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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 the codename of one of the supported formats. Some example:

Format typeCodename of the format
Document formats

mrv, cdx, cdxml, skc

Molecule file formats

mol rgf sdf rdf csmol, csrgf, cssdf, csrdf , csv,

cml , smarts, cxsmarts, smiles, cxsmiles, abbrevgroup, peptide

sybylmol2, pdb, xyz, inchi, inchikey, name

Graphics formats

jpeg, msbmp, png, pov, svg, emf, tiff, eps

Compression and Encoding

gzip, base64

Alternatively, use  

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

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

From files having doc, docx, ppt, pptx, xls, xls, odt, pdf, xml, html or txt format, Molconvert is able to recognize the name of compounds and convert it to any of the above mentioned output formats.

Options

Export options can be specified in the format string. The format descriptor and the options are separated by a colon, the options by commas.


-o fileWrite output to specified file instead of standard output
-mProduce multiple output files
-e charsetSet 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 stringRead 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 importoptions (can be omitted)
-f <string>Specify the import format and options
--smiles stringRead molecule from specified SMILES string
--smarts stringRead molecule from specified SMARTS string
--peptide stringRead molecule from specified peptide string
-gContinue with next molecule on error (default: exit on error)
-YRemove 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)
-Ufuse 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)
-FRemove small fragments, keep the largest
-c"f1 OP value&f2 OP value..."Filtering by the values of fields in the case of SDF import.
OP may be: =,<,>,<=,>=
--mol-fields-to-recordsConvert molecule type fields to separate records.
-vVerbose
-vvVery verbose (print stack trace at error)
-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 Fparameter is specified.
-3 [ : options]Calculate 3D coordinates
Options for coordinate calculation.
-H3D Help on options for 3D calculations. Detailed list on Clean 3d 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} 

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

 

Options:

 mrv

a, +a, +a_gen
General aromatization. Example: "XXX:a"
a_bas
Basic aromatization. Example: "XXX:a_bas"
a_loose 
Loose aromatization. Example: "XXX:a_loose"
a_ambig
Ambiguous aromatization. Example: "XXX:a_ambig"
-a, -a_gen
General Dearomatization. Example: "XXX:-a"
-a_huckel
Huckel dearomatization. Example: "XXX:-a_huckel"
-a_huckel_ex
Huckel dearomatization, throwing exception in case of failure. Example: "XXX:-a_huckel_ex"
H, +H
Add explicit Hydrogen atoms. Example: "XXX:H"
-H
Remove explicit Hydrogen atoms. Example: "XXX:-H"

Here, XXX can be any molecule or image format like mrv, mol, smiles, cxsmiles, abbrevgroup, cml, jpeg, png or svg, but aromatization options have no effect on formats which do not store bond orders like cube, pdb and xyz.

 cdx, cdxml

a, +a, +a_gen
General aromatization. Example: "XXX:a"
a_bas
Basic aromatization. Example: "XXX:a_bas"
a_loose 
Loose aromatization. Example: "XXX:a_loose"
a_ambig
Ambiguous aromatization. Example: "XXX:a_ambig"
-a, -a_gen
General Dearomatization. Example: "XXX:-a"
-a_huckel
Huckel dearomatization. Example: "XXX:-a_huckel"
-a_huckel_ex
Huckel dearomatization, throwing exception in case of failure. Example: "XXX:-a_huckel_ex"
H, +H
Add explicit Hydrogen atoms. Example: "XXX:H"
-H
Remove explicit Hydrogen atoms. Example: "XXX:-H"

Here, XXX can be any molecule or image format like mrv, mol, smiles, cxsmiles, abbrevgroup, cml, jpeg, png or svg, but aromatization options have no effect on formats which do not store bond orders like cube, pdb and xyz.

 skc

a, +a, +a_gen
General aromatization. Example: "XXX:a"
a_bas
Basic aromatization. Example: "XXX:a_bas"
a_loose 
Loose aromatization. Example: "XXX:a_loose"
a_ambig
Ambiguous aromatization. Example: "XXX:a_ambig"
-a, -a_gen
General Dearomatization. Example: "XXX:-a"
-a_huckel
Huckel dearomatization. Example: "XXX:-a_huckel"
-a_huckel_ex
Huckel dearomatization, throwing exception in case of failure. Example: "XXX:-a_huckel_ex"
H, +H
Add explicit Hydrogen atoms. Example: "XXX:H"
-H
Remove explicit Hydrogen atoms. Example: "XXX:-H"

