StollLab · mtessmer · Apr 11, 2026 · Apr 11, 2026 · Apr 11, 2026 · Apr 11, 2026
diff --git a/.github/workflows/PR_test.yml b/.github/workflows/PR_test.yml
@@ -2,20 +2,20 @@ name: Test on PR activity
 on:
   pull_request:
     branches:
-    - "**"
+      - "**"
 
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-13, windows-latest]
-        python-version: [3.11]
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ 3.11 ]
 
     steps:
       - uses: actions/checkout@v3
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
@@ -26,7 +26,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install rdkit
           pip install .
-      
+
       - name: Test with pytest
         run: |
           cd tests

diff --git a/README.md b/README.md
diff --git a/docs/source/_static/ligandens.png b/docs/source/_static/ligandens.png
diff --git a/docs/source/chilife.rst b/docs/source/chilife.rst
@@ -1,6 +1,6 @@
 chiLife Functions
 =================
-
+Some intro text
 General Functions
 -----------------
 
@@ -22,5 +22,15 @@ IO Functions
 .. automodule:: chilife.io
     :members: read_distance_distribution,
               read_library,
+              read_pdb,
+              read_cif,
+              read_sdf,
               save,
-              write_atoms
+              write_atoms,
+              write_cif,
+              write_sdf,
+              create_ccd_dicts,
+              join_ccd_info,
+
+
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -12,7 +12,6 @@
 #
 import os
 import sys
-from numpy.typing import ArrayLike
 sys.path.insert(0, os.path.abspath('.'))
 # sys.path.insert(0, os.path.abspath('../../../chilife'))
 
@@ -33,6 +32,7 @@
               'sphinx_mdinclude',
               'sphinx.ext.coverage',
               'sphinx.ext.napoleon',
+              'sphinx.ext.viewcode',
               'nbsphinx',
               'nbsphinx_link',
               'IPython.sphinxext.ipython_console_highlighting',
@@ -47,7 +47,8 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 autodoc_member_order = 'bysource'
-autodoc_type_aliases = {'ArrayLike': 'ArrayLike'}
+# autodoc_type_aliases = {'ArrayLike': 'ArrayLike'}
+autodoc_typehints_format = 'short'
 source_suffix = [".rst", ".md"]
 add_module_names = False
 python_use_unqualified_type_names = True
@@ -73,9 +74,28 @@
     'gallery/04-Adding_custom_spin_labels':'_static/customlabels.png',
     'gallery/06-Membrane_Docking': '_static/memdock.png',
     'gallery/10-Nucleic_acid_labels' : '_static/TUMLabeled.png',
-    'gallery/11-Arbitrary_molecular_labels': '_static/CMP501NCA.png'
+    'gallery/11-Arbitrary_molecular_labels': '_static/CMP501NCA.png',
+    'gallery/14-LigandEnsemble': '_static/ligandens.png',
     }
 # Add any paths that contain custom static files (such as style sheets) here,
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
+
+rst_prolog = """
+:github_url: https://github.com/mtessmer/chilife
+"""
+
+html_context = {
+    "display_github": True,
+    "github_user": "mtessmer",
+    "github_repo": "chilife",
+    "github_version": "main",
+    "conf_py_path": "/docs/source/",
+    "github_url": "https://github.com/mtessmer/chilife",
+}
+#
+# html_theme_options = {
+#     'repository_url': 'https://github.com/mtessmer/chiLife',
+#     'repository_name': 'chiLife',
+# }
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -18,3 +18,4 @@ Examples
     gallery/11-Arbitrary_molecular_labels.nblink
     gallery/12-Analyzing_MD_Simulations.nblink
     gallery/13-OpenMM_Score_Function.nblink
+    gallery/14-LigandEnsemble.nblink
diff --git a/docs/source/gallery/11-Arbitrary_molecular_labels.nblink b/docs/source/gallery/11-Arbitrary_molecular_labels.nblink
@@ -1,3 +1,3 @@
 {   
-"path": "../../../examples/11 - Arbitrary molecular labels/12 - Arbitrary molecular labels.ipynb"
+"path": "../../../examples/11 - Arbitrary molecular labels/11 - Arbitrary molecular labels.ipynb"
 }
diff --git a/docs/source/gallery/14-LigandEnsemble.nblink b/docs/source/gallery/14-LigandEnsemble.nblink
@@ -0,0 +1,4 @@
+{   
+"path": "../../../examples/14 - LigandEnsemble/14-LigandEnsemble.ipynb"
+}
+
diff --git a/docs/source/gallery/ligandens.png b/docs/source/gallery/ligandens.png
diff --git a/docs/source/ligand_utils.rst b/docs/source/ligand_utils.rst
@@ -0,0 +1,5 @@
+Ligand Utils
+=============
+
+.. automodule:: chilife.ligand_utils
+    :members:
diff --git a/docs/source/rotamer_ensemble.rst b/docs/source/rotamer_ensemble.rst
@@ -1,6 +1,6 @@
 .. _rotamer_ensemble:
 
