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

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

 molconvert jpeg:w100,Q95,#ffff00 nice.mol -o nice.jpg

(creates 100x100 JPEG image on yellow background, with 95% quality)

`-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` <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`"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<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 for file formats:

MRV

a, +a, +a_gen	General aromatization	mrv:a
a_bas	Basic aromatization	mrv:a_bas
a_loose	Loose aromatization	mrv:a_loose
a_ambig	Ambiguous aromatization	mrv:a_ambig
-a, -a_gen	General Dearomatization	mrv:-a
-a_huckel	Huckel dearomatization	mrv:-a_huckel
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure	mrv:-a_huckel_ex
H, +H	Add explicit Hydrogen atoms	mrv:H
-H	Remove explicit Hydrogen atoms	mrv:-H
+numbering	assigns atom numberings corresponding to the IUPAC name	mrv:+numbering

CDX, CDXML

a, +a, +a_gen	General aromatization	cdx:a
a_bas	Basic aromatization	cdx:a_bas
a_loose	Loose aromatization	cdx:a_loose
a_ambig	Ambiguous aromatization	cdx:a_ambig
-a, -a_gen	General Dearomatization	cdx:-a
-a_huckel	Huckel dearomatization	cdx:-a_huckel
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure	cdx:-a_huckel_ex
H, +H	Add explicit Hydrogen atoms	cdx:H
-H	Remove explicit Hydrogen atoms	cdx:-H
+numbering	assigns atom numberings corresponding to the IUPAC name	cdx:+numbering

SKC

a, +a, +a_gen	General aromatization	skc:a
a_bas	Basic aromatization	skc:a_bas
a_loose	Loose aromatization	skc:a_loose
a_ambig	Ambiguous aromatization	skc:a_ambig
-a, -a_gen	General Dearomatization	skc:-a
-a_huckel	Huckel dearomatization	skc:-a_huckel
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure	skc:-a_huckel_ex
H, +H	Add explicit Hydrogen atoms	skc:H
-H	Remove explicit Hydrogen atoms	skc:-H
+numbering	assigns atom numberings corresponding to the IUPAC name	skc:+numbering

CML

Export options

The argument of MolConverter, MolExporter and the getMol/getM functions (of the applets and beans) is the format string. The format specification ("cml") is followed by ":" and the selected option(s) for CML export.

CodeName	Explanation
a, +a, +a_gen	General aromatization.
a_bas	Basic aromatization.
a_loose	Loose aromatization.
a_ambig	Ambiguous aromatization.
-a, -a_gen	General Dearomatization.
-a_huckel	Huckel dearomatization.
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure.
H, +H	Add explicit Hydrogen atoms.
-H	Remove explicit Hydrogen atoms.
A	Atom attributes are stored in arrays. For 2D molecules, only the x, y coordinates are stored. This is a more compact form of storage than the default (using `<atom>` tags).
P	Create human readable output: put new XML elements in new lines and indent for embedded elements.
CN	The accuracy of the exported coordinates can be given: N is the length of the decimals of the coordinate, 0 < N ≤ 9
D	This option is important if the molecule has parity information and has 0 dimension. By default during the export, a clean method is invoked on the structure and the generated coordinates and wedge information are exported into CML format but NOT the parity information. However, using this option coordinates and wedge information are not generated but parity information is exported. Attention: When a CML file containing parity information is imported to Marvin older than 5.8, the parity information will be displayed wrong!
I	Ignore unexportable molecule properties. Without this option the exporter will throw an exception when reach an unexportable property.
BOM	Write the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8.

For example: cml:A or cml:C5.

MDL MOL

Import options

Codename	Explanation
Xsg	Expand all S-groups.
Usg	Ungroup all S-groups.
Fsg	Ungroup S-groups with 3 or more attachment points.
bXXX	Set the C-C bond length used in the molfile. The molecule file is supposed to store coordinates in 1.54Å/XXX units. Marvin uses Å units internally, thus coordinates are rescaled by factor 1.54/XXX at import if XXX is a nonzero number. If XXX = 0, then coordinates are not rescaled (default setting for 3D molecules if option 'b' is not used). If XXX = A, then coordinates are rescaled to transform the molfile's average C-C bond length to 1.54 Å (default setting for 2D molecules). Examples: "caffeine.mol{b0}" or "caffeine.mol{b1.54}" (bond lengths are in angstroms), "caffeine.mol{b0.825}" (bond lengths are in ISISDraw's units), "caffeine-V3.mol{bA}" (average bond length calculation, same as default).
nomolp	Read molecule type data fields (`$DTYPE $MFMT` and `$RFMT` in RDfiles) as strings instead of Molecule objects.
skipMMRV	Neglect ChemAxon/Marvin specific lines in the properties block. Such lines are in the following format: `M MRV` ... They should be skipped if the file is converted with non-ChemAxon software, which preserved them but made them invalid, e.g. by changing the total number of atoms and bonds.
skipAtomValue	Disables the import of "Atom values" from the given ctfile.
z	Carbon atoms with "Z" as alias string are converted to R-group attachment points.

