Joelib Tutorial




НазваниеJoelib Tutorial
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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 Error: Reference source not found

1. Installing JOELib Error: Reference source not found

Java Development Kit (JDK) Error: Reference source not found

Ant - XML based makefile mechanism Error: Reference source not found

Installing and starting JOELib Error: Reference source not found

Linux/Unix Error: Reference source not found

Windows 2000/NT Error: Reference source not found

Windows 95/98/XP Error: Reference source not found

Matlab toolbox Error: Reference source not found

Using another JDK Error: Reference source not found

2. JOELib basics Error: Reference source not found

Atoms Error: Reference source not found

Accessing atoms Error: Reference source not found

Chemical properties Error: Reference source not found

Bonds Error: Reference source not found

Accessing bonds Error: Reference source not found

Chemical properties Error: Reference source not found

Molecule Error: Reference source not found

Basics Error: Reference source not found

Chemical properties Error: Reference source not found

3. Molecule operation methods and classes Error: Reference source not found

Molecule Error: Reference source not found

Molecule data entries Error: Reference source not found

Molecule descriptors Error: Reference source not found

Set and get descriptor data entries Error: Reference source not found

Using external calculated descriptors Error: Reference source not found

Available descriptors Error: Reference source not found

Writing your own descriptor and result classes Error: Reference source not found

SMiles ARbitrary Target Specification (SMARTS)-substructure search Error: Reference source not found

SMARTS basics Error: Reference source not found

SMARTS definition Error: Reference source not found

Programmable Atom Typer (PATTY) Error: Reference source not found

SMARTS based structure modification Error: Reference source not found

Processes and filters Error: Reference source not found

Processes (internal, Java) Error: Reference source not found

Process filters Error: Reference source not found

External processes Error: Reference source not found

Input and output Error: Reference source not found

Supported input and output formats Error: Reference source not found

XML respective Chemical Markup Language (CML) Error: Reference source not found

CACTVS's clear text format (CTX) Error: Reference source not found

Image writers (BMP, GIF, JPEG, PPM) Error: Reference source not found

Joint Commitee on Atomic and Molecular Physical Data (JCAMP) Error: Reference source not found

Protein Data Base (PDB) Error: Reference source not found

Portable Adobe Document Format (PDF) Error: Reference source not found

Persistence Of Vision (POV) Ray Tracer Error: Reference source not found

Structured Data File (SDF) Error: Reference source not found

Simplified Molecular Input Line Entry System (SMILES) Error: Reference source not found

Sybyl (MOL2) Error: Reference source not found

Tinker (TINKER) Error: Reference source not found

Writing your own import/export filter Error: Reference source not found

Assigning atom types, aromatic flags, hybridization and hydrogens Error: Reference source not found

Assigning aromaticity flags Error: Reference source not found

Assigning atom hybridizations Error: Reference source not found

Assigning atom types Error: Reference source not found

Assigning implicite hydrogens Error: Reference source not found

Calculate descriptors and/or assign special atomtypes Error: Reference source not found

