OEChem - C++ Theory Manual
Version 1.3.1
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OEChem - C++ Theory
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Contents
Front Matter
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
4.1.1 Dimension
4.1.2 Energy
4.1.3 Rxn
4.1.4 Title
4.2 Derived Properties of Molecules
4.2.1 NumAtoms, NumBonds
4.2.2 GetMaxAtomIdx, GetMaxBondIdx
4.2.3 GetAtom, GetBond
4.2.4 GetAtoms, GetBonds
4.3 Manipulating SD File Tagged Data
4.3.1 Storing SD Data on a Molecule
4.3.2 Retrieving SD Data from a Molecule
4.3.3 Deleting SD Data from a Molecule
4.3.4 SD Data Example
4.4 Properties of Multi-Conformer Molecules
4.4.1 GetConf and GetConfs
4.4.2 Use of the conformer state
4.4.3 Use of the conformers as first-class objects
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
6.1.1 AtomicNum
6.1.2 FormalCharge
6.1.3 ImplicitHCount
6.1.4 Isotope
6.1.5 PartialCharge
6.1.6 Hyb
6.1.7 IntType
6.1.8 Name
6.1.9 Type
6.1.10 RxnRole
6.1.11 MapIdx
6.1.12 InRing
6.1.13 SymmetryClass
6.1.14 Aromatic
6.2 Derived Properties of Atoms
6.2.1 GetDegree
6.2.2 GetExplicitDegree
6.2.3 GetExplicitHCount
6.2.4 GetExplicitValence
6.2.5 GetHvyDegree
6.2.6 GetHvyValence
6.2.7 GetParent
6.2.8 GetTotalHCount
6.2.9 GetValence
6.2.10 GetIdx
6.2.11 IsCarbon
6.2.12 IsConnected
6.2.13 IsHalogen
6.2.14 IsHydrogen
6.2.15 IsMetal
6.2.16 IsNitrogen
6.2.17 IsOxygen
6.2.18 IsPhosphorus
6.2.19 IsPolarHydrogen
6.2.20 IsSulfur
7. Properties of Bonds
7.1 Stored Properties of Bonds
7.1.1 Order
7.1.2 Aromatic
7.1.3 InRing
7.1.4 IntType
7.1.5 Type
7.1.6 Bgn
7.1.7 End
7.2 Derived Properties of Bonds
7.2.1 GetBgnIdx
7.2.2 GetEndIdx
7.2.3 GetNbr
7.2.4 GetParent
7.2.5 IsRotor
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 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
15.2.1 OETriposAtomTypes
15.2.2 OETriposAtomTypeNames
15.2.3 OETriposTypeNames
15.2.4 OETriposAtomNames
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
20.3.1 OEGetAverageWeight
20.3.2 OEGetDefaultMass
20.3.3 OEGetCovalentRadius
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
27.1.1 Biological Hierarchies
27.1.2 Set Theory to the Rescue
27.1.3 OEChem Examples
27.1.4 Data Modeling Bibliography
27.2 Stored Properties of Residues
27.2.1 AlternateLocation
27.2.2 BFactor
27.2.3 ChainID
27.2.4 FragmentNumber
27.2.5 HetAtom
27.2.6 InsertCode
27.2.7 ModelNumber
27.2.8 Name
27.2.9 ResidueNumber
27.2.10 Occupancy
27.2.11 SecondaryStructure
27.2.12 SerialNumber
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
29.1.1 Atom Primitives
29.1.2 Bond Primitives
29.1.3 Logical Operators
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
32.9.1 Parameters that are of type file
32.9.2 Parameter files
32.9.3 Molecule 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
About this document ...
OEChem - C++ Theory Manual
Version 1.3.1
Previous:
Front Matter
Up:
OEChem - C++ Theory
Next:
List of Tables
Documentation released on July 30, 2004.