Here, XXX can be any molecule or image format like mrv, mol, smiles, cxsmiles, abbrevgroup, cml, jpeg, png or svg, but aromatization options have no effect on formats which do not store bond orders like cube, pdb and xyz.

 peptide

1   1-letter Peptide Sequence

3   3-letter Peptide Sequence

 inchi

Export options

CodenameExplanation
H, +H
Add explicit Hydrogen atoms.
-H
Remove explicit Hydrogen atoms.
Srel
Force relative stereo.
SAbs
Force absolute stereo
NEWPS
Narrow end of wedge points to stereocenter (default: both)
RecMet
Include reconnected metals results
FixedH
Mobile H Perception Off (Default: On)
AuxNone
Omit auxiliary information (default: Include)
NoADP
Disable Aggressive Deprotonation (for testing only)
Compress
Compressed output
DoNotAddH
Don't add H according to usual valences: all H are explicit
Key
Exports the InChIKey as well
Woff
Do not display warnings
 inchikey

Export options

CodenameExplanation
H, +H
Add explicit Hydrogen atoms.
-H
Remove explicit Hydrogen atoms.
Srel
Force relative stereo.
SAbs
Force absolute stereo
NEWPS
Narrow end of wedge points to stereocenter (default: both)
RecMet
Include reconnected metals results
FixedH
Mobile H Perception Off (Default: On)
AuxNone
Omit auxiliary information (default: Include)
NoADP
Disable Aggressive Deprotonation (for testing only)
Compress
Compressed output
DoNotAddH
Don't add H according to usual valences: all H are explicit
Key
Exports the InChIKey as well
Woff
Do not display warnings
 name

Import options


CodenameExplanation
ocr

converts names containing OCR (optical character recognition) error.
Example: convert the defective name "3-rnethyl-l-methoxynaphthalene" to SMILES

molconvert 'smiles:T*' -s '3-rnethyl-l-methoxynaphthalene' -f name:ocr
-systematic

disable conversion of systematic names

-commondisable conversion of common names (such as aspirin)
-elementsdisable conversion of the name of chemical elements, for instance carbon, sodium, .... Even though "carbon" is not converted, "methane" still is, since it is a molecule name for CH4, not an element.
-ionsdisable conversion of atomic ion syntax, for instance "Ca2+".
-groupsdisable conversion of groups and fragments, such as "oxo" or "methyl".
-casdisable the conversion of CAS registry numbers
-casNamesdisable the conversion of CAS names
nameField=FIELDsets the field/property that stores the original name. By default, the molecule title is used.
dict=PATH specify the location of the custom dictionary. Example: name:dict=C:\Users\Me\MyDictionary.smi .
webservice=URL enable the usage of a custom webservice at the given URL

Some of these options are mainly useful when configuring which names Document to Structure recognizes.

To enable an option, a + sign can be used before the option name. For instance, both forms ocr and +ocr are accepted to enable this option.

 Click here to expand...




a, +a, +a_gen
General aromatization. Example: "XXX:a"
a_bas
Basic aromatization. Example: "XXX:a_bas"
a_loose 
Loose aromatization. Example: "XXX:a_loose"
a_ambig
Ambiguous aromatization. Example: "XXX:a_ambig"
-a, -a_gen
General Dearomatization. Example: "XXX:-a"
-a_huckel
Huckel dearomatization. Example: "XXX:-a_huckel"
-a_huckel_ex
Huckel dearomatization, throwing exception in case of failure. Example: "XXX:-a_huckel_ex"
H, +H
Add explicit Hydrogen atoms. Example: "XXX:H"
-H
Remove explicit Hydrogen atoms. Example: "XXX:-H"

Here, XXX can be any molecule or image format like mrv, mol, smiles, cxsmiles, abbrevgroup, cml, jpeg, png or svg, but aromatization options have no effect on formats which do not store bond orders like cube, pdb and xyz.

mol:V2for exporting position variation bond to MDL mol v2000

 

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

    molconvert smiles foo.html