Difference between revisions of "File formats/Converters"
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File Formats
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* 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'') | *: (''this needs verification and detailed explanation, but is possible; search the scripting documentation and the email lists for hints'') | ||
| − | * Convert SMILES<sup>1D</sup> to JME<sup>1D</sup>, InChI<sup>1D</sup>, MOL<sup>2D</sup>, SDF<sup>2D</sup>, PDB<sup>3D</sup>, GIF<sup>2D</sup>, PNG<sup>2D</sup>,... using the CACTVS server at NIH: | + | * Convert SMILES<sup>1D</sup>, InChI<sup>1D</sup> or InChIKeys<sup>1D</sup><br> to JME<sup>1D</sup>, InChI<sup>1D</sup>, MOL<sup>2D</sup>, SDF<sup>2D</sup>, XYZ<sup>3D</sup>, PDB<sup>3D</sup>, MOL2<sup>3D</sup>, GIF<sup>2D</sup>, PNG<sup>2D</sup>,... using the CACTVS server at NIH:<br>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=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=pdb | ||
Revision as of 19:31, 8 September 2010
Converter software for coordinate file formats
How to convert your file from one format to another:
Using downloaded software
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.
- 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.
- (this needs verification and detailed explanation, but is possible; search the scripting documentation and the email lists for hints)
- Convert SMILES1D, InChI1D or InChIKeys1D
to JME1D, InChI1D, MOL2D, SDF2D, XYZ3D, PDB3D, MOL23D, GIF2D, PNG2D,... using the CACTVS 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
