Difference between revisions of "File formats/Converters"

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(Balloon)
 
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== Using downloaded software ==
 
== Using downloaded software ==
 
* [http://www.openbabel.org/ Open Babel]
 
* [http://www.openbabel.org/ Open Babel]
 +
* [http://users.abo.fi/mivainio/balloon/ Balloon] calculates 3D atomic coordinates from 1D or 2D information on connectivity. It can generate an ensemble of conformations. It may also assign partial charges to atoms. It runs in a command-line on Linux, Mac OS X or Microsoft Windows.
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:* Reads either a SMILES, an {{file|sdf}} file or a {{file|mol2}} file
 +
:* Outputs 3D atomic coordinates in an {{file|sdf}} file or a {{file|mol2}} file and atomic partial charges in the latter format.
  
 
== Online ==
 
== Online ==
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*: 39 input formats, 48 output formats; by file upload; Java-based.
 
*: 39 input formats, 48 output formats; by file upload; Java-based.
 
* [http://www.webqc.org/molecularformatsconverter.php Molecular Formats Converter] in the WebQC.Org Chemical Portal, by Vitalii Vanovschi.
 
* [http://www.webqc.org/molecularformatsconverter.php Molecular Formats Converter] in the WebQC.Org Chemical Portal, by Vitalii Vanovschi.
*: 50 input formats, 57 output formats; allows to add or delete hydrogens; by file upload or by text entry.
+
*: 50 input formats, 57 output formats; allows to add or delete hydrogens; by file upload or by text entry. Returns result in a text box.
 
* [http://www.molecular-networks.com/online_demos/convert_demo.html Online demonstration of the CONVERT program] by Molecular Networks.
 
* [http://www.molecular-networks.com/online_demos/convert_demo.html Online demonstration of the CONVERT program] by Molecular Networks.
 
*: 34 output formats; by file upload.
 
*: 34 output formats; by file upload.
 
* Jmol 12 (application and signed applet) can load text strings in SMILES or JME formats and convert them to 3D models using external web servers.
 
* Jmol 12 (application and signed applet) can load text strings in SMILES or JME formats and convert them to 3D models using external web servers.
*: (''this needs verification and detailed explanation, but is possible; search the scripting documentation and the email lists for hints'')
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*: See [[File formats/Chemical Structure]] for details.
* Convert SMILES to JME, InChI, MOL, SDF, PDB, GIF,... using the CACTVS server at NIH:
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* Convert SMILES<sup>1D</sup>, InChI<sup>1D</sup> or InChIKeys<sup>1D</sup><br> to InChI<sup>1D</sup>, JME<sup>2D</sup>, MOL<sup>3D</sup>, SDF<sup>3D</sup>, XYZ<sup>3D</sup>, PDB<sup>3D</sup>, MOL2<sup>3D</sup>, GIF<sup>2D</sup>, PNG<sup>2D</sup>,... using the CACTUS server at NIH:<br>Examples:
*: example:
 
 
  http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme
 
  http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme
  http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=mol
+
http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=pdb
 +
  http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=mol&get3d=True

Latest revision as of 11:45, 17 March 2019

File Formats

Converter software for coordinate file formats

How to convert your file from one format to another:

Using downloaded software

  • Open Babel
  • Balloon calculates 3D atomic coordinates from 1D or 2D information on connectivity. It can generate an ensemble of conformations. It may also assign partial charges to atoms. It runs in a command-line on Linux, Mac OS X or Microsoft Windows.
  • Reads either a SMILES, an File icon.gifsdf file or a File icon.gifmol2 file
  • Outputs 3D atomic coordinates in an File icon.gifsdf file or a File icon.gifmol2 file and atomic partial charges in the latter format.

Online

  • E-BABEL Interactive Molecular Structure Formats Interconversion Program. Part of the Virtual Computational Chemistry Laboratory; uses the Open Babel engine.
    39 input formats, 48 output formats; by file upload; Java-based.
  • Molecular Formats Converter in the WebQC.Org Chemical Portal, by Vitalii Vanovschi.
    50 input formats, 57 output formats; allows to add or delete hydrogens; by file upload or by text entry. Returns result in a text box.
  • Online demonstration of the CONVERT program by Molecular Networks.
    34 output formats; by file upload.
  • Jmol 12 (application and signed applet) can load text strings in SMILES or JME formats and convert them to 3D models using external web servers.
    See File formats/Chemical Structure for details.
  • Convert SMILES1D, InChI1D or InChIKeys1D
    to InChI1D, JME2D, MOL3D, SDF3D, XYZ3D, PDB3D, MOL23D, GIF2D, PNG2D,... using the CACTUS server at NIH:
    Examples:
http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme
http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=pdb
http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=mol&get3d=True

Contributors

AngelHerraez