1. Python
- 1.1 A Bit About Learning Python
- 1.2 Python versions
- 1.3 Platform Notes
- 1.4 Installing Python from Source
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
- 2.5 Getting Started with Python-OEChem
3. Manipulating Molecules
- 3.1 Creating Molecule Objects
- 3.2 Reusing Molecules
- 3.3 Creating a Molecule from SMILES
- 3.4 Generating a SMILES from a Molecule
4. Reading and Writing Molecules
- 4.1 Using OEChem oemolstreams
- 4.2 Reading Molecules with a Generator Method
- 4.3 Molecular File Formats
- 4.4 Molecule Input and Output with Files
- 4.5 Compressed Molecule Input and Output
- 4.6 Format control from the command line
- 4.7 Flavored Reading and Writing of Molecules
- 4.8 Writing Const Molecules
- 4.9 Writing molecules to string streams
5. Properties of Molecules
- 5.1 Generic Data
- 5.2 Stored Properties of Molecules
- 5.3 Derived Properties of Molecules
- 5.4 Manipulation of Tagged Data
6. OEMols and OEGraphMols
- 6.1 Preparation
- 6.2 Multi-conformer and single-conformer molecules
- 6.3 Conformers
- 6.4 Properties of Multi-Conformer Molecules
- 6.5 Reading Multi-conformer molecules
- 6.6 Dude, where's my SD Data?
7. Traversing the Atoms and Bonds of a Molecule
- 7.1 Looping over the Atoms and Bonds of a Molecule
- 7.2 Looping over the Bonds of an Atom
- 7.3 Looping over the Neighbors of an Atom
- 7.4 Looping over subsets of Atoms or Bonds
- 7.5 Using OEChem C++ Iterators Directly
8. Properties of Atoms
- 8.1 Stored Properties of Atoms
- 8.2 Derived Properties of Atoms
9. Properties of Bonds
- 9.1 Stored Properties of Bonds
- 9.2 Derived Properties of Bonds
10. Atom, Bond and Conformer Indices
11. Creating Atoms, Bonds and Conformers
- 11.1 Using NewAtom and NewBond
- 11.2 Implicit vs. Explicit Hydrogen Atoms
- 11.3 Updating Implicit Hydrogen Counts
- 11.4 Making Hydrogen Atoms Implicit
- 11.5 Making Hydrogen Atoms Explicit
- 11.6 Sprouting Hydrogens in 3D
- 11.7 Using NewConf
12. Connectivity Processing
- 12.1 Determining Bonds From 3D Coordinates
- 12.2 Kekule Form Assignment
- 12.3 Perceiving Bond Orders
13. Ring Processing
- 13.1 Cycle Membership
- 13.2 Number of Ring Bonds to an Atom
- 13.3 Testing for Membership in a Given Ring Size
- 13.4 Determining Smallest Ring Membership
- 13.5 Identifying Connected Components
- 13.6 Identifying Ring Systems
- 13.7 Smallest Set of Smallest Rings (SSSR) considered Harmful
14. Aromaticity Processing
- 14.1 Aromaticity and Hückel's 4n+2 rule
- 14.2 Aromaticity Models in OEChem
- 14.3 Clearing Aromaticity
15. Stereochemistry Processing
- 15.1 Atom Stereochemistry
- 15.2 Bond Stereochemistry
16. Atom and Bond Typing
- 16.1 Integer Atom Types and Type Names
- 16.2 Tripos Atom Typing
- 16.3 Tripos Bond Typing
- 16.4 Generic Tripos Type Functions
- 16.5 Writing a Sybyl mol2 file using OEWriteMol2File
- 16.6 MacroModel Atom Typing
- 16.7 Generic MacroModel Type Functions
17. Formal and Partial Charges
- 17.1 Assigning Formal Charges
- 17.2 Working with Partial Charges
- 17.3 Determining Net Charge on a Molecule
- 17.4 Calculating Gasteiger Partial Charges
18. Pattern Matching
- 18.1 Substructure Search
- 18.2 Maximum Common Substructure Search
  - 18.2.1 Exhaustive and approximate MCSS
  - 18.2.2 MCS scoring functions: OEMCSFunc
- 18.3 Clique Search
- 18.4 OEExprOpts Namespace
19. Coordinate Handling
- 19.1 Getting and Setting Coordinates of Atoms and Molecules
  - 19.1.1 C Array Wrappers
- 19.2 Coordinate Manipulation
20. Logging and Error Handling
- 20.1 OEErrorHandler
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 Python
- 22.4 Composition Functors in OEChem
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. 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. SMARTS Pattern Matching
- 29.1 SMARTS Syntax
30. Reactions
- 30.1 Normalization Reactions
- 30.2 Library Generation
31. License handling
32. OEChem Class Hierarchy: Why in the world are there 6 molecules?!
- 32.1 Atoms, Bond, Conformers, and Molecules
- 32.2 Objects and Free-Functions
- 32.3 Programming Layers: The Deep and Twisted Path
33. Bibliography
34. Release Notes
- 34.1 OEChem 1.6.1
- 34.2 OEChem 1.6.0
- 34.3 OEChem 1.5.1
  - 34.3.1 Bug fixes
  - 34.3.2 New features
- 34.4 OEChem 1.5.0
- 34.5 OEChem 1.4.2
- 34.6 OEChem 1.4.1
- 34.7 OEChem 1.4.0
- 34.8 OEChem 1.3.4
- 34.9 OEChem 1.3.3
- 34.10 OEChem 1.3.2
- 34.11 OEChem 1.3.1
- 34.12 OEChem 1.3.0
Index

				OEChem - Python Theory Manual

				OEChem - Python Theory Manual

Contents