinSequence

rowan_python-3.1.12/docs/api/user.md

@@ -0,0 +1,18 @@
+# User
+
+::: rowan.user
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - User
+        - Organization
+        - OrganizationRole
+        - SubscriptionPlan
+        - IndividualSubscription
+        - whoami

rowan_python-3.1.12/docs/api/webhooks.md

@@ -0,0 +1,16 @@
+# Webhooks
+
+::: rowan.user
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - get_webhook_secret
+        - create_webhook_secret
+        - rotate_webhook_secret
+        - verify_webhook_secret

rowan_python-3.1.12/docs/api/workflow.md

@@ -0,0 +1,23 @@
+# Workflow
+
+::: rowan.workflows.base
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+      members:
+        - Workflow
+        - WorkflowResult
+        - WorkflowError
+        - DispatchInfo
+        - Message
+        - submit_workflow
+        - retrieve_workflow
+        - retrieve_workflows
+        - list_workflows
+        - batch_submit_workflow
+        - batch_poll_status

rowan_python-3.1.12/docs/images/favicon.svg

@@ -0,0 +1,3 @@
+<svg width="48" height="48" viewBox="0 0 48 48" fill="none" xmlns="http://www.w3.org/2000/svg">
+<path d="M23.9999 0.100006C28.8538 0.100006 32.7894 4.06917 32.7894 8.96587C32.7894 10.7904 32.2414 12.485 31.3049 13.8946C32.3442 12.5606 33.7738 11.5125 35.4936 10.9487C40.1098 9.4354 45.0674 11.9846 46.5675 16.6415C48.0671 21.2983 45.542 26.3001 40.926 27.8134C39.207 28.3769 37.441 28.3759 35.8234 27.9137C37.4013 28.4988 38.8306 29.5461 39.8931 31.0212C42.7458 34.9825 41.8749 40.5264 37.949 43.4049C34.0221 46.2831 28.5256 45.4063 25.6725 41.445C24.6097 39.9691 24.0636 38.2735 23.9999 36.5778C23.9362 38.2733 23.3916 39.9691 22.3287 41.445C19.4757 45.4063 13.9804 46.284 10.0537 43.4063C6.12684 40.5279 5.25514 34.9828 8.10823 31.0212C9.17046 29.5463 10.599 28.4988 12.1765 27.9137C10.5592 28.3755 8.79387 28.3768 7.07529 27.8134C2.45914 26.3003 -0.0672141 21.2985 1.43234 16.6415C2.93236 11.9844 7.89139 9.4354 12.5075 10.9487C14.2241 11.5115 15.651 12.5573 16.6897 13.8879C15.7563 12.4798 15.2119 10.7871 15.2119 8.96587C15.2119 4.0693 19.1463 0.100293 23.9999 0.100006ZM30.9434 14.397C29.3352 16.4856 26.8245 17.8318 23.9999 17.8318C21.1781 17.8317 18.6686 16.4891 17.0605 14.4037C18.5297 16.5911 19.0211 19.4143 18.1492 22.1219C17.2765 24.8304 15.2327 26.8222 12.7685 27.7199C15.2856 26.9848 18.1005 27.3871 20.3846 29.0612C22.6696 30.7365 23.9165 33.3144 23.9999 35.9578C24.0836 33.314 25.3325 30.7351 27.618 29.0598C29.9008 27.3872 32.7132 26.985 35.2288 27.7186C32.7659 26.82 30.7241 24.8279 29.8521 22.1206C28.9795 19.4106 29.4712 16.585 30.9434 14.397Z" fill="#24B256"/>
+</svg>

