JOELib

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JOELib

JOELib2 logo, which is the word JOELib written in the fictional Tengwar script of J. R. R. Tolkien, followed by a Roman numeral 2.

Original author(s)| Joerg Kurt Wegner
Developer(s)| JOELib development team
Initial release| 9 November 2001; 23 years ago (2001-11-09)
Stable release|

2007-03-03 / 3 March 2007; 17 years ago (2007-03-03)

Preview release|

2009-06-08 / 8 June 2009; 15 years ago (2009-06-08)

Repository|

* sourceforge.net/p/joelib/svn/HEAD/tree/

Written in| Java
Operating system| Cross-platform: Windows, Unix, Linux, macOS
Platform| IA-32, x86-64
Available in| English
Type| Cheminformatics, molecular modelling
License| GPL 2.0
Website| sourceforge.net/projects/joelib

JOELib is computer software, a chemical expert system used mainly to interconvert chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other operating systems supporting the programming language Java. It is free and open-source software distributed under the GNU General Public License (GPL) 2.0.

## History

[edit]

JOELib and OpenBabel were derived from the OELib Cheminformatics library.

## Logo

[edit]

The project logo is just the word JOELib in the Tengwar script of J. R. R. Tolkien. The letters are grouped as JO-E-Li-b. Vowels are usually grouped together with a consonant, but two following vowels must be separated by a helper construct.

## Major features

[edit]

* Chemical expert system
* Query and substructure search (based on Simplified molecular-input line-entry system (SMARTS), a SMILES extension
* Clique detection
* QSAR
* Data mining
* Molecule mining, special case of Structured Data Mining
* Feature–descriptor calculation
* Partition coefficient, log P
* Rule-of-five
* Partial charges
* Fingerprint calculation
* etc.
* Chemical file formats
* Chemical table file: MDL Molfile, SD format
* SMILES
* Gaussian
* Chemical Markup Language
* MOPAC

## See also

[edit]

* OpenBabel \- C++ version of JOELib-OELib
* Jmol
* Chemistry Development Kit (CDK)
* Comparison of software for molecular mechanics modeling
* Blue Obelisk
* Molecule editor
* List of free and open-source software packages

## References

[edit]

* The Blue Obelisk-Interoperability in Chemical Informatics, Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck, Jörg K. Wegner, and Egon L. Willighagen, J. Chem. Inf. Model.; 2006; doi:10.1021/ci050400b

## External links

[edit]

* Official website at SourceForge
* Algorithm dictionary

* v
* t
* e

Computational chemistry software

Cheminformatics|

| Free software|

* Avalon Cheminformatics Toolkit
* Bioclipse
* Blue Obelisk
* Chemistry Development Kit
* ECCE
* JOELib
* OELib
* Open Babel
* RDKit

|

Proprietary|

* Canvas
* Chemicalize
* Discovery Studio

Chemical kinetics|

| Free software|

* APBS
* Cantera
* KPP

|

Proprietary|

* Autochem
* Chemical WorkBench
* CHEMKIN
* COSILAB
* DelPhi
* Khimera

Molecular modelling
and
visualization|

List of molecular graphics systems

| Free software|

* Ascalaph Designer
* Avogadro
* BALL
* Biskit
* Gabedit
* Ghemical
* Jmol
* Molekel
* PyMOL
* QuteMol
* RasMol

|

Proprietary|

* Abalone
* ACD/ChemSketch
* Atomistix ToolKit
* ChemDraw
* ChemWindow
* EzMol
* Gaussian
* Maestro
* MarvinSketch
* MarvinView
* MODELLER
* Molecular Operating Environment
* SAMSON
* Spartan
* UCSF Chimera
* VMD

Molecular docking|

List of protein-ligand docking software

| Free software|

* AutoDock
* AutoDock Vina
* FlexAID
* rDock

|

Proprietary|

* Glide
* LeDock
* Molecular Operating Environment

Molecular dynamics|

| Free software|

* CP2K
* GROMACS
* LAMMPS
* OpenMM
* PLUMED

|

Proprietary|

* Abalone
* AMBER
* CHARMM
* CPMD
* Desmond
* GROMOS
* NAMD

Quantum chemistry|

List of quantum chemistry and solid-state physics software

| Free software|

* ABINIT
* ACES (CFOUR)
* AIMAll
* BigDFT
* COLUMBUS
* CONQUEST
* CP2K
* Dalton
* DIRAC
* DP code
* FLEUR
* FreeON
* MADNESS
* MOPAC
* MPQC
* NWChem
* Octopus
* OpenMolcas
* PARSEC
* PSI
* PyQuante
* PySCF
* Quantum ESPRESSO (PWscf)
* RMG
* SIESTA
* VB2000
* YAMBO code

|

Proprietary|

* ADF
* AMPAC
* DMol3
* CADPAC
* CASINO
* CASTEP
* CPMD
* CRUNCH
* CRYSTAL
* Firefly
* GAMESS (UK)
* GAMESS (US)
* Gaussian
* Jaguar
* MOLCAS
* MOLPRO
* ONETEP
* OpenAtom
* ORCA
* PLATO
* PQS
* Q-Chem
* Quantemol
* Scigress
* Spartan
* TeraChem
* TURBOMOLE
* VASP
* WIEN2k
* XMVB

Skeletal structure drawing|

| Free software|

* JChemPaint
* Molsketch
* XDrawChem

|

Proprietary|

* ACD/ChemSketch
* BIOVIA Draw
* ChemDoodle
* ChemDraw
* ChemWindow
* JME Molecule Editor
* MarvinSketch

Others|

* Aqion
* Eulim
* EXC code
* GenX
* GSim
* Mercury
* CrystalExplorer
* ICM (ICM-Browser)
* Materials Studio
* Molden
* OpenChrom
* SASHIMI

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