Molecule File Conversion with MolConverter

Version 5.9.4

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

Usage

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

The outformat argument must be one of the following strings:

mrv	(document formats)
mol, rgf, sdf, rdf, csmol, csrgf, cssdf, csrdf, cml, smiles, cxsmiles, abbrevgroup, peptide, sybyl, mol2, pdb, xyz, inchi, name, cdx, cdxml, skc	(molecule file formats)
jpeg, msbmp, png, pov, ppm, svg, emf	(graphics formats)
gzip, base64	(compression and encoding)

Alternatively, use

molconvert [options] query-encoding [files...]

to query the automatically detected encodings of the specified molecule files.

Options

-o file	Write output to specified file instead of standard output
-m	Produce multiple output files
-e charset	Set the input character encoding. The encoding must be supported by Java.
-e [in]..[out]	Set the input (in) and/or output (out) character encodings. Examples: UTF-8, ASCII, Cp1250 (Windows Eastern European), Cp1252 (Windows Latin 1), ms932 (Windows Japanese).
-s string	Read molecule from specified SMILES, SMARTS or peptide string (try to recognize its format)
-s string{format:options}	Read molecule from the string in the specified format (can be omitted), using the specified import options (can be omitted)
--smiles string	Read molecule from specified SMILES string
--smarts string	Read molecule from specified SMARTS string
--peptide string	Read molecule from specified peptide string
-g	Continue with next molecule on error (default: exit on error)
-Y	Remove explicit H atoms
-I <range>	process input molecules with molecule index (1-based) falling into the specified range (e.g. 5-8,15 refers to molecules 5,6,7,8,15)
-U	fuse input molecules and output the union
-R <file>[:<range>]	fuse fragments to input molecule(s) from file with specified mol index range range syntax: "-5,10-20,25,26,38-" (e.g. -R frags.mrv:20-)
-R<i> <file>[:<range>]	fuse R<i> definition members to input molecule(s) from file in specified index range (e.g. -R1 rdef1.mrv:5-8,19)
-R<i>:<1|2> <file>[:<range>]	fuse R<i> definition members to input molecule(s) from file in specified index range, filter molecules having 1 (2, resp.) attachment points (e.g. -R1:2 rdef1.mrv:-3,8-10)
-F	Remove small fragments, keep the largest
-c "f1OPvalue&f2OPvalue..."	Filtering by the values of fields in the case of SDF import. OP may be: =,<,>,<=,>=
--mol-fields-to-records	Convert molecule type fields to separate records.
-v	Verbose
-vv	Very verbose (print stack trace at error)
-n	Skip valence checking
-2[:options][:F<i1><i2>...,<iN>]	Calculate 2D coordinates Options for coordinate calculation. Performs partial clean with fixed atom coordinates for atoms <i1><i2>...,<iN> (1-based indexes) if the F parameter is specified.
-3[:options]	Calculate 3D coordinates Options for coordinate calculation.
-H3D	Detailed list on Clean3D options

Import options can be specified between braces, in one of the following forms:

filename{options}
filename{MULTISET,options}	to merge molecules into one that contains multiple atom sets
filename{format:}	to skip automatic format recognition
filename{format:options}
filename{format:MULTISET,options}

Export options are the same as the cml and mrv export options.

You can also pass options to Java VM when you run the application from command line.

Examples

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