Molconvert

Molconverter is a command line program in Marvin Suite and JChem that converts between various file types.

Syntax

molconvert [options] outformat[:exportoptions] [files...]

The outformat stands for one of the supported formats.

Chemical Formats

Image Formats

Molconvert Options

Export options

The format specific export option can be specified with the format descriptor.The outformat value and the options are separated by a colon, the options by commas.

The following example creates a 100x100 pixel JPEG image on yellow background, with 95% quality molconvert jpeg:w100,Q95,#ffff00 nice.mol -o nice.jpg

Import options

The format specific import options can be specified between braces, in one of the following forms:

Format specific options

You can also use the Basic export options for all formats.

Examples

Example

1. Printing the SMILES string of a molecule in a molfile

   molconvert smiles caffeine.mol

2. Dearomatizing an aromatic molecule:

   molconvert smiles:-a -s "c1ccccc1"

3. Aromatizing a molecule:

   molconvert smiles:a -s "C1=CC=CC=C1"

   (The default general aromatization is used.)

4. Aromatizing a molecule using the basic algorithm:

   molconvert smiles:a_bas -s "CN1C=NC2=C1C(=O)N(C)C(=O)N2C"

5. Converting a SMILES file to MDL Molfile

   molconvert mol caffeine.smiles -o caffeine.mol

6. Making an SDF from molfiles:

   molconvert sdf *.mol -o molecules.sdf

7. Printing the encodings of SDfiles in the working directory:

   molconvert query-encoding *.sdf

8. SMILES to Molfile with optimized 2D coordinate calculation, converting double bonds with unspecified cis/trans to "either"

   molconvert -2:2e mol caffeine.smiles -o caffeine.mol

9. 2D coordinate calculation with optimization and fixed atom coordinates for atoms 1, 5, 6:

   molconvert -2:2:F1,5,6 mol caffeine.mol

10. Import a file as XYZ, do not try to recognize the file format:

    molconvert smiles "foo.xyz{xyz:}"

    Note: This is just an example. XYZ and other formats known by Marvin are always recognized (send us a bug report otherwise), so the specification of the input format is usually not needed. It is only relevant if a user-defined import module is used.

11. Import a file as XYZ, with bond-length cut-off = 1.4, and max. number of Carbon connections = 4, export to SMILES:

    molconvert smiles "foo.xyz{f1.4C4}"

12. Import a file as Gzipped XYZ, with the same import options as in the previous example:

    molconvert smiles "foo.xyz.gz{gzip:xyz:f1.4C4}"

13. Like the previous example but merge the molecules into one molecule that contains multiple atom sets. MDL molfile is exported.

    molconvert mol "foo.xyz.gz{gzip:xyz:MULTISET,f1.4C4}"

14. Import an SDF and export a table containing selected molecules with columns: SMILES, ID, and logP:

    molconvert smiles -c "ID<=1000&logP>=-2&logP<=4" -T "ID:logP" foo.sdf

15. Fuse R2 definition from file, filter fragments with 1 attachment point:

    molconvert mrv in.mrv -R2:1 rdef.mrv

16. Fuse fragments from file (note, that the input molecule, which the fragments are fused to, should also be specified):

    molconvert mrv in.mrv -R frags.mrv

17. Generate all common names for a structure:

    molconvert "name:common,all" -s tylenol

18. Generate the most popular common name for a structure (It fails if none is known.):

    molconvert name:common -s viagra

19. Generate SMILES from those molecules that names are mentioned in a file foo.html:

    molconvert smiles foo.html