Jbabel
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Jbabel is a GUI front-end of Open Babel. Open Babel is an open-source project used for converting various chemical data file types. To use Open Babel you must install it on your computer, whereas Jbabel is accessible over the internet from any computer that has Java installed. Jbabel is also designed to do mass file conversions.
[edit] Getting Started
[edit] Install Java
To begin using Jbabel, you will need to install Java. Java can be downloaded from Sun's website. Choose the Java Runtime Environment (JRE) 6 download. You will need to accept the license agreement, and then download the version for your operating system. Please choose a 32 bit version if possible. If you are using windows, simply double click the executable when it is done downloading and follow the instructions.
If you are using linux, you will need to change the file permissions of the installer file. Open a terminal and locate the file. Type "chmod +x 'filename'" without quotes, where 'filename' is the name of the file you downloaded. If you downloaded the rpm version, you will now need to log in as the root user. Next, simply type that same filename and press enter to execute the installer. The license agreement will display. You will have to press the spacebar several times and type yes to accept the agreement, and it will begin to install.
[edit] Starting the Interface
Jbabel is a Java-based GUI front-end for the open-source Open Babel, a C++ program used to convert chemical data into various formats. The GUI runs via Java Web Start. You can start it through the command line by typing "javaws http://fireball.phys.wvu.edu/jbabel/Jbabel.jnlp" without quotes. Alternatively, you can configure your web browser to start the GUI by clicking on that link. See the Help:Contents page for instructions.
[edit] Using Jbabel
[edit] Add Files
Click the Add button to open the file chooser. By default, it will only display supported file types. Select one or more files to add, and press ok. You may repeat this step to get files from different folders. Your files will be displayed in the left column. Jbabel does not simply convert all the files in the left column. You must now highlight one or more files in the left column to convert. This is to prevent unwanted file conversions. To select multiple files, hold the control button.
[edit] Remove Files
To remove files from the input files column, highlight them in the left-most column (you can hold down the Shift or Control key on your keyboard to select multiple files), then click the "Remove File(s)" button.
[edit] Selecting Conversion File Types
Select one or more formats exactly as you have highlighted input files.
[edit] Converting Files
After you have selected input files and formats, simply press the Convert button. Jbabel will upload your files to fireball.phys.wvu.edu, convert them to the specified formats, and download the converted files. A total of <# of input files> * <# of formats> files will be converted. The converted files will be put in the directory in which they came.
All files converted by Jbabel will be retained on the server, and may be used for any purpose. Do not use Jbabel if you want your files private.
[edit] View Log
If you suspect Jbabel has not converted you files correctly, you can click the log button. The output of Jbabel's conversions will be show, and any errors can be seen.
[edit] View Converted Files
To view your converted file, simply select a file in the right column and press view converted file. If multiple files are selected, only the first file is opened.
[edit] Supported File Types
Open Babel currently supports over 80 chemical file formats. However, some formats are Read-Only, or Write-Only. Read-Only formats mean your input files can be of this type, but you cannot convert other input files into this type. Write-Only formats can only be written to. You cannot convert files of these types to other formats. Below is a table listing the supported file types and their available operations.
(Details on each file type can be found here.)
