Tidied Files NO_JIRA

Author: apeel-ccdc

assets/save_script.gif

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+# Analyse Disorder and Geometry
+
+## Summary
+
+This script demonstrates how to analyse crystallographic disorder and evaluate molecular geometry using the Cambridge Structural Database (CSD) Python API. It inspects disorder groups in a crystal structure, activates specific disorder configurations, identifies unusual torsion angles, and visualises torsion histograms using Matplotlib.
+
+## Requirements
+
+CSD Python API (v 3.5.0 or later)
+
+Matplotlib (v 3.9.4 or later)
+
+## Licensing Requirements
+
+CSD-Core
+
+## Instructions on Running
+
+In a command prompt run `python analyse_disorder.py`.
+
+## Author
+
+Andrew J. Peel (2025-09-29)
+
+> For feedback or to report any issues please contact [support@ccdc.cam.ac.uk](mailto:support@ccdc.cam.ac.uk)

scripts/Disorder_Mogul-MOG-003/ReadMe.md

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+#! /usr/bin/env python
+###############################################################################
+#
+# 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
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2025-09-29: created by Andrew J. Peel, Cambridge Crystallographic Data Centre
+#
+###############################################################################
+
+from ccdc.io import EntryReader
+from ccdc.conformer import GeometryAnalyser
+import matplotlib.pyplot as plt
+
+# Read CSD entry
+entry_reader = EntryReader('CSD')
+purzio_entry = entry_reader.entry('PURZIO')
+print(f'Refcode: {purzio_entry.identifier}')
+
+# Get crystal
+purzio_crystal = purzio_entry.crystal
+
+# Examine disorder groups
+print(f'Crystal has disorder: {purzio_crystal.has_disorder}')
+print(f'Number of disorder assemblies: '
+      f'{len(purzio_crystal.disorder.assemblies)}')
+for i, assembly in enumerate(purzio_crystal.disorder.assemblies, start=1):
+    print(f'Assembly {i} has {len(assembly.groups)} disorder groups.')
+
+# Activate disorder assembly, group 1 of 2
+first_assembly = purzio_crystal.disorder.assemblies[0]
+first_group = first_assembly.groups[0]
+first_group.activate()
+
+print(f'Activated assembly_id: {first_assembly.id}')
+print(f'Activated group_id: {first_assembly.active.id}')
+print(f'Occupancy of disorder group: {first_group.occupancy:.3f}')
+
+# Examine the molecules
+mol = purzio_crystal.molecule
+print(f'Number of molecules in crystal: '
+      f'{len( mol.components)}')
+
+# Select component by index
+comp_index = 0
+
+# Examine the first molecule
+comp = mol.components[comp_index]
+print(f'Analysing molecule {comp_index + 1} of '
+      f'{len(mol.components)}')
+
+# Check if this molecule is disordered
+if any([atom.occupancy < 1 for atom in comp.atoms]):
+    print('This molecule is disordered.')
+else:
+    print('This molecule is not disordered.')
+
+# Identify disordered atoms
+print([(atom.label, atom.occupancy) for atom in comp.atoms
+      if atom.occupancy < 1])
+
+# Create an instance of geometry analyser
+engine = GeometryAnalyser()
+
+# Adjust settings - exclude organometallics and powder structures
+engine.settings.organometallic_filter = 'organics_only'
+engine.settings.powder_filter = True
+
+# Analyse geometry
+geom_analysed_mol = engine.analyse_molecule(comp)
+
+# For example, look at torsion measurements
+for torsion in geom_analysed_mol.analysed_torsions:
+    if torsion.unusual and torsion.enough_hits:
+        print(f'Unusual torsion: {",".join(torsion.atom_labels)}  '
+              f'Torsion: {torsion.value:.3f} °')
+
+# Accessing histogram data
+# Take example of an unusual torsion
+unusual_tors = [t for t in geom_analysed_mol.analysed_torsions
+                if t.unusual and t.enough_hits]
+
+# Retrieves the first occurance of specified torsion
+tor_query = next(t for t in unusual_tors if
+                 t.atom_labels == ['C39', 'C28', 'C29', 'C30'])
+
+counts = tor_query.histogram()
+
+# Create histogram
+n_bins = len(counts)
+bin_min, bin_max = 0, 180
+bin_width = (bin_max - bin_min) / n_bins
+bin_edges = [bin_min + i * bin_width for i in range(n_bins + 1)]
+
+plt.figure(figsize=(8, 5))
+plt.bar(
+    bin_edges[:-1],
+    counts,
+    width=bin_width,
+    edgecolor="black",
+    align="edge",
+    color="limegreen"
+)
+
+# Red line for torsion value
+torsion_val = tor_query.value
+plt.axvline(
+    torsion_val,
+    color="red",
+    linestyle="--",
+    linewidth=2
+)
+
+# Add text label above the histogram, slightly shifted
+y_max = max(counts)
+plt.text(
+    torsion_val + 2,     # shift slightly right
+    y_max * 0.9,         # place near the top
+    f"{torsion_val:.2f}°",
+    color="red",
+    fontsize=10,
+    rotation=90,
+    va="bottom"
+)
+
+plt.xlabel("Torsion Angle (degrees)")
+plt.ylabel("Count of Observation Hits")
+plt.title(f"Histogram for torsion {tor_query.atom_labels}")
+plt.xlim(bin_min, bin_max)
+
+plt.show()
+
+print('\n----------------------------------\n')
+print('Now using disorder combinations\n')
+
+# Interate over disorder combinations
+for comb_id, combination in enumerate(purzio_crystal.disorder.combinations):
+    for comp_id, component in enumerate(purzio_crystal.molecule.components):
+        print(f'Combination_id {comb_id}, Component_id {comp_id}')
+        analysed_mol = engine.analyse_molecule(component)
+        unusual_tors = [t for t in analysed_mol.analysed_torsions
+                        if t.enough_hits and t.unusual]
+        if len(unusual_tors) > 0:
+            for t in unusual_tors:
+                print(f'Unusual torsion: {",".join(t.atom_labels)}'
+                      f'  Torsion: {t.value:.3f} °')
+        else:
+            print('No unusual torsions with enough hits.')
+        print()