JOELib

JOELib Tutorial

Contents

Users/Publications

JOELib Tutorial

	Contents
	Preface
	Installation
	Basics
	Functionalities
	Utilities
	Maintenance
	Descriptors
	Algorithms
	Interfaces
	Interfaces JNI
	Interface ML
	Documentation
	Examples
	Applications
	Support
	Structures
	Bibliography
	Glossary
	Index

JOELib2 Tutorial

Acknowledgements

Research at WSI-RA

Software at WSI-RA

WSI-RA Department

JOELib Tutorial

A Java based cheminformatics/computational chemistry package

Dipl. Chem. Jörg K. Wegner

Copyright © 2002, 2003, 2004 Dept. Cognitive Systems, University of Tübingen, Germany, Jörg K. Wegner

Updated

$Date: 2004/12/06 15:30:57 $

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Documents

PS, PDF, RTF versions of this tutorial are available.

Plucker E-Book versions: HiRes-color, HiRes-grayscale (recommended), HiRes-black/white, color, grayscale, black/white

Table of Contents

1. Installing JOELib

Java Development Kit (JDK)

Ant - XML based makefile mechanism

Installing and starting JOELib

Linux/Unix
Windows 2000/NT
Windows 95/98/XP

Matlab toolbox

Using another JDK

2. JOELib basics

Accessing atoms
Chemical properties

Accessing bonds
Chemical properties

Basics
Chemical properties

3. Molecule operation methods and classes

Molecule data entries
Molecule descriptors

SMiles ARbitrary Target Specification (SMARTS)-substructure search

SMARTS basics
SMARTS definition
Programmable Atom Typer (PATTY)
SMARTS based structure modification

Processes and filters

Processes (internal, Java)
Process filters
External processes

Input and output

Supported input and output formats
Writing your own import/export filter

Assigning atom types, aromatic flags, hybridization and hydrogens

Assigning aromaticity flags
Assigning atom hybridizations
Assigning atom types
Assigning implicite hydrogens
Calculate descriptors and/or assign special atomtypes

4. Used utilities

Development
Maintenance

5. Descriptors

Native values

Number of acidic groups
Number of aliphatic hydroxy groups
Number of aromatic bonds
Number of basic groups
Fraction of rotatable bonds
Geometrical diameter
Geometrical radius
Geometrical shape coefficient
Graph shape coefficient
Number of Hydrogen Bond Acceptors (HBA) 1
Number of Hydrogen Bond Acceptors (HBA) 2
Number of Hydrogen Bond Donors (HBD) 1
Number of Hydrogen Bond Donors (HBD) 2
Number of heavy bonds
Number of heterocycles
Number of hydrophobic groups
Kier Shape 1
Kier shape 2
Kier shape 3
Octanol/Water partition coefficient (logP)
Molar refractivity (MR)
Molecular weight (MW)
Number of atoms
Number of boron atoms
Number of bromine atoms
Number of bonds
Number of chlorine atoms
Number of halogen atoms
Number of iodine atoms
Number of fluorine atoms
Number of nitrogen atoms
Number of oxygen atoms
Number of phosphorus atoms
Number of sulfur atoms
Number of -NO₂ groups
Number of -OSO atoms
Polar surface area (PSA)
Number of rotatable bonds
Number of -SO groups
Number of -SO₂ atoms
Topological diameter
Topological radius
Zagreb index 1
Zagreb index 2

Atom properties

Atom in acceptor
Atom in conjugated environment
Atom in donor or acceptor
Atom in donor
Atom in ring
Atom is terminal carbon
Atom is negative
Atom is positive
Atom masss
Valence
Van der Waals volume
Conjugated electrotopological state
Electrogeometrical state
Electron affinity
Electronegativity after Pauling
Electrotopological state
Gasteiger-Marsili
Graph potentials
Intrinsic topological state

Fingerprints

Pharmacophore fingerprint

Transformations

Moreau-Broto topological autocorrelation
Burden modified eigenvalues
Global topological charge
Radial distribution function (RDF)

6. Algorithms

Breadth First Search (BFS)
Depth First Search (DFS)
Topological distance matrix
Geometrical distance matrix
Morgan: Unique atom numbering

7. Interfaces to other libraries

Interfaces to Java libraries

Chemical Development Kit (CDK)
Weka data mining library

Interfaces to C/C++ libraries using the Java native interface (JNI)

