Theory

OEChem Theory

Introduction to Molecules

• Molecules
  • Construction and Destruction
  • Construction from SMILES
  • Reuse
  • Unique Representation
    • InChI
• Molecule Reading and Writing
  • Molecule Streams
  • File Formats
  • File Input and Output
  • String Input and Output
  • Compressed Input and Output
  • Command Line Format Control
  • Flavored Input and Output
  • Molecular Property Preservation
• Tagged Data Manipulation
  • SD Tagged Data Manipulation
  • Multi-conformer molecules
  • CSV File Format
  • PDB Tagged Data Manipulation
  • CIF File Format
  • mmCIF Metadata Manipulation
  • mmCIF Header Perception

Atoms and Bonds

• Atom and Bond Traversal
  • Iterators
  • Atom and Bond Iteration
  • Bonds of an Atom Iteration
  • Atom Neighbor Iteration
  • Atom or Bond Subset Iteration
  • Iterator Methods
• Atom, Bond, and Conformer Indices
  • Unique Identifiers
  • Parallel Data Structures
  • Indices for Molecule Lookup Considered Harmful
• Atom Properties
  • Read/Write Atom Properties
  • Read Only Atom Properties
  • Attach Generic Data to Atoms
• Bond Properties
  • Read/Write Bond Properties
  • Read Only Bond Properties
  • Attach Generic Data to Bonds
• Valence Models
  • MDL Valence Model
  • OpenEye Valence Model
    • OpenEye Charge Model
    • OpenEye Hydrogen Count Model

Molecules

• Molecule Properties
  • Read/Write Molecule Properties
  • Title
  • Atoms and Bonds
  • Atom and Bond Creation
  • Attach Generic Data to Molecules
• Ring Perception
  • Cycle Membership
  • Membership in a Given Ring Size
  • Smallest Ring Membership
  • Connected Components Identification
  • Ring Systems Identification
  • Smallest Set of Smallest Rings (SSSR) Considered Harmful
• Aromaticity Perception
  • Aromaticity and Hückel’s rule
  • Aromaticity Models in OEChem TK
  • Clearing Aromaticity
  • Input/Output Aromaticity
• Connectivity Perception
  • Connectivity From 3D Coordinates
  • Bond Order Perception
  • Kekulé Form Assignment
  • Kekulé Assignment of New Bonds
• Stereochemistry Perception
  • Atom Chirality
  • Atom Stereochemistry
  • Bond Chirality
  • Bond Stereochemistry
  • CIP Stereo Perception
• Formal and Partial Charges
  • Formal Charges Assignment
  • Gasteiger Partial Charge Calculation
• 2D Coordinate Generation
  • User-Defined Ring Dictionary
• Molecule Styling
  • OE3DMolStyle
  • Atom Labeling
  • Styling and Typing
  • Colorer

Molecule Algorithms

• Pattern Matching
  • Substructure Search
  • Maximum Common Substructure Search
  • Exhaustive and approximate MCSS
  • MCS scoring functions
  • Clique Search
  • OEExprOpts Namespace
• Substructure Search with MDL Queries
  • MDL Query Interpretation
  • Supported MDL Query Features
  • Aromaticity
  • Aromaticity with Generic Atoms
  • Explicit Hydrogens
• Reactions
  • Normalization Reactions
  • Library Generation
    • Initialization with SMIRKS
    • Starting Materials
    • Valence Correction Modes
    • Explicit Hydrogen Handling
    • Implicit Hydrogen Handling
    • Automatic Valence Correction
    • Reactant Tracking
    • Atom Mapping
    • MDL Reaction Query File
    • Hydrogens on the Reactant Side
    • Product Kekulization

Advanced OEChem

• Multi-conformer Molecules
  • OEMols
  • Conformers
  • Conformer Iteration
  • Conformer Creation
  • Input and Output
  • Dude, where’s my SD data?
• Molecular Database Handling
  • Opening and Reading
  • Direct Data Access
  • Title Access
  • Index Files
  • Database Generic Data
  • Caveats
• Design Decisions
  • Abstract Base-Classes
  • Factory Functions
  • Smart Pointers
  • Query Molecules
  • Free-Functions
  • Programming Layers: The Deep and Twisted Path
• Multi-Threading
  • Input and Output Threads
  • Thread Safety
    • Classes
    • Functions
  • Memory Management
    • Thread Safety Options
    • Overriding the allocator
    • (Un)bounded Options
• Predicate Functors
  • Built-in Functors
    • Atom Functors
    • Atomic Number Functors
    • Bond Functors
    • Group Functors
    • Reaction Component Functors
    • Conformer Functors
    • Residue Data Functors
  • Composite Functors
  • User Defined Functors
  • Functor substructure-based matching
  • Molecule Partitioning
• OEMolRecord
  • Conformer data on records

Reference Appendices

• Periodic Table Functions
  • Atomic Symbol/Atomic Number
  • Element Properties
  • Atom Radius Functions
• SMILES Line Notation
  • Extensions to Daylight SMILES
• SMARTS Pattern Matching
  • SMARTS Syntax
  • Atom Primitives
  • Bond Primitives
  • Logical Operators
  • Examples
• Atom Stereo From Bond Stereo
  • Tertiary
  • Quaternary
• InChI validation

OESystem Theory

• Command Line Interface and Options
  • Application with Input, output, and Options
  • Application with Reference system, Input, output, and Options
  • Application with Input and output only
  • Adding custom parameters
  • Defining new options class
• Command Line Interface Definition
  • Parameter Value Access
  • Default Values
  • Requiring Parameters
  • Legal and Illegal Values and Ranges
  • Parameter Lists
  • Positional Parameters
  • Molecule Parameters
  • Command Line Help
  • Interface Definition Specification
• Generic Data
  • Attaching plain old data
  • Attaching data to atoms
  • Attaching other objects
• OERecord
  • Metadata on fields

OEBio Theory

Working With Macromolecules

• Biopolymers
  • Biopolymer Residues
  • Residue Naming Conventions
  • A Hierarchy View
  • Sequence Alignment
  • Crystal Symmetry
  • Protein Secondary Structure
  • Functors
  • Misc
• Protein Preparation
  • Processing Alternate Locations
  • Adding Hydrogens and Optimizing Hydrogen Bonds
  • Splitting Macromolecular Complexes
• Macromolecule Conformations
  • Alternate Locations
  • Dihedrals and Sidechain Rotamers
  • Swapping Ambiguous Isoelectronic Residue Atoms
• Interaction Perception
  • Interaction Hint Container
  • Interaction Hint Predicates
  • Accessing Calculated Interaction Hint Geometries
• Receptors
  • Contents of a Receptor
    • Negative Image
    • Constraints
      • Protein Constraints
      • Custom Constraints

OEGrid Theory

• Scalar Grids
  • Minimum and maximum
    • Data Access
  • Spatial Coordinates
  • Grid Indices
  • Grid Elements
    • Input and Output
    • Grid as Generic Data