JOELib Tutorial A Java based cheminformatics/computational chemistry package Dipl. Chem. Jörg K. Wegner JOELib Tutorial: A Java based cheminformatics/computational chemistry package by Dipl. Chem. Jörg K. Wegner Published $Date: 2004/03/16 09:16:14 $ Copyright © 2002, 2003, 2004 Dept. Computer Architecture, University of Tübingen, GermanyJörg K. Wegner Updated $Date: 2004/03/16 09:16:14 $ 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 (JOELibTutorial.ps), PDF (JOELibTutorial.pdf), RTF (JOELibTutorial.rtf) versions of this tutorial are available. Plucker E-Book (http://www.plkr.org) versions: HiRes-color (JOELib-HiRes-color.pdb), HiRes-grayscale (JOELib-HiRes-grayscale.pdb) (recommended), HiRes-black/white (JOELib-HiRes-bw.pdb), color (JOELib-color.pdb), grayscale (JOELib-grayscale.pdb), black/white (JOELib-bw.pdb) Revision History Revision $Revision: 1.5 $ $Date: 2004/03/16 09:16:14 $ $Id: JOELibTutorial.sgml,v 1.5 2004/03/16 09:16:14 wegner Exp $ Table of Contents Preface ........................................................................................................................................................i 1. Installing JOELib .................................................................................................................................1 Java Development Kit (JDK)............................................................................................................1 Ant - XML based makefile mechanism ............................................................................................1 Installing and starting JOELib ..........................................................................................................1 Linux/Unix ..............................................................................................................................1 Windows 2000/NT ..................................................................................................................2 Windows 95/98/XP .................................................................................................................2 Matlab toolbox..................................................................................................................................3 Using another JDK ..................................................................................................................3 2. JOELib basics .......................................................................................................................................4 Atoms................................................................................................................................................4 Accessing atoms ......................................................................................................................4 Chemical properties.................................................................................................................4 Bonds ................................................................................................................................................5 Accessing bonds ......................................................................................................................5 Chemical properties.................................................................................................................6 Molecule ...........................................................................................................................................7 Basics ......................................................................................................................................7 Chemical properties.................................................................................................................7 3. Molecule operation methods and classes ............................................................................................8 Molecule ...........................................................................................................................................8 Molecule data entries...............................................................................................................8 Molecule descriptors ...............................................................................................................8 Set and get descriptor data entries..................................................................................8 Using external calculated descriptors.............................................................................9 Available descriptors ...................................................................................................10 Writing your own descriptor and result classes ...........................................................10 SMiles ARbitrary Target Specification (SMARTS)-substructure search .......................................11 SMARTS basics ....................................................................................................................11 SMARTS definition...............................................................................................................11 Programmable Atom Typer (PATTY)...................................................................................12 SMARTS based structure modification.................................................................................12 Processes and filters........................................................................................................................13 Processes (internal, Java).......................................................................................................13 Process filters ........................................................................................................................13 External processes .................................................................................................................13 Input and output ..............................................................................................................................14 Supported input and output formats ......................................................................................14 XML respective Chemical Markup Language (CML).................................................15 CACTVS's clear text format (CTX).............................................................................16 Image writers (BMP, GIF, JPEG, PPM) ......................................................................18 iii Joint Commitee on Atomic and Molecular Physical Data (JCAMP)...........................17 Protein Data Base (PDB) .............................................................................................17 Portable Adobe Document Format (PDF)....................................................................18 Persistence Of Vision (POV) Ray Tracer ....................................................................18 Structured Data File (SDF) ..........................................................................................18 Simplified Molecular Input Line Entry System (SMILES) .........................................18 Sybyl (MOL2)..............................................................................................................19 Tinker (TINKER).........................................................................................................19 Writing your own import/export filter...................................................................................19 Assigning atom types, aromatic flags, hybridization and hydrogens..............................................19 Assigning aromaticity flags...................................................................................................20 Assigning atom hybridizations ..............................................................................................20 Assigning atom types ............................................................................................................20 Assigning implicite hydrogens ..............................................................................................20 Calculate descriptors and/or assign special atomtypes ..........................................................21 4. Used utilities........................................................................................................................................22 Development...................................................................................................................................22 Maintenance....................................................................................................................................22 5. Descriptors ..........................................................................................................................................24 Native values...................................................................................................................................24 Number of acidic groups .......................................................................................................24