-Side Chain Ensembles
+Molecular Ensembles
 =====================
 
 
@@ -17,10 +17,9 @@ acids.
 SpinLabel
 ---------
 
-The :class:`chilife.SpinLabel` object is the primary feature of χLife. :class:`chilife.SpinLabel` inherits from the
-:class:`chilife.RotamerEnsemble` object and therefore has all the same properties and methods . Additionally
-:class:`chilife.SpinLabel` have several other features unique to spin labels and useful for protein and spin label
-modeling.
+The :class:`chilife.SpinLabel` inherits from the :class:`chilife.RotamerEnsemble` object and therefore has all the same
+properties and methods. Additionally :class:`chilife.SpinLabel` have several other features unique to spin labels and
+useful for protein and spin label modeling.
 
 .. autoclass:: chilife.SpinLabel
     :members:
@@ -35,17 +34,42 @@ amino acids whether they are spin labels or other bifunctional non-canonical ami
 .. autoclass:: chilife.dRotamerEnsemble
     :members:
 
+
 dSpinLabel
 ----------
+The :class:`dSpinLabel` class is the radicalized extension of the :class:`dRotamerEnsemble`. It is used to model
+bifunctional spinl labels like RX and di-histidine copper capped with NTA.
 
 .. autoclass:: chilife.dSpinLabel
     :members:
     :exclude-members: copy
 
 
+LigandEnsemble
+--------------
+The :class:`LigandEnsemble` is the base class for ligands. Ligands, being free-floating structures rather than branches
+off a protein or nucleic acid chain, must be treated very differently than other ensemble objects. Nonetheless, the
+:class:`LigandEnsemble` API is designed to be used in a very similar manner to the :class:`RotamerEnsemble` and
+:class:`dRotamerEnsemble` class families.
+
+.. autoclass:: chilife.LigandEnsemble
+    :members:
+
+
+SpinLigand
+----------
+The :class:`SpinEnsemble` class extends :class:`LigandEnsemble` allowing for free radicals and can be used like a
+:class:`SpinLabel` to get distance distributions with other :class:`SpinLabel` like objects and visualize spin density.
+
+.. autoclass:: chilife.SpinLigand
+    :members:
+
+
 IntrinsicLabel
 --------------
+The :class:`IntrinsicLabel` class is designed to allow users to specify free radicals that are already present in a
+molecular system or protein structure such as metals in hemes and porphyrins, organic radicals like the tryptophan
+cation radical.
 
 .. autoclass:: chilife.IntrinsicLabel
     :members:
-
diff --git a/docs/source/utils.rst b/docs/source/utils.rst
@@ -6,5 +6,6 @@ Utils
 
     numba_utils
     protein_utils
+    ligand_utils
     alignments
     scoring
diff --git a/examples/09 - Bifunctional labels/09 - Bifunctional Labels.ipynb b/examples/09 - Bifunctional labels/09 - Bifunctional Labels.ipynb
@@ -37,11 +37,11 @@
     "\n",
     "# Create spin labels using the off-rotamer sampling method\n",
     "SL1 = xl.dSpinLabel('DCN', (6, 8), protein)\n",
-    "SL2 = xl.dSpinLabel('DCN', (28,32), protein)\n",
+    "SL2 = xl.dSpinLabel('DCN', (28, 32), protein)\n",
     "\n",
     "# Predict distance distributions over an experimental axis\n",
     "r, Pexp = np.loadtxt('Exp_Data.txt').T\n",
-    "Pexp /= np.trapz(Pexp, r)\n",
+    "Pexp /= np.trapezoid(Pexp, r)\n",
     "P = xl.distance_distribution(SL1, SL2, r=r)"
    ],
    "outputs": [],
@@ -60,6 +60,7 @@
    },
    "source": [
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "plt.style.use('chiLife')\n",
     "plt.rcParams.update({'font.size': 15})\n",
     "\n",
@@ -69,7 +70,6 @@
     "\n",
     "ax.plot(r, P, label='Model Prediction', color='C0')\n",
     "\n",
-    "\n",
     "ax.set_yticks([])\n",
     "ax.set_xlabel(r'distance ($\\rm\\AA$)')\n",
     "ax.legend(frameon=False)\n",

