Molconvert - User guide¶

Syntax¶

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

The outformat stands for one of the supported formats.

Chemical Formats

Format owner	Format name	Format type	Outformat value
Chemaxon	Marvin Document (MRV)	Document	mrv
Chemaxon	Chemaxon Object Notation (CXON)	Document	cxon
Chemaxon	Chemaxon Compressed Molfile	Molecule	csmol csrxn cssdf csrdf
Chemaxon	Chemaxon Extended SMILES	Molecule	cxsmiles
Chemaxon	Chemaxon Extended SMARTS	Molecule	cxsmarts
Chemaxon	Chemaxon SMILES Abbreviated Groups	Molecule	abbrevgroup
PerkinElmer Informatics	ChemDraw sketch file (CDX)	Document	cdx
Dassault Systemes	ISIS/Draw sketch file (SKC)	Document	skc
Dassault Systemes	CTFile formats	Molecule	mol rgf rxn sdf rdf
Daylight	SMILES	Molecule	smiles
Daylight	SMARTS	Molecule	smarts
IUPAC/InChI Trust	IUPAC InChI	Molecule	inchi
IUPAC/InChI Trust	IUPAC InChIKey	Hash	inchikey
IUPAC	IUPAC Name	Molecule	name
	Peptide Sequence	Molecule	peptide
	CSV	N/A	csv

Image Formats

Format name	Outformat value
Portable Network Graphics	png
MS Bitmap	bmp
JPEG	jpeg
Enhanced Windows Metafile	emf
Tag Image File Format	tiff
Encapsulated PostScript	eps

Molconvert 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 importoptions (can be omitted)
`-f` string	Specify the import format and options
`--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`	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` [:]	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>` [:]	fuse R definition members to input molecule(s) from file in specified index range (e.g. -R1 rdef1.mrv:5-8,19)
`-R<i>:<1\|2>` [:]	fuse R 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)
`-T "<f1>:<f2>:..."`	Export molecule properties , , ... with the result separated by tab characters. Supported in SMILES, SMARTS, CXSMILES, CXSMARTS, InChI, InChIKey (where the result is a single line). There is an option to export all properties with `-T "*"`.
`-F`	Remove 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-records`	Convert molecule type fields to separate records.
`-v`	Verbose
`-vv`	Very verbose (print stack trace at error)
`-2` [ `:` options] [ `:` F...,]	Calculate 2D coordinates Options for coordinate calculation. Performs partial clean with fixed atom coordinates for atoms ..., (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

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:

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

Format specific options¶

Format name	Export options	Import opions
MRV	>>
CXSMARTS,CXSMILES	>>	>>
CTFile formats (MOL, SDF, RXN, RDF, RGF)	>>	>>
SMILES, SMARTS	>>	>>
InChI,InChIKey	>>
Name	>>
Peptide	>>	>>

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

Examples¶

Example

Printing the SMILES string of a molecule in a molfile
1
molconvert smiles caffeine.mol
Dearomatizing an aromatic molecule:
1
molconvert smiles:-a -s "c1ccccc1"
Aromatizing a molecule:
1
molconvert smiles:a -s "C1=CC=CC=C1"
(The default general aromatization is used.)

Aromatizing a molecule using the basic algorithm:

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

Converting a SMILES file to MDL Molfile

1	`molconvert mol caffeine.smiles -o caffeine.mol`

Making an SDF from molfiles:
1
molconvert sdf *.mol -o molecules.sdf
Printing the encodings of SDfiles in the working directory:
1
molconvert query-encoding *.sdf
SMILES to Molfile with optimized 2D coordinate calculation, converting double bonds with unspecified cis/trans to "either"
1
molconvert -2:2e mol caffeine.smiles -o caffeine.mol
2D coordinate calculation with optimization and fixed atom coordinates for atoms 1, 5, 6:
1
molconvert -2:2:F1,5,6 mol caffeine.mol
Import a file as XYZ, do not try to recognize the file format:
1
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.
Import a file as XYZ, with bond-length cut-off = 1.4, and max. number of Carbon connections = 4, export to SMILES:
1
molconvert smiles "foo.xyz{f1.4C4}"
Import a file as Gzipped XYZ, with the same import options as in the previous example:
1
molconvert smiles "foo.xyz.gz{gzip:xyz:f1.4C4}"
Like the previous example but merge the molecules into one molecule that contains multiple atom sets. MDL molfile is exported.
1
molconvert mol "foo.xyz.gz{gzip:xyz:MULTISET,f1.4C4}"
Import an SDF and export a table containing selected molecules with columns: SMILES, ID, and logP:
1
molconvert smiles -c "ID<=1000&logP>=-2&logP<=4" -T "ID:logP" foo.sdf
Fuse R2 definition from file, filter fragments with 1 attachment point:
1
molconvert mrv in.mrv -R2:1 rdef.mrv
Fuse fragments from file (note, that the input molecule, which the fragments are fused to, should also be specified):
1
molconvert mrv in.mrv -R frags.mrv

Generate all common names for a structure:

1	`molconvert "name:common,all" -s tylenol`

Generate the most popular common name for a structure (It fails if none is known.):
1
molconvert name:common -s viagra
Generate SMILES from those molecules that names are mentioned in a file foo.html:
1
molconvert smiles foo.html