LibGhemical

Matlab interface

8. Documentation

DocBook and mathematical equations
DocBook and molecular structures

API documentation

9. JOELib examples and code snippets

Molecules
Special atom methods

Descriptors

Get and calculate descriptors
Create own descriptor classes

Processes and filters

Applying processes and filters

Import/Export

Import
Export
Simple Import/Export pipeline

Java interfaces
C/C++ interfaces using JNI
Matlab interface

Database access using the Java Database Connection (JDBC)

Miscellaneous

Point group symmetry calculation
Hash code calculation
Reading JCAMP-DX spectras
Create fragmented molecules
Combinatorial synthesis for generating virtual combinatorial libraries

10. Example applications

Options
Examples

ConvertSkip

Options
Examples

Options

Descriptor calculation

Options

EuklidianComparison

Options

Options

Point Group Symmetry

Options

11. Support

A. Summary of molecular structures

Bibliography

List of Tables
3-1. Predefined data types/names
3-2. Substructure search expressions
3-3. Supported file formats
3-4. Process of assigning atom types
3-5. Possible special atom type assignments (not implemented)
5-1. SMARTS definitions for assigning the conjugated atom property flag
5-2. Pharmacophore fingerprint definition
8-1. Molecular structures with atom numbers and special atom labels
8-2. Molecular structures with a delocalised ring
8-3. Molecular structures with retrosynthetic bond splittings
8-4. Molecular structures with electron transfer arrows
9-1. Simple database definition

List of Figures
6-1. Pseudocode for the BFS algorithm
6-2. Pseudocode for the DFS algorithm
6-3. Pseudocode for the Morgan labeling algorithm
6-4. Pseudocode for the Morgan renumbering algorithm

List of Examples
2-1. Using an iterator for accessing atoms
2-2. Using the atom index for accessing atoms
2-3. Bond iterator
3-1. Getting descriptor data entries
3-2. Setting descriptor data entries
3-3. SMARTS substructure search
3-4. Definition of IO types
9-1. Load molecules from large files sequentially
9-2. Load molecules from smaller files into memory
9-3. Add atoms to a molecule
9-4. Access atoms using a for statement
9-5. Access atoms using an AtomIterator
9-6. Access bonds using a for statement
9-7. Access bonds using an BondIterator
9-8. Access neighbour atoms using a NbrAtomIterator
9-9. Access bonds of an atom using a BondIterator
9-10. Get a list of all available descriptors
9-11. Get a list of all native value descriptors
9-12. Get a list of all atom property descriptors
9-13. Get and calculate descriptors using always a new instance (slow)
9-14. Get and calculate descriptors creating only one descriptor calculation instance (fast)
9-15. Create own native descriptor calculation classes
9-16. Create own atom property descriptor calculation classes
9-17. Get a molecule process by creating an instance
9-18. Get a molecule process by using the process factory
9-19. Use initialization method for a process (depends on the process!)
9-20. Get a molecule process pipe with filter functionalities
9-21. Apply a process to a molecule
9-22. Get molecule import classes
9-23. Get molecule export classes
9-24. Create molecule processing pipe
9-25. Chemical Development Kit (CDK) interface
9-26. Weka data mining interface
9-27. Create 3D coordinates using the Ghemical force field (molecular mechanics)
9-28. Load native descriptors under Matlab
9-29. Database access
9-30. Calculate point group symmetries
9-31. Calculate a molecule hashcode
9-32. Load JCAMP-DX spectras
9-33. Fragment molecules if they are disconnected (non-contiguous)
9-34. Generate molecules using R-Groups
10-1. Show help screen for Convert
10-2. Print molecules to standard output
10-3. Show help screen for ConvertSkip
10-4. Print molecules to standard output
10-5. Write flat file
10-6. Using conversion rule

List of Equations
5-1. Kier shape 1
5-2. Kier shape 1 (alternative formulation)
5-3. Kier shape 2
5-4. Kier shape 3
5-5. Zagreb index 1
5-6. Zagreb index 2
5-7. Conjugated electrotopological state
5-8. Conjugated topological distance
5-9. Electrogeometrical state
5-10. Electrotopological state
5-11. Orbital electronegativity based on atom charge
5-12. Graph potentials
5-13. Intrinsic topological state
5-14. Moreau-Broto autocorrelation
5-15. Radial distribution function

		Next
		Preface

Last changes: 10.12.2010, 13:05 CET (UTC/GMT +1 hour) wegner.
http://www.ra.cs.uni-tuebingen.de/software/joelib/tutorial/JOELibPrimer.html
© 2003 University of Tübingen, Germany