diff --git a/examples/12 - Analyzing MD simulations/.AR1A.xtc_offsets.npz b/examples/12 - Analyzing MD simulations/.AR1A.xtc_offsets.npz
diff --git a/examples/12 - Analyzing MD simulations/12 - Analyzing MD Simulations.ipynb b/examples/12 - Analyzing MD simulations/12 - Analyzing MD Simulations.ipynb
diff --git a/examples/12 - Analyzing MD simulations/1ubq_A28CYR.pdb b/examples/12 - Analyzing MD simulations/1ubq_A28CYR.pdb
@@ -733,7 +733,7 @@ ATOM      4 S1L  CYR A  28      41.113  22.404  12.342  0.60  1.00           S
 ATOM      5 C1L  CYR A  28      40.902  22.700  10.587  0.60  1.00           C  
 ATOM      6 C1R  CYR A  28      41.649  21.701   9.707  0.60  1.00           C  
 ATOM      7 C2R  CYR A  28      42.660  22.053   8.929  0.60  1.00           C  
-ATOM      8  C1  CYR A  28      41.403  20.210   9.539  0.60  1.00           C  
+ATOM      8  C1  CYR A  28      41.404  20.210   9.539  0.60  1.00           C  
 ATOM      9  C2  CYR A  28      43.181  21.048   8.029  0.60  1.00           C  
 ATOM     10  NN  CYR A  28      42.231  19.939   8.398  0.60  1.00           N  
 ATOM     11  ON  CYR A  28      42.425  18.730   8.022  0.60  1.00           O  
@@ -756,7 +756,7 @@ ATOM      6 C1R  CYR A  28      43.117  22.296  13.973  0.54  1.00           C
 ATOM      7 C2R  CYR A  28      43.607  23.561  14.205  0.54  1.00           C  
 ATOM      8  C1  CYR A  28      43.874  21.124  14.655  0.54  1.00           C  
 ATOM      9  C2  CYR A  28      44.785  23.470  15.131  0.54  1.00           C  
-ATOM     10  NN  CYR A  28      44.902  21.916  15.324  0.54  1.00           N  
+ATOM     10  NN  CYR A  28      44.902  21.916  15.323  0.54  1.00           N  
 ATOM     11  ON  CYR A  28      45.835  21.399  15.997  0.54  1.00           O  
 ATOM     12 C2D  CYR A  28      44.314  24.064  16.420  0.54  1.00           C  
 ATOM     13 C1D  CYR A  28      43.032  20.354  15.730  0.54  1.00           C  
@@ -839,7 +839,7 @@ ATOM      5 C1L  CYR A  28      42.185  23.263  11.196  0.29  1.00           C
 ATOM      6 C1R  CYR A  28      43.347  22.415  10.704  0.29  1.00           C  
 ATOM      7 C2R  CYR A  28      44.629  22.415  11.112  0.29  1.00           C  
 ATOM      8  C1  CYR A  28      43.198  21.468   9.523  0.29  1.00           C  
-ATOM      9  C2  CYR A  28      45.545  21.456  10.561  0.29  1.00           C  
+ATOM      9  C2  CYR A  28      45.546  21.456  10.561  0.29  1.00           C  
 ATOM     10  NN  CYR A  28      44.638  20.978   9.486  0.29  1.00           N  
 ATOM     11  ON  CYR A  28      45.044  19.901   8.929  0.29  1.00           O  
 ATOM     12 C2D  CYR A  28      45.801  20.312  11.589  0.29  1.00           C  
@@ -966,7 +966,7 @@ ATOM      6 C1R  CYR A  28      42.437  21.761  13.973  0.16  1.00           C
 ATOM      7 C2R  CYR A  28      42.869  22.771  14.678  0.16  1.00           C  
 ATOM      8  C1  CYR A  28      42.749  20.487  14.529  0.16  1.00           C  
 ATOM      9  C2  CYR A  28      43.643  22.438  15.852  0.16  1.00           C  
-ATOM     10  NN  CYR A  28      43.594  20.955  15.719  0.16  1.00           N  
+ATOM     10  NN  CYR A  28      43.594  20.955  15.718  0.16  1.00           N  
 ATOM     11  ON  CYR A  28      43.838  20.189  16.757  0.16  1.00           O  
 ATOM     12 C2D  CYR A  28      43.012  22.940  17.152  0.16  1.00           C  
 ATOM     13 C1D  CYR A  28      41.476  19.770  15.027  0.16  1.00           C