List of Tables
1. Introduction
- 1.1 OEChem and Informatics
- 1.2 How to Read this Manual
- 1.3 Getting Started with OEChem Molecules
- 1.4 Atoms and Bonds
2. Manipulating Molecules
- 2.1 Creating and Destroying Molecules
- 2.2 Reusing Molecules
- 2.3 Creating a Molecule from SMILES
- 2.4 Generating a SMILES from a Molecule
3. Reading and Writing Molecules
- 3.1 Using OEChem oemolstreams
- 3.2 Reading Molecules with Iterators
- 3.3 Molecular File Formats
- 3.4 Molecule Input and Output with Files
- 3.5 Compressed Molecule Input and Output
- 3.6 Format control from the command line
- 3.7 Flavored Reading and Writing of Molecules
- 3.8 Writing Const Molecules
- 3.9 Writing molecules to string streams
4. Properties of Molecules
- 4.1 Stored Properties of Molecules
- 4.2 Derived Properties of Molecules
- 4.3 Manipulation of Tagged Data
5. OEMols and OEGraphMols
- 5.1 Preparation
- 5.2 Multi-conformer and single-conformer molecules
- 5.3 Conformers
- 5.4 Properties of Multi-Conformer Molecules
- 5.5 Reading Multi-conformer molecules
- 5.6 Dude, where's my SD Data?
6. Traversing the Atoms and Bonds of a Molecule
- 6.1 OEChem Iterators
- 6.2 Looping over the Atoms and Bonds of a Molecule
- 6.3 Dereferencing the Iterator
- 6.4 Looping over the Bonds of an Atom
- 6.5 Looping over the Neighbors of an Atom
- 6.6 Looping over the Conformers of a Molecule
- 6.7 Looping over subsets of Atoms or Bonds
7. Properties of Atoms
- 7.1 Stored Properties of Atoms
- 7.2 Derived Properties of Atoms
8. Properties of Bonds
- 8.1 Stored Properties of Bonds
9. Atom, Bond, and Conformer Indices
10. Creating Atoms, Bonds, and Conformers
- 10.1 Using NewAtom and NewBond
- 10.2 Implicit vs. Explicit Hydrogen Atoms
- 10.3 Updating Implicit Hydrogen Counts
- 10.4 Making Hydrogen Atoms Implicit
- 10.5 Making Hydrogen Atoms Explicit
- 10.6 Sprouting Hydrogens in 3D
- 10.7 Using NewConf
11. Connectivity Processing
- 11.1 Determining bonds from 3D coordinates
- 11.2 Kekule Form Assignment
- 11.3 Perceiving Bond Orders
12. Ring Processing
- 12.1 Cycle Membership
- 12.2 Number of Ring Bonds to an Atom
- 12.3 Testing for Membership in a Given Ring Size
- 12.4 Determining Smallest Ring Membership
- 12.5 Identifying Connected Components
- 12.6 Identifying Ring Systems
- 12.7 Smallest Set of Smallest Rings (SSSR) considered Harmful
13. Aromaticity Processing
- 13.1 Aromaticity and Hückel's 4n+2 rule
- 13.2 Aromaticity Models in OEChem
- 13.3 Clearing Aromaticity
14. Stereochemistry Processing
- 14.1 Atom Stereochemistry
- 14.2 Bond Stereochemistry
15. Atom and Bond Typing
- 15.1 Integer Atom Types and Type Names
- 15.2 Tripos Atom Typing
- 15.3 Tripos Bond Typing
- 15.4 Generic Tripos Type Functions
- 15.5 Writing a Sybyl mol2 file using OEWriteMol2File
- 15.6 MacroModel Atom Typing
- 15.7 Generic MacroModel Type Functions
16. Formal and Partial Charges
- 16.1 Assigning Formal Charges
- 16.2 Working with Partial Charges
- 16.3 Determining Net Charge on a Molecule
- 16.4 Calculating Gasteiger Partial Charges
17. Pattern Matching
- 17.1 Substructure Search
- 17.2 Maximum Common Substructure Search
  - 17.2.1 Exhaustive and approximate MCSS
  - 17.2.2 MCS scoring functions: OEMCSFunc
- 17.3 Clique Search
- 17.4 OEExprOpts Namespace
18. OEQMols and Queries in OEChem
