Difference between revisions of "File formats/Converters"
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File Formats
AngelHerraez (talk | contribs) (→Online) |
AngelHerraez (talk | contribs) (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. | ||
| + | :* 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 == | ||
| Line 9: | Line 12: | ||
*: 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. | ||
| − | *: | + | *: See [[File formats/Chemical Structure]] for details. |
| − | * Convert SMILES to JME | + | * 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: |
| − | |||
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
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.
- Reads either a SMILES, an
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
