Cookbook documentation

• Entry examples
  • Create indexes of useful information for subsets of CSD entries
  • Filter the CSD using a ccdc.search.Search.Settings instance
  • Use python’s string formatting method to generate an HTML report
• Crystal examples
  • Generating molecular assemblies
  • Analysis of HBond dimensionality
  • Descriptor HTML report
  • Analysing crystal morphologies
  • Charting crystal morphologies
  • Functional groups of a crystal’s HBonds
  • A simple spreadsheet of hydrogen bond coordination likelihoods
  • Exploring hydrogen bond coordination models
  • Charting hydrogen bond propensities
• Molecular processing examples
  • Standardising, converting and filtering molecules
• Search examples
  • Torsion angle preferences in drug-like molecules
  • Similarity search with maximum common substructure highlighted
  • Hit processor example
  • Protein-ligand search
• Geometry analysis examples
  • Generating a HTML report
  • Extracting the CSD hits of the analysis distributions
  • Filtering a set of conformers
• Powder pattern examples
  • Comparing powder patterns
  • Calculating many powder patterns
• Packing similarity examples
  • Comparing similarity measures
• Utility examples
  • Matplotlib plots and HTML generators
  • Timing python code
• Cavity examples
  • Compare cavities in proteins using histograms
  • Overlay pairs of proteins based on their contained cavities
  • Compare XML cavity files
  • Compare cavities using multiple cores
  • Compare cavities stored in an SQLite database
  • Scan an SQLite database for ligands in related cavities
  • Download and extract the PDB header for a cavity
  • Find the most buried cavity area using k-means clustering and use it for subcavity comparisons
  • Evaluate enrichment in cavity comparison
  • Create a subcavity and use it for comparisons
  • Perform subcavity comparisons and filter out results from structures homologous to the query
  • Perform a k-leave-one-out cross-validation
• Screening examples
  • Field-based virtual screening
• Protein Examples
  • Protein Chain Binding Site Superposition Search
• Docking examples
  • Docking and Rescoring
  • Interactive docking
  • Testing fitness functions
  • Ensemble docking
  • Searching docked structures
• Pharmacophore Examples
  • Creating a pharmacophore model
  • Creating a feature database
  • Creating a feature database from generated conformers
  • Creating a feature database from docking results
  • An example of a search
  • Extract annotations defined in a feature database
  • Creating an annotation file for the CSD
• Particle examples
  • Slip planes
  • Surface
• InChI examples
  • Accessing InChIs for CSD Entries
  • Generating InChIs for molecules
• Hydrogen bond propensities examples
  • Hydrogen bond propensities calculation in docx report
  • Multi-component hydrogen bond propensities calculation in docx report