19. Coordinate Handling
- 19.1 Getting and Setting Coordinates of Atoms and Molecules
- 19.2 Coordinate Manipulation
  - 19.2.1 Molecular Geometry Routines
20. Error Handling
21. Periodic Table Functions
- 21.1 Obtaining the Atomic Symbol of an Atom/Element
- 21.2 Obtaining the Atomic Number from an Atomic Symbol
- 21.3 Properties of the Elements
- 21.4 Handling Isotopes
  - 21.4.1 OEIsCommonIsotope
  - 21.4.2 OEGetIsotopicWeight
- 21.5 Calculating Molecular Weight of a Compound
22. Predicate Functors
- 22.1 Introduction
- 22.2 operator() and function pointers
- 22.3 Functors have State
- 22.4 OEUnaryPredicate
- 22.5 Call-Backs
- 22.6 Predefined OEChem Functors
- 22.7 Using Your oOn Functors in OEChem
- 22.8 Composition Functors in OEChem
- 22.9 Predicates as a subset of Functors
23. Molecular File Formats
- 23.1 SMILES File Format
  - 23.1.1 OEParseSmiles
  - 23.1.2 OECreateCanSmiString
- 23.2 MDL File Format (SD and Mol)
  - 23.2.1 OEReadMDLFile
  - 23.2.2 OEWriteMDLFile
- 23.3 Sybyl Mol2 File Format
  - 23.3.1 OEReadMol2File
  - 23.3.2 OEWriteMol2File
- 23.4 PDB File Format
  - 23.4.1 OEReadPDBFile
  - 23.4.2 OEWritePDBFile
- 23.5 MacroModel File Format
  - 23.5.1 OEReadMacroModelFile
  - 23.5.2 OEWriteMacroModelFile
- 23.6 XYZ File Format
  - 23.6.1 OEReadXYZFile
  - 23.6.2 OEWriteXYZFile
- 23.7 FASTA Sequence File Format
  - 23.7.1 OEReadFASTAFile
  - 23.7.2 OEWriteFASTAFile
24. I/O Utilities
- 24.1 oestream
- 24.2 oeistream
- 24.3 oeostream
- 24.4 oefstream
- 24.5 oegzstream
- 24.6 oesstream
- 24.7 oestdstream
- 24.8 OEOpenStream and OECloseStream
25. Miscellaneous Utilities
- 25.1 OEStopwatch
- 25.2 OEDots
26. SMILES Line Notation
- 26.1 Daylight SMILES
- 26.2 Extensions to Daylight SMILES
27. Biopolymer Residues
- 27.1 Ontology and Schema Fragility
- 27.2 Stored Properties of Residues
- 27.3 A Hierarchy View of Residue Data
28. Valence Models
- 28.1 The MDL Valence Model
- 28.2 The OpenEye Valence Model
  - 28.2.1 The OpenEye Charge Model
  - 28.2.2 The OpenEye Hydrogen Count Model
29. Reactions
- 29.1 Normalization Reactions
- 29.2 Library Generation
30. OEBinary Version 2 Format
- 30.1 OEBinary Format Specification
31. OpenEye Command Line Interface
- 31.1 Overview
- 31.2 Configure the OEInterface
  - 31.2.1 Compiling the text configuration file into a program
  - 31.2.2 Configuring Examples
- 31.3 Parsing the Command Line
  - 31.3.1 OEParseCommandLine
  - 31.3.2 OEParseCommandLineLW
- 31.4 Command line help
- 31.5 Parameter Categories
- 31.6 Ordering parameters and Categories
- 31.7 Requiring Parameters
- 31.8 Accessing parameter values
- 31.9 Types of Parameters
- 31.10 Parameter Ranges and Legal/Illegal Values
- 31.11 Parameter Aliases/Shortcuts
32. Design Decisions
- 32.1 Atoms, Bond, Conformers, and Molecules
- 32.2 Objects and Free-Functions
- 32.3 Programming Layers: The Deep and Twisted Path
A. SMARTS Pattern Matching
- A.1 SMARTS Syntax
B. Bibliography
C. Release Notes
- C.1 OEChem 1.6.1
- C.2 OEChem 1.6.0
- C.3 OEChem 1.5.1
  - C.3.1 Bug fixes
  - C.3.2 New features
- C.4 OEChem 1.5.0
- C.5 OEChem 1.4.2
- C.6 OEChem 1.4.1
- C.7 OEChem 1.4.0
- C.8 OEChem 1.3.4
- C.9 OEChem 1.3.3
- C.10 OEChem 1.3.2
- C.11 OEChem 1.3.1
- C.12 OEChem 1.3.0
Index

				OEChem - C++ Theory Manual

				OEChem - C++ Theory Manual

Contents