rowan_python-3.1.12/docs/index.md

@@ -0,0 +1,106 @@
+![Rowan](images/RowanLogoLarge.png){ width="320" }
+
+# Rowan Python API
+
+The `rowan` package is the official Python client for the [Rowan](https://rowansci.com) computational
+chemistry platform. Submit workflows, poll or stream results, and manage
+molecules, proteins, folders, and projects—all from plain Python.
+
+## Installation
+
+=== "pip"
+
+    ```bash
+    pip install rowan-python
+    ```
+
+=== "pixi"
+
+    ```bash
+    pixi add --pypi rowan-python
+    ```
+
+=== "uv"
+
+    ```bash
+    uv add rowan-python
+    ```
+
+## Authentication
+
+Create an API key on your [account page](https://labs.rowansci.com/account), then either export
+it as an environment variable or set it directly on the module:
+
+```python
+import os
+
+os.environ["ROWAN_API_KEY"]  # picked up automatically, or...
+
+import rowan
+
+rowan.api_key = "rowan-sk..."
+```
+
+!!! tip "Working in a shared process?"
+    Use [`rowan.api_credentials`](api/api-keys.md) to scope a key to a single `with` block instead
+    of setting it globally — handy for multi-tenant scripts or test suites.
+
+## Quickstart
+
+This example runs a geometry optimization on isoprene and streams each optimization step as it
+completes:
+
+```python title="quickstart.py" linenums="1"
+import rowan
+
+folder = rowan.get_folder("examples")  # (1)!
+
+workflow = rowan.submit_basic_calculation_workflow(
+    initial_molecule=rowan.Molecule.from_smiles("CC(=C)C=C"),
+    preset="rapid_semiempirical",  # (2)!
+    tasks=["optimize"],
+    name="Isoprene Optimization",
+    folder=folder,
+)
+
+print(f"View workflow at: https://labs.rowansci.com/calculation/{workflow.uuid}")
+
+for result in workflow.stream_result(poll_interval=3):  # (3)!
+    if result.calculation_uuid:
+        mols = rowan.retrieve_calculation_molecules(result.calculation_uuid)
+        print(f"  {len(mols)} opt steps, energy={mols[-1].get('energy') if mols else None}")
+
+print(result)  # (4)!
+```
+
+1. Folders are created on first use — no need to pre-create them in the UI.
+2. Presets bundle a method, basis set, and corrections into one named choice. See
+   [Basic Calculation](workflows/basic-calculation.md) for the full list and when to use each one.
+3. `stream_result` polls the API and yields an updated result after every optimization step,
+   instead of blocking until the whole workflow finishes.
+4. The final yielded result is the completed workflow — same object you'd get from `workflow.result`
+   after `workflow.wait()`.
+
+## What's next
+
+<div class="grid cards" markdown>
+
+-   :material-flask-outline: **Workflows**
+
+    ---
+
+    Every Rowan workflow's submit function, settings, and result type, grouped by molecular
+    modeling, property prediction, protein–ligand, spectrometry, and cheminformatics.
+
+    [:octicons-arrow-right-24: Browse workflows](workflows/basic-calculation.md)
+
+-   :material-code-braces: **Objects**
+
+    ---
+
+    `Molecule`, `Protein`, `Folder`, `Project`, `Workflow`, `Calculation`, and the account/API-key
+    types every workflow builds on.
+
+    [:octicons-arrow-right-24: Browse objects](api/workflow.md)
+
+</div>

rowan_python-3.1.12/docs/stylesheets/colors.css

@@ -0,0 +1,76 @@
+/* Rowan brand palette */
+:root > * {
+  --color-light: #FFFFFF;
+  --color-offlight: #F4F5F4;
+  --color-neutral: #DDDDDD;
+
+  --color-subtle: #6E716E;
+  --color-dark: #181D18;
+
+  --color-border-primary: #74967E;
+  --color-border-secondary: #BACBBF;
+
+  --color-form-text: #5A7763;
+  --color-form-placeholder: #9CADA1;
+  --color-link-text: #5A7763;
+
+  --color-primary-bright: #24B256;
+  --color-primary-std: #189143;
+  --color-primary-hover: #14793B;
+  --color-primary-active: #0C5C30;
+  --color-primary-disabled: #7AA982;
+
+  /* Header + top nav-tabs bar: offlight background instead of a solid green fill */
+  --md-primary-fg-color: var(--color-offlight);
+  --md-primary-fg-color--light: var(--color-light);
+  --md-primary-fg-color--dark: var(--color-offlight);
+  --md-primary-bg-color: var(--color-dark);
+  --md-primary-bg-color--light: var(--color-subtle);
+
+  /* Accent: links, buttons, focus rings, and (via --md-typeset-a-color below) the
+     current-page highlight in the sidebar nav. Material defaults --md-typeset-a-color
+     to --md-primary-fg-color, which would make it offlight-on-white and invisible —
+     pin it to the brand green explicitly instead. */
+  --md-accent-fg-color: var(--color-primary-std);
+  --md-accent-fg-color--transparent: #1891431a;
+  --md-accent-bg-color: var(--color-light);
+  --md-typeset-a-color: var(--color-primary-std);
+}
+
+/* Material's collapsed search box is a translucent-black pill tuned for a dark
+   header; against our light header it read as a dark gray box. Use a plain
+   light input instead. */
+.md-search__form {
+  background-color: var(--color-neutral);
+}
+
+.md-search__form:hover {
+  background-color: var(--color-border-secondary);
+}
+
+/* Material hardcodes each admonition type's accent color (tip = teal, #00bfa5)
+   rather than deriving it from the theme palette — recolor "tip" to match brand green. */
+.md-typeset .admonition.tip,
+.md-typeset details.tip {
+  border-color: var(--color-primary-std);
+}
+
+.md-typeset .admonition.tip:focus-within,
+.md-typeset details.tip:focus-within {
+  box-shadow: 0 0 0 0.2rem var(--md-accent-fg-color--transparent);
+}
+
+.md-typeset .tip > .admonition-title,
+.md-typeset .tip > summary {
+  background-color: var(--md-accent-fg-color--transparent);
+}
+
+.md-typeset .tip > .admonition-title::before,
+.md-typeset .tip > summary::before {
+  background-color: var(--color-primary-std);
+}
+
+.md-typeset .tip > .admonition-title::after,
+.md-typeset .tip > summary::after {
+  color: var(--color-primary-std);
+}

