Descriptive documentation

• Quick primer to using the CSD Python API
  • Introduction
  • Starting a Python interactive shell
  • Accessing database entries, crystals and molecules from the CSD
  • Reading and writing molecules
  • Searching the CSD
  • Conformational geometry analysis
  • Interaction preference analysis
• Using the CSD Python API with Mercury and Hermes
• Reading and writing molecules and crystals
  • Introduction
  • Supported file formats
  • Reading molecules
  • Reading crystals
  • Writing molecules
  • Writing crystals
  • Reading Entries
  • Writing Entries
  • Default crystal
  • Working with multiple databases
• Working with entries
  • Introduction
• Working with crystals
  • Introduction
  • Accessing crystallographic properties
  • Miller Indices
  • Disordered Structures and Suppressed Atoms
  • Crystallographic Contacts
  • Crystallographic Hydrogen Bonds
  • Manipulating crystals
  • Contact and HBond expansion
  • Packing and Slicing
  • Polymer Expansion
• Disorder in crystal structure
  • Introduction
• Working with molecules, atoms and bonds
  • Introduction
  • A ccdc.molecule.Molecule can contain several molecules
  • Standardising and editing molecules
  • Accessing molecular properties
  • Rings
  • Working with string representations of Mol2 and SDF files
  • Close Contacts
  • Hydrogen Bonds
  • HBond Criterion
  • Accessing atomic properties
  • Accessing bond properties
• Editing molecules
  • Introduction
  • Atom editing
  • Bond editing
  • Molecule editing
  • Building molecules from scratch
  • Changing molecular geometry
  • Tidying up
• Search philosophy
• Text-numeric searching
  • Introduction
  • Searching the CSD using text numeric searches
  • Peptide sequence searches
• Substructure searching
  • Introduction
  • Setting up a substructure
  • Setting up and running a substructure search
  • Substructure search hits
  • Create a substructure from scratch
  • Substructure searching with geometric measurements
  • Substructure searching with geometric constraints
  • Search filters
  • Interactive Hit Processing
• Similarity searching
  • Introduction
  • Similarity search
• Reduced cell searching
  • Introduction
  • Performing reduced cell searches
• Combined searches
• Conformer generation and molecular minimisation
  • Introduction
  • Conformer Generation
  • Molecular Minimisation
• Field-based virtual screening
  • Introduction
  • Screening Workflow
  • Library Screening of actives and decoys
• Working with proteins
  • Introduction
  • Accessing protein properties
  • Manipulating proteins
  • A ccdc.protein.Protein is a ccdc.molecule.Molecule too
  • Superposing protein chains and binding sites
• Working with cavities
  • Introduction
  • Accessing cavity properties
  • Subcavities
  • Comparing cavities
• Docking and scoring
  • Introduction
  • Setting up a docking run
  • Interactive docking
  • Rescoring
  • Protein and Ligand Preparation
  • Output File Write Options
  • Setting up ensemble docking with waters
• Pharmacophore searching
  • Introduction
  • Features and Pharmacophore Queries
  • Creating Feature definitions
  • Feature Databases
  • Pharmacophore Searching
  • Creating Feature Databases
• Protein-ligand searching
• SMARTS implementation
  • Extensions to the SMARTS Language
  • Supported features since version 3.0.13
  • Unsupported features
  • Aromaticity and its relationship to SMARTS searching
  • Hydrogen treatment in CSD Searching
• Molecular geometry analysis
  • Introduction
  • The molecular geometry analysis engine
  • Geometry analysis settings
  • Performing a geometry analysis on a molecule
  • Analysing the results
  • Molecular geometry analysis with multiple data libraries
• Particle
  • Surface
  • Slip Planes
• Analysing molecular interactions preferences
  • Introduction
  • Central and contact groups and libraries
  • Accessing the underlying interaction data
  • Matching functional groups to molecules
• Interaction Maps
  • Introduction
  • Use Cases
  • Other Settings
• Crystal packing similarity
  • Introduction
  • Using the Packing Similarity API
• Generating 2D diagrams of molecules
  • Introduction
  • Generating 2D diagrams
  • Accessing diagrams from CSD entries
  • Highlighting atom selections in diagrams
  • Diagram generation settings
  • Generating ChemDraw XML file
• Descriptors
  • Introduction
  • Pore Analyser
  • Powder patterns
  • Statistical descriptors
  • Principle axes aligned molecules
• Graph Sets
• HBond Propensities
  • Settings
  • Basic operation
  • Functional Groups
  • Fitting data
  • Analysis
  • Regression
  • Propensities
  • Propensity Groupings
• HBond Coordination
• Hydrogen Bond Statistics
  • Basic operation
  • Hydrogen Bond interactions search
  • Plotting HBS distance and angle data as Histograms
• Solvate Analyser
  • Introduction
• Aromatics Analyser
  • Introduction
• Morphology
• VisualHabit
• SMILES to 3D conversion
  • Reading SMILES
  • 3D Generation
  • 2D Generation
• CSD Landscape Generator
  • CSD Landscape Generator API Usage
  • Shape Database Creation
• Working with Crystal Structure Prediction Databases
  • Introduction
  • Accessing the CSP database
• Working with Crystal Structure Predictions
  • Introduction
  • Accessing the crystal structure
  • Accessing the computed properties
  • Accessing the CSP metadata fields
• Solubility Platform
  • Ingestion
  • Searching for notes
  • Detailed API Documentation
• Warnings
  • Python Warning Control
• Utilities
  • Introduction
  • Logger
  • Histograms
  • Grids
  • Licence
• Predicted Properties
  • Organic Semi Conductor Properties