ccdc-opensource · CRingroseCCDC · May 27, 2026
diff --git a/.yamllint.yml b/.yamllint.yml
@@ -5,11 +5,11 @@
 # Project Homepage: https://github.com/adrienverge/yamllint
 #
 # Overriding rules in files:
-# http://yamllint.readthedocs.io/en/latest/disable_with_comments.html
+# https://yamllint.readthedocs.io/en/latest/disable_with_comments.html
 ---
 extends: default
 
-# Rules documentation: http://yamllint.readthedocs.io/en/latest/rules.html
+# Rules documentation: https://yamllint.readthedocs.io/en/latest/rules.html
 rules:
   document-start: disable
   line-length:

diff --git a/api_paper_2024/example_2/about_entry.py b/api_paper_2024/example_2/about_entry.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_2/language_processing.py b/api_paper_2024/example_2/language_processing.py
@@ -23,7 +23,7 @@
 pages  ="7233-7241",
 publisher  ="The Royal Society of Chemistry",
 doi  ="10.1039/D0CE00045K",
-url  ="http://dx.doi.org/10.1039/D0CE00045K",
+url  ="https://dx.doi.org/10.1039/D0CE00045K",
 """
 # For now, to prevent deprecation warnings tripping things up
 import warnings

diff --git a/api_paper_2024/example_2/references.py b/api_paper_2024/example_2/references.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_2/url_requesting.py b/api_paper_2024/example_2/url_requesting.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_4/mercury_metal_voronoi.py b/api_paper_2024/example_4/mercury_metal_voronoi.py
@@ -1,6 +1,6 @@
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_4/mercury_molecular_voronoi.py b/api_paper_2024/example_4/mercury_molecular_voronoi.py
@@ -1,6 +1,6 @@
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_4/voronoi.py b/api_paper_2024/example_4/voronoi.py
@@ -1,6 +1,6 @@
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_5/particle_shape.py b/api_paper_2024/example_5/particle_shape.py
@@ -1,6 +1,6 @@
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_5/shape_classification.py b/api_paper_2024/example_5/shape_classification.py
@@ -1,6 +1,6 @@
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/api_paper_2024/example_5/visualiser.py b/api_paper_2024/example_5/visualiser.py
@@ -1,6 +1,6 @@
 #
 # This script can be used for any purpose without limitation subject to the
-# conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
 #
 # This permission notice and the following statement of attribution must be
 # included in all copies or substantial portions of this script.

diff --git a/notebooks/API_Training_Exercises/01_Simple_Report.ipynb b/notebooks/API_Training_Exercises/01_Simple_Report.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/00_Background/00_Background.ipynb b/notebooks/Discovery/00_Background/00_Background.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",
@@ -501,7 +501,7 @@
    "source": [
     "### RDKit\n",
     "\n",
-    "As noted above, the Python API is primarily intended as a means of programatically accessing the CSD and the various tools provided by the CCDC. It is not currently intended to be a full-featured cheminformatics toolkit, although the Molecule API can certainly be used for a variety of chemiformatics tasks. Where functionality is not present in the Molecule API, we normally use the [RDKit](http://rdkit.org/docs/index.html), as it is freely-available, powerful and well-supported."
+    "As noted above, the Python API is primarily intended as a means of programatically accessing the CSD and the various tools provided by the CCDC. It is not currently intended to be a full-featured cheminformatics toolkit, although the Molecule API can certainly be used for a variety of chemiformatics tasks. Where functionality is not present in the Molecule API, we normally use the [RDKit](https://rdkit.org/docs/index.html), as it is freely-available, powerful and well-supported."
    ]
   },
   {

diff --git a/notebooks/Discovery/01_CSD_Search/01_Substructure_searching_the_CSD.ipynb b/notebooks/Discovery/01_CSD_Search/01_Substructure_searching_the_CSD.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",
@@ -526,10 +526,10 @@
      "evalue": "'NoneType' object is not subscriptable",
      "output_type": "error",
      "traceback": [
-      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[1;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[1;32mIn[26], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m (\u001b[43mconquest_df\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mRefcode\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m \u001b[38;5;241m==\u001b[39m connser_df[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mRefcode\u001b[39m\u001b[38;5;124m'\u001b[39m])\u001b[38;5;241m.\u001b[39mall()\n",
-      "\u001b[1;31mTypeError\u001b[0m: 'NoneType' object is not subscriptable"
+      "\u001B[1;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[1;31mTypeError\u001B[0m                                 Traceback (most recent call last)",
+      "Cell \u001B[1;32mIn[26], line 1\u001B[0m\n\u001B[1;32m----> 1\u001B[0m \u001B[38;5;28;01massert\u001B[39;00m (\u001B[43mconquest_df\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43mRefcode\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m]\u001B[49m \u001B[38;5;241m==\u001B[39m connser_df[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mRefcode\u001B[39m\u001B[38;5;124m'\u001B[39m])\u001B[38;5;241m.\u001B[39mall()\n",
+      "\u001B[1;31mTypeError\u001B[0m: 'NoneType' object is not subscriptable"
      ]
     }
    ],

