Disulfides

.github/workflows/gh-ci.yaml

@@ -24,7 +24,7 @@ defaults:
 
 jobs:
   main-tests:
-    if: "github.repository == 'yoshanuikabundi/openff-pablo'"
+    if: "github.repository == 'openforcefield/openff-pablo'"
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

AUTHORS.md

@@ -4,7 +4,7 @@ OpenFF Pablo was created by Josh Mitchell in 2025.
 
 
 All contributing authors are listed in this file below.
-The repository history at https://github.com/yoshanuikabundi/openff-pablo
+The repository history at https://github.com/openforcefield/openff-pablo
 and the CHANGELOG show individual code contributions.
 
 ## Chronological list of authors

CONTRIBUTING.md

@@ -4,12 +4,12 @@ We welcome all contributions to OpenFF Pablo!
 
 Contributions can take many forms, such as:
 
-* sharing bug reports or feature requests through the [Issue Tracker](https://github.com/yoshanuikabundi/openff-pablo/issues)
+* sharing bug reports or feature requests through the [Issue Tracker](https://github.com/openforcefield/openff-pablo/issues)
 * asking or answering questions, or otherwise joining in on discussions
 * adding bug fixes, new features, or otherwise improving the code
 * adding or improving documentation
 
-The second two options both involve making a [pull request](https://github.com/yoshanuikabundi/openff-pablo/pulls) .
+The second two options both involve making a [pull request](https://github.com/openforcefield/openff-pablo/pulls) .
 
 There are many existing guides on how to make a contribution to an open
 source project on GitHub. In short, the steps are to:

README.md

@@ -2,13 +2,13 @@ OpenFF Pablo
 ==============================
 [//]: # (Badges)
 
-| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/yoshanuikabundi/openff-pablo.svg)](https://github.com/openforcefield/openff-pablo/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/openforcefield/openff-pablo/latest)  [![Documentation Status](https://readthedocs.org/projects/openff-pablo/badge/?version=latest)](https://openff-pablo.readthedocs.io/en/latest/?badge=latest)                                                                                                                                                                                                                        |
+| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-pablo.svg)](https://github.com/openforcefield/openff-pablo/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/openforcefield/openff-pablo/latest)  [![Documentation Status](https://readthedocs.org/projects/openff-pablo/badge/?version=latest)](https://openff-pablo.readthedocs.io/en/latest/?badge=latest)                                                                                                                                                                                                                        |
 | :----------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| **Status**         | [![GH Actions Status](https://github.com/yoshanuikabundi/openff-pablo/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-pablo/actions?query=branch%3Amain+workflow%3Agh-ci) |
+| **Status**         | [![GH Actions Status](https://github.com/openforcefield/openff-pablo/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-pablo/actions?query=branch%3Amain+workflow%3Agh-ci) |
 
 New, independent implementation of `Topology.from_pdb`
 
-OpenFF Pablo is bound by a [Code of Conduct](https://github.com/yoshanuikabundi/openff-pablo/blob/main/CODE_OF_CONDUCT.md).
+OpenFF Pablo is bound by a [Code of Conduct](https://github.com/openforcefield/openff-pablo/blob/main/CODE_OF_CONDUCT.md).
 
 ### Installation
 
@@ -72,8 +72,8 @@ pip install -e ".[test,doc]"
 
 ### Copyright
 
-The OpenFF Pablo source code is hosted at https://github.com/yoshanuikabundi/openff-pablo
-and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/yoshanuikabundi/openff-pablo/blob/main/LICENSE)).
+The OpenFF Pablo source code is hosted at https://github.com/openforcefield/openff-pablo
+and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/openforcefield/openff-pablo/blob/main/LICENSE)).
 
 Copyright (c) 2025, Josh Mitchell
 

docs/conf.py

@@ -241,7 +241,7 @@
 html_theme_options = {
     # Repository integration
     # Set the repo url for the link to appear
-    "repo_url": "https://github.com/yoshanuikabundi/openff-pablo",
+    "repo_url": "https://github.com/openforcefield/openff-pablo",
     # The name of the repo. If must be set if repo_url is set
     "repo_name": "openff-pablo",
     # Must be one of github, gitlab or bitbucket

docs/tests.md

@@ -13,6 +13,8 @@ Pablo has a (developing) PDB test suite.
     - Coverage <input type="text" id="pdb-filter-1" onkeyup="filterTable(1)" placeholder="Filter..." style="display: block; width: 8rem">
 *   - 5ap1_prepared.pdb
     - ACE/NME caps, `unique_molecules`
+*   - 193L_prepared.pdb
+    - disulfides, all 20 canonical amino acids, charged terminii, charged canonical AA side chains
 :::
 
 <script>