File formats/Converters

File Formats

• General information
• Coordinates
• Chemical structure
• Compressed
• Converters
• Images
• Ray Tracing
• Surfaces
• 3D Objects
• Scripting
• Exporting / saving files
• Support for bond orders
• Support for isotopes
• Support for stereochemistry

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 sdf file or a mol2 file
• Outputs 3D atomic coordinates in an sdf file or a mol2 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 SMILES^1D, InChI^1D or InChIKeys^1D
  to InChI^1D, JME^2D, MOL^3D, SDF^3D, XYZ^3D, PDB^3D, MOL2^3D, GIF^2D, PNG^2D,... 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