NO_JIRA Added Pharmacophore generator script to create CrossMiner queries from Ligand Overlay outputs. Includes basic tests and examples.

Author: CRingroseCCDC

scripts/discovery/overlay_to_pharmacophore/cluster.py

@@ -1,3 +1,12 @@
+"""
+This script can be used for any purpose without limitation subject to the
+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.
+
+"07/08/2026n": created by the Cambridge Crystallographic Data Centre
+"""
+
 from collections import defaultdict
 
 import numpy as np

scripts/discovery/overlay_to_pharmacophore/crossminer_search.py

@@ -1,3 +1,12 @@
+"""
+This script can be used for any purpose without limitation subject to the
+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.
+
+"07/08/2026": created by the Cambridge Crystallographic Data Centre
+"""
+
 from pathlib import Path
 
 from ccdc.pharmacophore import Pharmacophore

scripts/discovery/overlay_to_pharmacophore/datastructures.py

@@ -1,3 +1,12 @@
+"""
+This script can be used for any purpose without limitation subject to the
+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.
+
+"07/08/2026": created by the Cambridge Crystallographic Data Centre
+"""
+
 from __future__ import annotations
 
 from dataclasses import dataclass

scripts/discovery/overlay_to_pharmacophore/main.py

@@ -4,7 +4,7 @@
 This permission notice and the following statement of attribution must be
 included in all copies or substantial portions of this script.
 
-"date of creation": created by the Cambridge Crystallographic Data Centre
+"07/08/2026": created by the Cambridge Crystallographic Data Centre
 """
 
 import argparse

scripts/discovery/overlay_to_pharmacophore/overlay.py

@@ -1,3 +1,12 @@
+"""
+This script can be used for any purpose without limitation subject to the
+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.
+
+"07/08/2026": created by the Cambridge Crystallographic Data Centre
+"""
+
 from functools import cached_property
 
 import numpy as np

scripts/discovery/overlay_to_pharmacophore/tests/tests.py

@@ -1,3 +1,12 @@
+"""
+This script can be used for any purpose without limitation subject to the
+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.
+
+"07/08/2026": created by the Cambridge Crystallographic Data Centre
+"""
+
 from pathlib import Path
 
 import pytest

scripts/discovery/overlay_to_pharmacophore/write_query.py

@@ -1,3 +1,12 @@
+"""
+This script can be used for any purpose without limitation subject to the
+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.
+
+"07/08/2026": created by the Cambridge Crystallographic Data Centre
+"""
+
 from pathlib import Path
 
 from datastructures import PharmFeaturePoint