Merge pull request #157 from StollLab/mkpep

refactoring, exampels, and docs
StollLab · Aug 15, 2024 · 8cd8705 · 8cd8705
2 parents 6e261cd + 771bb3a
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diff --git a/README.md b/README.md
@@ -1,13 +1,22 @@
 <p align="center">
    <a href="https://stolllab.github.io/chiLife/">
-      <img src="https://img.shields.io/badge/docs-latest-brightgreen.svg" height="60">
+      <img src="https://github.com/StollLab/chiLife/raw/main/img/chiLife_logo.png" width="300">
+   </a>
+</p>
+
+<p align="center">
+   <a href="https://stolllab.github.io/chiLife/">
+      <img src="https://img.shields.io/badge/docs-latest-brightgreen.svg" width="300">
    </a>
 </p>
 
 
-|                       :exclamation:   News   :exclamation:                                |                       
-|-------------------------------------------------------------------------------------------|
-| chiLife now supports arbitrary backbone attachments including DNA and RNA labels and more!| 
+| **UPDATES**                                                                                                                   |
+|-------------------------------------------------------------------------------------------------------------------------------|
+| 2024.8.15 : chiLife 1.0 released!                                                                                             |
+| 2024.8.15 : chiLife can now be used to create arbitrary peptides with natural and NCAAs. Checkout the `make_peptide` function. |
+| 2024.8.15 : chiLife can make NCAA structures from smiles. Checkout `smiles2residue`. Note: Requires RDKit to be installed.    | 
+| chiLife now supports arbitrary backbone attachments including DNA and RNA labels and more!                                    | 
 
 
 

diff --git a/... Arbitrary molecular lables/CMP501NCA.png → docs/source/_static/CMP501NCA.png b/... Arbitrary molecular lables/CMP501NCA.png → docs/source/_static/CMP501NCA.png
diff --git a/...s/11 - Nucleic acid labels/TUMLabeled.png → docs/source/_static/TUMLabeled.png b/...s/11 - Nucleic acid labels/TUMLabeled.png → docs/source/_static/TUMLabeled.png
diff --git a/docs/source/_static/chiLife_logo.png b/docs/source/_static/chiLife_logo.png
diff --git a/docs/source/_static/chiLife_logo_enclosed.png b/docs/source/_static/chiLife_logo_enclosed.png
diff --git a/docs/source/_static/customlabels.png b/docs/source/_static/customlabels.png
diff --git a/docs/source/_static/memdock.png b/docs/source/_static/memdock.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,7 +18,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'χLife'
+project = 'chiLife'
 copyright = '2022, Maxx Tessmer'
 author = 'Maxx Tessmer'
 
@@ -47,7 +47,7 @@
 # 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'}
 source_suffix = [".rst", ".md"]
 add_module_names = False
 python_use_unqualified_type_names = True
@@ -66,12 +66,16 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-
+html_static_path = ['_static']
+html_logo = '_static/chiLife_logo.png'
+
+nbsphinx_thumbnails = {
+    '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'
+    }
 # 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".
-
-
-
-html_static_path = ['_static']
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -7,9 +7,12 @@ Examples
     :glob:
 