| Extension | File Type | Read-Only | Write-Only |
|---|---|---|---|
| acr | Carine ASCI Crystal | ||
| alc | Alchemy | ||
| arc | Accelrys/MSI Biosym/Insight II CAR | Yes | |
| bgf | MSI BGF | ||
| box | Dock 3.5 Box | ||
| bs | Ball and Stick | ||
| c3d1 | Chem3D Cartesian 1 | ||
| c3d2 | Chem3D Cartesian 2 | ||
| caccrt | Cacao Cartesian | ||
| cache | CAChe MolStruct | Yes | |
| cacint | Cacao Internal | Yes | |
| can | Canonical SMILES | ||
| car | Accelrys/MSI Biosym/Insight II | Yes | |
| cc | CCC | Yes | |
| cdx | ChemDraw binary | Yes | |
| cdxml | ChemDraw CDXML | ||
| cht | Chemtool [W] | Yes | |
| cif | Chiron Interchange | ||
| cml | Chemical Markup Language | ||
| cmlr | CML Reaction | ||
| com | Gaussian 98/03 Cartesian Input | Yes | |
| copy | Copies raw text | Yes | |
| crk2d | Chemical Resource Kit 2D diagram | ||
| crk3d | Chemical Resource Kit 3D | ||
| csr | Accelrys/MSI Quanta CSR | Yes | |
| cssr | CSD CSSR | Yes | |
| ct | ChemDraw Connection Table | ||
| dmol | DMol3 coordinates | ||
| ent | Protein Data Bank | ||
| fa | FASTA | Yes | |
| fasta | FASTA | Yes | |
| fch | Gaussian formatted checkpoint file | Yes | |
| fchk | Gaussian formatted checkpoint file | Yes | |
| fck | Gaussian formatted checkpoint file | Yes | |
| feat | Feature | ||
| fh | Fenske-Hall Z-Matrix | Yes | |
| fix | SMILES FIX | Yes | |
| fpt | Fingerprint | Yes | |
| fract | Free Form Fractional | ||
| fs | Open Babel FastSearching Index | ||
| fsa | FASTA | Yes | |
| g03 | Gaussian98/03 Output | Yes | |
| g98 | Gaussian98/03 Output | Yes | |
| gam | GAMESS Output | Yes | |
| gamin | GAMESS Input | Yes | |
| gamout | GAMESS Output | Yes | |
| gau | Gaussian 98/03 Cartesian Input | Yes | |
| gjc | Gaussian 98/03 Cartesian Input | Yes | |
| gjf | Gaussian 98/03 Cartesian Input | Yes | |
| gpr | Ghemical | ||
| gr96 | GROMOS96 | Yes | |
| hin | HyperChem HIN | ||
| inchi | IUPAC InChI descriptor | Yes | |
| inp | GAMESS Input [W] | Yes | |
| ins | ShelX | Yes | |
| jin | Jaguar input | Yes | |
| jout | Jaguar output | Yes | |
| mdl | MDL MOL | ||
| mmd | MacroModel | ||
| mmod | MacroModel | ||
| mol | MDL MOL | ||
| mol2 | Sybyl Mol2 | ||
| molreport | Open Babel molecule report | Yes | |
| moo | MOPAC Output | Yes | |
| mop | MOPAC Cartesian | ||
| mopcrt | MOPAC Cartesian | ||
| mopout | MOPAC Output | Yes | |
| mpc | MOPAC Cartesian | ||
| mpd | Sybyl descriptor | Yes | |
| mpqc | MPQC output | Yes | |
| mpqcin | MPQC simplified input | Yes | |
| nw | NWChem input | Yes | |
| nwo | NWChem output | Yes | |
| pc | PubChem | Yes | |
| pcm | PCModel | ||
| pdb | Protein Data Bank | ||
| pov | POV-Ray input | Yes | |
| pqs | Parallel Quantum Solutions | ||
| prep | Amber Prep | Yes | |
| qcin | Q-Chem input | Yes | |
| qcout | Q-Chem output | Yes | |
| report | Open Babel report | Yes | |
| res | ShelX | Yes | |
| rxn | MDL RXN | ||
| sd | MDL MOL | ||
| sdf | MDL MOL | ||
| smi | SMILES | ||
| sy2 | Sybyl Mol2 | ||
| tdd | Thermo | ||
| test | Test | Yes | |
| tmol | TurboMole Coordinate | ||
| txyz | Tinker MM2 | Yes | |
| unixyz | UniChem XYZ | ||
| vmol | ViewMol | ||
| xed | XED | Yes | |
| xml | General XML | Yes | |
| xyz | XYZ cartesian coordinates | ||
| yob | YASARA.org YOB | ||
| zin | ZINDO input | Yes |