rowan_python-3.1.12/docs/workflows/admet.md

@@ -0,0 +1,11 @@
+# ADMET
+
+::: rowan.workflows.admet
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/analogue-docking.md

@@ -0,0 +1,11 @@
+# Analogue Docking
+
+::: rowan.workflows.analogue_docking
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/basic-calculation.md

@@ -0,0 +1,11 @@
+# Basic Calculation
+
+::: rowan.workflows.basic_calculation
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/batch-docking.md

@@ -0,0 +1,11 @@
+# Batch Docking
+
+::: rowan.workflows.batch_docking
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/binding-affinity.md

@@ -0,0 +1,11 @@
+# Binding Affinity
+
+::: rowan.workflows.binding_affinity
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/bond-dissociation-energy.md

@@ -0,0 +1,11 @@
+# Bond Dissociation Energy
+
+::: rowan.workflows.bde
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/conformer-search-settings.md

@@ -0,0 +1,21 @@
+# Conformer Search Settings
+
+::: stjames.conformers
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]
+
+::: stjames.trajectory_clustering
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/conformer-search.md

@@ -0,0 +1,11 @@
+# Conformer Search
+
+::: rowan.workflows.conformer_search
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/covalent-inhibitor-scan.md

@@ -0,0 +1,11 @@
+# Covalent Inhibitor Scan
+
+::: rowan.workflows.covalent_inhibitor_scan
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/descriptors.md

@@ -0,0 +1,11 @@
+# Descriptors
+
+::: rowan.workflows.descriptors
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/docking.md

@@ -0,0 +1,11 @@
+# Docking
+
+::: rowan.workflows.docking
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/double-ended-ts-search.md

@@ -0,0 +1,11 @@
+# Double-Ended TS Search
+
+::: rowan.workflows.double_ended_ts_search
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/electronic-properties.md

@@ -0,0 +1,11 @@
+# Electronic Properties
+
+::: rowan.workflows.electronic_properties
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/fukui.md

@@ -0,0 +1,11 @@
+# Fukui
+
+::: rowan.workflows.fukui
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/hydrogen-bond-donor-acceptor-strength.md

@@ -0,0 +1,11 @@
+# Hydrogen Bond Donor/Acceptor Strength
+
+::: rowan.workflows.hydrogen_bond_donor_acceptor_strength
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/interaction-energy-decomposition.md

@@ -0,0 +1,11 @@
+# Interaction Energy Decomposition
+
+::: rowan.workflows.interaction_energy_decomposition
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/ion-mobility.md

@@ -0,0 +1,11 @@
+# Ion Mobility
+
+::: rowan.workflows.ion_mobility
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]

rowan_python-3.1.12/docs/workflows/irc.md

@@ -0,0 +1,11 @@
+# IRC
+
+::: rowan.workflows.irc
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^_"]