     gallery/01-Basic_Spin_Labeling.nblink
-    gallery/02-SDSL_Site_Screen.nblink
-    gallery/03-Adding_Custom_Spin_Lables.nblink
-    gallery/04-Repacking_with_MCMC_Sampling.nblink
-    gallery/05-Membrane_Docking.nblink
-    gallery/06-Custom_Energy_Function.nblink
+    gallery/02-Simple_SDSL_site_pair_screen.nblink
+    gallery/03-SDSL_Site_Screen.nblink
+    gallery/04-Adding_custom_spin_labels.nblink
+    gallery/05-Repacking_with_MCMC_Sampling.nblink
+    gallery/06-Membrane_Docking.nblink
+    gallery/07-Custom_Energy_Function.nblink
     gallery/09-Bifunctional_Labels.nblink
+    gallery/10-Nucleic_acid_labels.nblink
+    gallery/11-Arbitrary_molecular_labels.nblink
diff --git a/docs/source/gallery/02-SDSL_Site_Screen.nblink b/docs/source/gallery/02-SDSL_Site_Screen.nblink
diff --git a/docs/source/gallery/02-Simple_SDSL_site_pair_screen.nblink b/docs/source/gallery/02-Simple_SDSL_site_pair_screen.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/02 - Simple SDSL site pair screen/02 - Simple SDSL site pair screen.ipynb"
+}
diff --git a/docs/source/gallery/03-Adding_Custom_Spin_Lables.nblink b/docs/source/gallery/03-Adding_Custom_Spin_Lables.nblink
diff --git a/docs/source/gallery/03-SDSL_Site_Screen.nblink b/docs/source/gallery/03-SDSL_Site_Screen.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/03 - SDSL site screen for conformational change/03-SDSL Site Screen.ipynb"
+}
diff --git a/docs/source/gallery/04-Adding_custom_spin_labels.nblink b/docs/source/gallery/04-Adding_custom_spin_labels.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/04 - Adding custom spin labels/04 - Adding custom spin labels.ipynb"
+}
diff --git a/docs/source/gallery/04-Repacking_with_MCMC_Sampling.nblink b/docs/source/gallery/04-Repacking_with_MCMC_Sampling.nblink
diff --git a/docs/source/gallery/05-Membrane_Docking.nblink b/docs/source/gallery/05-Membrane_Docking.nblink
diff --git a/docs/source/gallery/05-Repacking_with_MCMC_Sampling.nblink b/docs/source/gallery/05-Repacking_with_MCMC_Sampling.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/05 - Repacking with MCMC sampling/05-Repacking with MCMC sampling.ipynb"
+}
diff --git a/docs/source/gallery/06-Custom_Energy_Function.nblink b/docs/source/gallery/06-Custom_Energy_Function.nblink
diff --git a/docs/source/gallery/06-Membrane_Docking.nblink b/docs/source/gallery/06-Membrane_Docking.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/06 - Membrane Docking/06-Membrane Docking.ipynb"
+}
diff --git a/docs/source/gallery/07-Custom_Energy_Function.nblink b/docs/source/gallery/07-Custom_Energy_Function.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/07 - Custom energy functions/07 - Custom energy functions.ipynb"
+}
diff --git a/docs/source/gallery/10-Nucleic_acid_labels.nblink b/docs/source/gallery/10-Nucleic_acid_labels.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/10 - Nucleic acid labels/10 - Nucleic acid labels.ipynb"
+}
diff --git a/docs/source/gallery/11-Arbitrary_molecular_labels.nblink b/docs/source/gallery/11-Arbitrary_molecular_labels.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/11 - Arbitrary molecular labels/12 - Arbitrary molecular labels.ipynb"
+}
diff --git a/docs/source/gallery/12-Analyzing_MD_simulations.nblink b/docs/source/gallery/12-Analyzing_MD_simulations.nblink
@@ -0,0 +1,3 @@
+{   
+"path": "../../../examples/12 - Analyzing MD simulations/12 - Analyzing MD Simulations.ipynb"
+}
diff --git a/...s/12 - Arbitrary molecular lables/CMP.png → docs/source/gallery/CMP.png b/...s/12 - Arbitrary molecular lables/CMP.png → docs/source/gallery/CMP.png
diff --git a/docs/source/gallery/CMP501NCA.png b/docs/source/gallery/CMP501NCA.png
diff --git a/docs/source/gallery/CMP501NCAsm.png b/docs/source/gallery/CMP501NCAsm.png
diff --git a/...s/12 - Arbitrary molecular lables/NCA.png → docs/source/gallery/NCA.png b/...s/12 - Arbitrary molecular lables/NCA.png → docs/source/gallery/NCA.png
diff --git a/... - Arbitrary molecular lables/NCA_opt.png → docs/source/gallery/NCA_opt.png b/... - Arbitrary molecular lables/NCA_opt.png → docs/source/gallery/NCA_opt.png
diff --git a/docs/source/gallery/TUMLabeled.png b/docs/source/gallery/TUMLabeled.png
diff --git a/.../11 - Nucleic acid labels/alt_aln_pos.png → docs/source/gallery/alt_aln_pos.png b/.../11 - Nucleic acid labels/alt_aln_pos.png → docs/source/gallery/alt_aln_pos.png
diff --git a/docs/source/gallery/customlabels.png b/docs/source/gallery/customlabels.png
diff --git a/docs/source/gallery/memdock.png b/docs/source/gallery/memdock.png
diff --git a/examples/11 - Nucleic acid labels/tum.png → docs/source/gallery/tum.png b/examples/11 - Nucleic acid labels/tum.png → docs/source/gallery/tum.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,5 +1,5 @@
-χLife
-======
+chiLife (χLife)
+===============
 
 .. mdinclude:: ../../README.md
 

diff --git a/docs/source/rotamer_libraries.rst b/docs/source/rotamer_libraries.rst
@@ -2,8 +2,18 @@
 Rotamer Libraries
 =================
 
+.. note::
+    As of version 0.4.0 chiLife supports custom rotamer libraries with arbitrary backbones. This allows for the
+    creation of rotamer libraries for nucleic acids, as well as libraries that can be used to modify ligands or
+    glycans.
+
+    We have added an example of how to create a nucleic acid label and a ligand label in the :ref:`Examples`
+    section.
+
+
 .. _custom-rotamer-libraries:
 