4. Used utilities Error: Reference source not found

Development Error: Reference source not found

Maintenance Error: Reference source not found

5. Descriptors Error: Reference source not found

Native values Error: Reference source not found

Number of acidic groups Error: Reference source not found

Number of aliphatic hydroxy groups Error: Reference source not found

Number of aromatic bonds Error: Reference source not found

Number of basic groups Error: Reference source not found

Fraction of rotatable bonds Error: Reference source not found

Geometrical diameter Error: Reference source not found

Geometrical radius Error: Reference source not found

Geometrical shape coefficient Error: Reference source not found

Graph shape coefficient Error: Reference source not found

Number of Hydrogen Bond Acceptors (HBA) 1 Error: Reference source not found

Number of Hydrogen Bond Acceptors (HBA) 2 Error: Reference source not found

Number of Hydrogen Bond Donors (HBD) 1 Error: Reference source not found

Number of Hydrogen Bond Donors (HBD) 2 Error: Reference source not found

Number of heavy bonds Error: Reference source not found

Number of heterocycles Error: Reference source not found

Number of hydrophobic groups Error: Reference source not found

Kier Shape 1 Error: Reference source not found

Kier shape 2 Error: Reference source not found

Kier shape 3 Error: Reference source not found

Octanol/Water partition coefficient (logP) Error: Reference source not found

Molar refractivity (MR) Error: Reference source not found

Molecular weight (MW) Error: Reference source not found

Number of atoms Error: Reference source not found

Number of boron atoms Error: Reference source not found

Number of bromine atoms Error: Reference source not found

Number of bonds Error: Reference source not found

Number of chlorine atoms Error: Reference source not found

Number of halogen atoms Error: Reference source not found

Number of iodine atoms Error: Reference source not found

Number of fluorine atoms Error: Reference source not found

Number of nitrogen atoms Error: Reference source not found

Number of oxygen atoms Error: Reference source not found

Number of phosphorus atoms Error: Reference source not found

Number of sulfur atoms Error: Reference source not found

Number of -NO2 groups Error: Reference source not found

Number of -OSO atoms Error: Reference source not found

Polar surface area (PSA) Error: Reference source not found

Number of rotatable bonds Error: Reference source not found

Number of -SO groups Error: Reference source not found

Number of -SO2 atoms Error: Reference source not found

Topological diameter Error: Reference source not found

Topological radius Error: Reference source not found

Zagreb index 1 Error: Reference source not found

Zagreb index 2 Error: Reference source not found

Atom properties Error: Reference source not found

Atom in acceptor Error: Reference source not found

Atom in conjugated environment Error: Reference source not found

Atom in donor or acceptor Error: Reference source not found

Atom in donor Error: Reference source not found

Atom in ring Error: Reference source not found

Atom is terminal carbon Error: Reference source not found

Atom is negative Error: Reference source not found

Atom is positive Error: Reference source not found

Atom masss Error: Reference source not found

Valence Error: Reference source not found

Van der Waals volume Error: Reference source not found

Conjugated electrotopological state Error: Reference source not found

Electrogeometrical state Error: Reference source not found

Electron affinity Error: Reference source not found

Electronegativity after Pauling Error: Reference source not found

Electrotopological state Error: Reference source not found

Gasteiger-Marsili Error: Reference source not found

Graph potentials Error: Reference source not found

Intrinsic topological state Error: Reference source not found

Fingerprints Error: Reference source not found

Pharmacophore fingerprint Error: Reference source not found

Transformations Error: Reference source not found

Moreau-Broto topological autocorrelation Error: Reference source not found

Burden modified eigenvalues Error: Reference source not found

Global topological charge Error: Reference source not found

Radial distribution function (RDF) Error: Reference source not found

6. Algorithms Error: Reference source not found

Breadth First Search (BFS) Error: Reference source not found

Depth First Search (DFS) Error: Reference source not found

Topological distance matrix Error: Reference source not found

Geometrical distance matrix Error: Reference source not found

Morgan: Unique atom numbering Error: Reference source not found

7. Interfaces to other libraries Error: Reference source not found

Interfaces to Java libraries Error: Reference source not found

Chemical Development Kit (CDK) Error: Reference source not found

Weka data mining library Error: Reference source not found

Interfaces to C/C++ libraries using the Java native interface (JNI) Error: Reference source not found

LibGhemical Error: Reference source not found

Matlab interface Error: Reference source not found

8. Documentation Error: Reference source not found

DocBook Error: Reference source not found

DocBook and mathematical equations Error: Reference source not found

DocBook and molecular structures Error: Reference source not found

API documentation Error: Reference source not found

9. JOELib examples and code snippets Error: Reference source not found

Molecule Error: Reference source not found

Molecules Error: Reference source not found

Load and store molecules Error: Reference source not found

Modify molecules Error: Reference source not found

Access atoms and bonds of a molecule Error: Reference source not found

Special atom methods Error: Reference source not found

Access the neighbour atoms of an atom Error: Reference source not found

Access the bonds of an atom Error: Reference source not found

Descriptors Error: Reference source not found

Get and calculate descriptors Error: Reference source not found

Create own descriptor classes Error: Reference source not found

Processes and filters Error: Reference source not found

Applying processes and filters Error: Reference source not found

Import/Export Error: Reference source not found

Import Error: Reference source not found

Get molecule import classes Error: Reference source not found

Export Error: Reference source not found

Get molecule export classes Error: Reference source not found

Simple Import/Export pipeline Error: Reference source not found

Create molecule processing pipe Error: Reference source not found

Interfaces Error: Reference source not found

Java interfaces Error: Reference source not found

Chemical Development Kit (CDK) Error: Reference source not found

Weka data mining interface Error: Reference source not found

C/C++ interfaces using JNI Error: Reference source not found

Some Java implementions to test Ghemical Error: Reference source not found

Matlab interface Error: Reference source not found

Matlab to Java connection Error: Reference source not found

Java to Matlab connection Error: Reference source not found

Database Error: Reference source not found

Database access using the Java Database Connection (JDBC) Error: Reference source not found

Miscellaneous Error: Reference source not found

Point group symmetry calculation Error: Reference source not found

Hash code calculation Error: Reference source not found

Reading JCAMP-DX spectras Error: Reference source not found

Create fragmented molecules Error: Reference source not found

Combinatorial synthesis for generating virtual combinatorial libraries Error: Reference source not found

10. Example applications Error: Reference source not found

Convert Error: Reference source not found

Options Error: Reference source not found

Examples Error: Reference source not found

ConvertSkip Error: Reference source not found

Options Error: Reference source not found

Examples Error: Reference source not found

Comparison Error: Reference source not found

Options Error: Reference source not found

Descriptor calculation Error: Reference source not found

Options Error: Reference source not found

EuklidianComparison Error: Reference source not found

Options Error: Reference source not found

Statistic Error: Reference source not found

Options Error: Reference source not found

Point Group Symmetry Error: Reference source not found

Options Error: Reference source not found

11. Support Error: Reference source not found

A. Summary of molecular structures Error: Reference source not found

Bibliography Error: Reference source not found

Glossary Error: Reference source not found

Index Error: Reference source not found
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