diff --git a/notebooks/Discovery/01_CSD_Search/02_Similarity_searching_the_CSD.ipynb b/notebooks/Discovery/01_CSD_Search/02_Similarity_searching_the_CSD.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/01_CSD_Search/03_MCS_searching_the_CSD.ipynb b/notebooks/Discovery/01_CSD_Search/03_MCS_searching_the_CSD.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/02_Protein_Ligand/01_Protein_Ligand_Searching.ipynb b/notebooks/Discovery/02_Protein_Ligand/01_Protein_Ligand_Searching.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/02_Protein_Ligand/02_API_Protein-Ligand_search_for_FAD.ipynb b/notebooks/Discovery/02_Protein_Ligand/02_API_Protein-Ligand_search_for_FAD.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/03_Molecular_geometries/Molecular_geometries.ipynb b/notebooks/Discovery/03_Molecular_geometries/Molecular_geometries.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",
@@ -16,6 +16,13 @@
     "```"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": ""
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/notebooks/Discovery/04_Conformer_generation/Conformer_generation.ipynb b/notebooks/Discovery/04_Conformer_generation/Conformer_generation.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/05_Molecular_interactions/Molecular_interactions.ipynb b/notebooks/Discovery/05_Molecular_interactions/Molecular_interactions.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/06_Interaction_maps/Interaction_maps.ipynb b/notebooks/Discovery/06_Interaction_maps/Interaction_maps.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/07_Cavities/Cavities.ipynb b/notebooks/Discovery/07_Cavities/Cavities.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/07_Cavities/pdbe_get.ps1 b/notebooks/Discovery/07_Cavities/pdbe_get.ps1
@@ -1,13 +1,13 @@
 function pdbe_get() {

    Param([string]$pdb_code)
 
     $pdb_code = $pdb_code.ToLower()
 
-    $uri = [System.Uri]"http://www.ebi.ac.uk/pdbe/entry-files/download/pdb${pdb_code}.ent"
+    $uri = [System.Uri]"https://www.ebi.ac.uk/pdbe/entry-files/download/pdb${pdb_code}.ent"
 
     $pdb_file = Join-Path -Path $(Convert-Path '.') -ChildPath $uri.Segments[-1]  # Absolute path for output file
 
    $wc = New-Object System.Net.WebClient

    $wc.DownloadFile($uri, $pdb_file)

diff --git a/notebooks/Discovery/08_Docking/00a_Input_for_GOLD.ipynb b/notebooks/Discovery/08_Docking/00a_Input_for_GOLD.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",
@@ -26,7 +26,7 @@
     "\n",
     "For optimal performance, GOLD requires a good-quality 3D ligand structure as input. The CSD [Molecule API](https://downloads.ccdc.cam.ac.uk/documentation/API/modules/molecule_api.html) and [Conformer API](https://downloads.ccdc.cam.ac.uk/documentation/API/modules/conformer_api.html) can now be used together to generate such structures. This notebook is designed to show how this can be done.\n",
     "\n",
-    "Note that it is assumed that the input structures are all in the desired charge and tautomeric states. No protonation/deprotonation or tautomer standardization/enumeration is done here. This is currently out of scope for the [CSD Python API](https://downloads.ccdc.cam.ac.uk/documentation/API/index.html), but we recommend [RDKit](http://www.rdkit.org/docs/GettingStartedInPython.html) to those who wish to investigate it further."
+    "Note that it is assumed that the input structures are all in the desired charge and tautomeric states. No protonation/deprotonation or tautomer standardization/enumeration is done here. This is currently out of scope for the [CSD Python API](https://downloads.ccdc.cam.ac.uk/documentation/API/index.html), but we recommend [RDKit](https://www.rdkit.org/docs/GettingStartedInPython.html) to those who wish to investigate it further."
    ]
   },
   {

diff --git a/notebooks/Discovery/08_Docking/00b_Input_for_GOLD-RDKit.ipynb b/notebooks/Discovery/08_Docking/00b_Input_for_GOLD-RDKit.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",
@@ -26,7 +26,7 @@
     "\n",
     "For optimal performance, GOLD requires good-quality 3D ligand structures as input (note that it only requires a single conformer as it performs flexible docking based on the input structure). Now, the [Conformer API](https://downloads.ccdc.cam.ac.uk/documentation/API/modules/conformer_api.html) can be used to generate a 3D structure that reflects conformational preferences observed in the CSD and thus provides ideal input for GOLD. This process is illustrated in the notebook [00a_Input_for_GOLD](./00a_Input_for_GOLD.ipynb).\n",
     "\n",
-    "However, if this tool is not available (_e.g._ for licencing reasons), we recommend the use of [RDKit](http://rdkit.org/) to generate an initial 3D structure.\n",
+    "However, if this tool is not available (_e.g._ for licencing reasons), we recommend the use of [RDKit](https://rdkit.org/) to generate an initial 3D structure.\n",
     "\n",
     "Note that it is assumed that the input structures are all in the desired charge and tautomeric states. No protonation/deprotonation or tautomer standardization/enumeration is done here."
    ]

diff --git a/notebooks/Discovery/08_Docking/01_Docking_foreground.ipynb b/notebooks/Discovery/08_Docking/01_Docking_foreground.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/08_Docking/02_Docking_background_conf.ipynb b/notebooks/Discovery/08_Docking/02_Docking_background_conf.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/08_Docking/03_Docking_interactive.ipynb b/notebooks/Discovery/08_Docking/03_Docking_interactive.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/08_Docking/04_Docking_interactive_conf.ipynb b/notebooks/Discovery/08_Docking/04_Docking_interactive_conf.ipynb
@@ -7,7 +7,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",

diff --git a/notebooks/Discovery/08_Docking/05_Parameter_tests.ipynb b/notebooks/Discovery/08_Docking/05_Parameter_tests.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "```\n",
     "This script can be used for any purpose without limitation subject to the\n",
-    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
     "\n",
     "This permission notice and the following statement of attribution must be\n",
     "included in all copies or substantial portions of this script.\n",