+
 ---------------------------------
 Creating Custom Rotamer Libraries
 ---------------------------------

diff --git a/examples/02 - Simple SDSL site pair screen/02 - Simple SDSL site pair screen.ipynb b/examples/02 - Simple SDSL site pair screen/02 - Simple SDSL site pair screen.ipynb
@@ -1,18 +1,24 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "558eb854-221c-4ef3-ae64-2b49a4d9a298",
    "metadata": {},
+   "cell_type": "markdown",
+   "source": "# Simple SDSL site pair screen",
+   "id": "75e838cf0ee2702b"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": 1,
    "source": [
     "from itertools import combinations\n",
     "from tqdm import tqdm\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt \n",
     "import chilife as xl"
-   ]
+   ],
+   "id": "558eb854-221c-4ef3-ae64-2b49a4d9a298"
   },
   {
    "cell_type": "code",

diff --git a/...mational change/02-SDSL Site Screen.ipynb → ...mational change/03-SDSL Site Screen.ipynb b/...mational change/02-SDSL Site Screen.ipynb → ...mational change/03-SDSL Site Screen.ipynb
diff --git a/... Custom Spin Lables/ 2lzm_many_labels.pdb → ... custom spin labels/ 2lzm_many_labels.pdb b/... Custom Spin Lables/ 2lzm_many_labels.pdb → ... custom spin labels/ 2lzm_many_labels.pdb
diff --git a/...bles/03 - Adding custom spin labels.ipynb → ...bels/04 - Adding custom spin labels.ipynb b/...bles/03 - Adding custom spin labels.ipynb → ...bels/04 - Adding custom spin labels.ipynb
@@ -84,6 +84,11 @@
     "\n",
     "xl.save(T109R3A, T109NBA, T109GD3, T4L)\n"
    ]
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "![labels](customlabels.png)"
   }
  ],
  "metadata": {

diff --git a/...g Custom Spin Lables/GD3/GD3_Ensemble.pdb → ...g custom spin labels/GD3/GD3_Ensemble.pdb b/...g Custom Spin Lables/GD3/GD3_Ensemble.pdb → ...g custom spin labels/GD3/GD3_Ensemble.pdb
diff --git a/...Adding Custom Spin Lables/GD3/weights.txt → ...Adding custom spin labels/GD3/weights.txt b/...Adding Custom Spin Lables/GD3/weights.txt → ...Adding custom spin labels/GD3/weights.txt
diff --git a/...g Custom Spin Lables/NBA/NBA_Ensemble.pdb → ...g custom spin labels/NBA/NBA_Ensemble.pdb b/...g Custom Spin Lables/NBA/NBA_Ensemble.pdb → ...g custom spin labels/NBA/NBA_Ensemble.pdb
diff --git a/...Adding Custom Spin Lables/NBA/weights.txt → ...Adding custom spin labels/NBA/weights.txt b/...Adding Custom Spin Lables/NBA/weights.txt → ...Adding custom spin labels/NBA/weights.txt
diff --git a/...g Custom Spin Lables/R3A/R3A_Ensemble.pdb → ...g custom spin labels/R3A/R3A_Ensemble.pdb b/...g Custom Spin Lables/R3A/R3A_Ensemble.pdb → ...g custom spin labels/R3A/R3A_Ensemble.pdb
diff --git a/...Adding Custom Spin Lables/R3A/weights.txt → ...Adding custom spin labels/R3A/weights.txt b/...Adding Custom Spin Lables/R3A/weights.txt → ...Adding custom spin labels/R3A/weights.txt
diff --git a/examples/04 - Adding custom spin labels/customlabels.png b/examples/04 - Adding custom spin labels/customlabels.png
diff --git a/...embrane Docking/05-Membrane Docking.ipynb → ...embrane Docking/06-Membrane Docking.ipynb b/...embrane Docking/05-Membrane Docking.ipynb → ...embrane Docking/06-Membrane Docking.ipynb
@@ -120,6 +120,11 @@
     "plt.legend()\n",
     "plt.show()\n"
    ]
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "![docked](memdock.png)"
   }
  ],
  "metadata": {

diff --git a/examples/06 - Membrane Docking/memdock.png b/examples/06 - Membrane Docking/memdock.png
diff --git a/...nal Labels/10 - Bifunctional Labels.ipynb → ...nal labels/09 - Bifunctional Labels.ipynb b/...nal Labels/10 - Bifunctional Labels.ipynb → ...nal labels/09 - Bifunctional Labels.ipynb
diff --git a/... - Bifunctional Labels/DCNip2_drotlib.zip → ... - Bifunctional labels/DCNip2_drotlib.zip b/... - Bifunctional Labels/DCNip2_drotlib.zip → ... - Bifunctional labels/DCNip2_drotlib.zip
diff --git a/... - Bifunctional Labels/DCNip4_drotlib.zip → ... - Bifunctional labels/DCNip4_drotlib.zip b/... - Bifunctional Labels/DCNip4_drotlib.zip → ... - Bifunctional labels/DCNip4_drotlib.zip
diff --git a/...les/10 - Bifunctional Labels/Exp_Data.txt → ...les/09 - Bifunctional labels/Exp_Data.txt b/...les/10 - Bifunctional Labels/Exp_Data.txt → ...les/09 - Bifunctional labels/Exp_Data.txt