OEChem - C++ Theory Manual
Version 1.3.1

OpenEye Scientific Software, Inc.

OpenEye Scientific Software, Inc.
3600 Cerrillos Road, Suite 1107
Santa Fe, NM 87507
www.eyesopen.com
support@eyesopen.com

July 30, 2004

Front Matter
Contents
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
4. Properties of Molecules
- 4.1 Stored Properties of Molecules
- 4.2 Derived Properties of Molecules
- 4.3 Manipulating SD File Tagged Data
- 4.4 Properties of Multi-Conformer Molecules
5. Traversing the Atoms, Bonds of a Molecule
- 5.1 OEChem Iterators
- 5.2 Looping over the Atoms and Bonds of a Molecule
- 5.3 Dereferencing the Iterator
- 5.4 Looping over the Bonds of an Atom
- 5.5 Looping over the Neighbors of an Atom
- 5.6 Looping over the Conformers of a Molecule
- 5.7 Looping over subsets of Atoms or Bonds
6. Properties of Atoms
- 6.1 Stored Properties of Atoms
- 6.2 Derived Properties of Atoms
7. Properties of Bonds
- 7.1 Stored Properties of Bonds
- 7.2 Derived Properties of Bonds
8. OEMols and OEGraphMols
- 8.1 Preparation
- 8.2 Multi-conformer and single-conformer molecules
- 8.3 Conformers
- 8.4 Reading Multi-conformer molecules
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 Huckel'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
- 17.3 Clique Search
- 17.4 OEExprOpts Namespace
18. Coordinate Handling
19. Error Handling
20. Periodic Table Functions
- 20.1 Obtaining the Atomic Symbol of an Atom/Element
- 20.2 Obtaining the Atomic Number from an Atomic Symbol
- 20.3 Properties of the Elements
- 20.4 Handling Isotopes
  - 20.4.1 OEIsCommonIsotope
  - 20.4.2 OEGetIsotopicWeight
- 20.5 Calculating Molecular Weight of a Compound
21. OEQMols and Queries in OEChem
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 own 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
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. SMARTS Pattern Matching
- 29.1 SMARTS Syntax
30. Reactions
- 30.1 Normalization Reactions
- 30.2 Library Generation
31. OEBinary Version 2 Format
- 31.1 OEBinary Format Specification
32. OpenEye Command Line Interface
- 32.1 Compiling a text file into a C++ program
- 32.2 Configuring OEInterface
- 32.3 Parsing the Command Line
  - 32.3.1 OEParseCommandLine
  - 32.3.2 OEParseCommandLineLW
- 32.4 Command line help
- 32.5 Parameter Categories
- 32.6 Ordering parameters and Categories
- 32.7 Requiring Parameters
- 32.8 Accessing parameter values
- 32.9 Types of Parameters
- 32.10 Parameter Ranges and Legal/Illegal Values
- 32.11 Parameter Aliases/Shortcuts
33. Design Decisions
- 33.1 Atoms, Bond, Conformers, and Molecules
- 33.2 Objects and Free-Functions
- 33.3 Programming Layers: The Deep and Twisted Path
A. Bibliography
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