1. Java
- 1.1 Java versions
- 1.2 Basic installation instructions
  - 1.2.1 Windows Example
  - 1.2.2 Linux/Mac OS X Example
- 1.3 Java, Windows and Stack size
  - 1.3.1 Modify the actual java.exe executable
  - 1.3.2 Spawn a second thread for your OEChem code
2. Introduction
- 2.1 OEChem and Informatics
- 2.2 How to Read this Manual
- 2.3 Getting Started with OEChem Molecules
- 2.4 Atoms and Bonds
3. Manipulating Molecules
- 3.1 Creating a Molecule from SMILES
- 3.2 Generating a SMILES from a Molecule
  - 3.2.1 OECreateCanSmiString
4. Reading and Writing Molecules
- 4.1 Using OEChem oemolstreams
- 4.2 Molecular File Formats
- 4.3 Molecule Input and Output with Files
- 4.4 Compressed Molecule Input and Output
- 4.5 Format control from the command line
- 4.6 Flavored Reading and Writing of Molecules
- 4.7 Writing Const Molecules
- 4.8 Writing molecules to string streams
5. Iterators in OEChem
- 5.1 Introduction
- 5.2 Java-style Iteration
- 5.3 C++-style Iteration
6. Properties of Molecules
- 6.1 Stored Properties of Molecules
- 6.2 Derived Properties of Molecules
- 6.3 Manipulation of Tagged Data
7. OEMols and OEGraphMols
- 7.1 Preparation
- 7.2 Multi-conformer and single-conformer molecules
- 7.3 Conformers
- 7.4 Properties of Multi-Conformer Molecules
- 7.5 Reading Multi-conformer molecules
- 7.6 Dude, where's my SD Data?
8. Traversing the Atoms and Bonds of a Molecule
- 8.1 Looping over the Atoms and Bonds of a Molecule
- 8.2 Looping over the Bonds of an Atom
- 8.3 Looping over the Neighbors of an Atom
- 8.4 Looping over subsets of Atoms or Bonds
9. Properties of Atoms
- 9.1 Stored Properties of Atoms
- 9.2 Derived Properties of Atoms
10. Properties of Bonds
- 10.1 Stored Properties of Bonds
- 10.2 Derived Properties of Bonds
11. Atom, Bond and Conformer Indices
12. Creating Atoms, Bonds and Conformers
- 12.1 Using NewAtom and NewBond
- 12.2 Implicit vs. Explicit Hydrogen Atoms
- 12.3 Updating Implicit Hydrogen Counts
- 12.4 Making Hydrogen Atoms Implicit
- 12.5 Making Hydrogen Atoms Explicit
- 12.6 Sprouting Hydrogens in 3D
- 12.7 Using NewConf
13. Connectivity Processing
- 13.1 Determining Bonds From 3D Coordinates
- 13.2 Kekule Form Assignment
- 13.3 Perceiving Bond Orders
14. Ring Processing
- 14.1 Cycle Membership
- 14.2 Number of Ring Bonds to an Atom
- 14.3 Testing for Membership in a Given Ring Size
- 14.4 Determining Smallest Ring Membership
- 14.5 Identifying Connected Components
- 14.6 Identifying Ring Systems
- 14.7 Smallest Set of Smallest Rings (SSSR) considered Harmful
15. Aromaticity Processing
- 15.1 Aromaticity and Hückel's 4n+2 rule
- 15.2 Aromaticity Models in OEChem
- 15.3 Clearing Aromaticity
16. Stereochemistry Processing
- 16.1 Atom Stereochemistry
- 16.2 Bond Stereochemistry
17. Atom and Bond Typing
- 17.1 Integer Atom Types and Type Names
- 17.2 Tripos Atom Typing
- 17.3 Tripos Bond Typing
- 17.4 Generic Tripos Type Functions
- 17.5 Writing a Sybyl mol2 file using OEWriteMol2File
- 17.6 MacroModel Atom Typing
- 17.7 Generic MacroModel Type Functions
18. Formal and Partial Charges
- 18.1 Assigning Formal Charges
- 18.2 Working with Partial Charges
- 18.3 Determining Net Charge on a Molecule
- 18.4 Calculating Gasteiger Partial Charges
19. Pattern Matching
- 19.1 Substructure Search
- 19.2 Maximum Common Substructure Search
  - 19.2.1 Exhaustive and approximate MCSS
  - 19.2.2 MCS scoring functions: OEMCSFunc
- 19.3 Clique Search
- 19.4 OEExprOpts Namespace
20. Coordinate Handling
- 20.1 Getting and Setting Coordinates of Atoms and Molecules
- 20.2 Coordinate Manipulation
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 Functions
- 22.1 Callbacks
- 22.2 Predefined OEChem Functors
- 22.3 Writing your own Functors in Java
- 22.4 Composition Functors in OEChem
23. Molecular File Formats
- 23.1 MDL File Format (SD and Mol)
  - 23.1.1 OEReadMDLFile
  - 23.1.2 OEWriteMDLFile
- 23.2 Sybyl Mol2 File Format
  - 23.2.1 OEReadMol2File
  - 23.2.2 OEWriteMol2File
- 23.3 PDB File Format
  - 23.3.1 OEReadPDBFile
  - 23.3.2 OEWritePDBFile
- 23.4 MacroModel File Format
  - 23.4.1 OEReadMacroModelFile
  - 23.4.2 OEWriteMacroModelFile
- 23.5 XYZ File Format
  - 23.5.1 OEReadXYZFile
  - 23.5.2 OEWriteXYZFile
- 23.6 FASTA Sequence File Format
  - 23.6.1 OEReadFastaFile
  - 23.6.2 OEWriteFastaFile
24. Miscellaneous Utilities
- 24.1 OEStopWatch
- 24.2 OEDots
25. The SMILES Line Notation
- 25.1 Daylight SMILES
- 25.2 Extensions to Daylight SMILES
26. Biopolymer Residues
- 26.1 Ontology and Schema Fragility
- 26.2 Stored Properties of Residues
- 26.3 A Hierarchy View of Residue Data
27. Valence Models
- 27.1 The MDL Valence Model
- 27.2 The OpenEye Valence Model
  - 27.2.1 The OpenEye Charge Model
  - 27.2.2 The OpenEye Hydrogen Count Model
28. SMARTS Pattern Matching
- 28.1 SMARTS Syntax
29. Reactions
- 29.1 Normalization Reactions
- 29.2 Library Generation
30. License handling
31. OEChem Class Hierarchy: Why in the world are there 6 molecules?!
- 31.1 Atoms, Bond, Conformers, and Molecules
- 31.2 Objects and Free-Functions
- 31.3 Programming Layers: The Deep and Twisted Path
32. Logging and Error Handling
- 32.1 OEErrorHandler
33. Appendix
34. Bibliography
35. Release Notes
- 35.1 OEChem 1.6.1
- 35.2 OEChem 1.6.0
- 35.3 OEChem 1.5.1
  - 35.3.1 Bug fixes
  - 35.3.2 New features
- 35.4 OEChem 1.5.0
- 35.5 OEChem 1.4.2
- 35.6 OEChem 1.4.1
- 35.7 OEChem 1.4.0
- 35.8 OEChem 1.3.4
- 35.9 OEChem 1.3.3
- 35.10 OEChem 1.3.2
- 35.11 OEChem 1.3.1
- 35.12 OEChem 1.3.0
Index

				OEChem - Java Theory Manual

				OEChem - Java Theory Manual

Contents