Export options

Codename	Explanation
a, +a, +a_gen	General aromatization.	XXX:a
a_bas	Basic aromatization.	XXX:a_bas
a_loose	Loose aromatization.	XXX:a_loose
a_ambig	Ambiguous aromatization.	XXX:a_ambig
-a, -a_gen	General Dearomatization.	XXX:-a
-a_huckel	Huckel dearomatization.	XXX:-a_huckel
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure.	XXX:-a_huckel_ex
H, +H	Add explicit Hydrogen atoms.	XXX:H
-H	Remove explicit Hydrogen atoms.	XXX:-H
+numbering	assigns atom numberings corresponding to the IUPAC name	XXX:+numbering
V2 or V3	Force writing V2 or V3 (extended) molfiles. The default format is V2 for simple molecules, V3 if the number of atoms or bonds exceeds 999, in case of reactions with Rgroups or there is enhanced stereo in the molecule.	mol:V3
P	Write floating point numbers with maximum precision. Only meaningful for V3 molfiles.	mol:V3P
bXXX	Set C-C bond length. If XXX is nonzero, then the exported atom coordinates are rescaled by XXX / 1.54. If XXX = 0, then coordinates are not rescaled. Examples: "mol:b0" or "mol:b1.0" (bond lengths are in angstroms), "mol:b1.0a" (set bond length, aromatize). Default: 0.825 in V2 format for 2D molecules, 1.54 (Å units) (which means no rescaling) in any other case.
ec	Convert to enhanced stereo representation, considering the chiral flag. Only meaningful with option V3. (Chiral centers are grouped into ABS or an AND stereo group, depending on the chiral flag. When the input molecule contained any enhanced stereo labels, the unlabeled stereo centers always will form a new AND group.)	mol:V3ec
ea	Convert to enhanced stereo representation, assuming absolute stereochemistry. Only meaningful with option V3. (Chiral centers are grouped into the ABS group. In case the input molecule already contains enhanced stereo labels, the behaviour is similar to the one described at option ec above.)	mol:V3ea
cc	Write CHIRAL flag if there are only ABS enhanced stereo labels in the molecule. Only meaningful with option V2.	mol:V2cc
omitClean0D	Omits the clean operation while exporting 0D molecules into ctfile format with V2 compatibility which is the default. This clean was introduced in 5.4 because the ctfile format cannot contain stereo information without coordinates.	mol:omitClean0D
BOM	Write the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8.	mol:BOM

SMILES, SMARTS

Import options

`--smiles` string	Read molecule from specified SMILES string
`--smarts` string	Read molecule from specified SMARTS string
f {fFIELD1,fFIELD2,...}	Import data fields from a multi-column file. The fields should be separated by tab character. The first column contains the SMILES/SMARTS strings, the second may contain the molecule name or the data field called FIELD1, the following columns contain the other fields.	molconvert sdf "foo.smi{fname,fID}" reads the smiles string, the name and the ID from the foo.smi file and converts it to SDF format.
d	Import with Daylight compatibility for query H. In daylight smarts, H is only considered as H atom when the atom expression has the syntax [<mass>H<charge><map>] (mass, charge and map are optional). Otherwise it is considered as query H count. Examples: [!H!#6] without d option is imported as an atom which is not H and not C. However with d option it is imported as an atom which has not one H attached, and which is not C. Use "H1" or "#1" or "#1A" instead of "H" to avoid ambiguous meaning of H. "H1" always means query H count. "#1" always means H atom, "#1A" means aliphatic H atom.
c	Ignore fixing of double bond stereo information in small rings, also ignore fixing of aromatic bonds to aliphatic if necessary. Double bonds in small rings (ring size < 8) is imported automatically with CIS stereo information. If c options is set, the double bond stereo information is not changed to CIS during the import. By default the bond is aromatic between two aromatic atom. But this is not true e.g. in case of biphenyl where the bond connecting the two aromatic ring is single. If biphenyl is represented with the SMILES string: "c1ccc(cc1)c1ccccc1" then it is necessary to set the bond between the two rings to single. If the molecule is exported by ChemAxon tools, the single bond between two aromatic atom is always explicitly written to avoid any confusion, so fixing aromatic bonds to aliphatic can be avoided.
Z	Import compressed smiles. The compressed format must be specified explicitly, as it is not recognized by the importer automatically.

After importing SMILES, invoking of MoleculeGraph.clearCashedInfo method is recommended in order to remove cashed information which results increased molecule size.

Export options

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

Codename	Explanation

a, +a, +a_gen	General aromatization.
a_bas	Basic aromatization.
a_loose	Loose aromatization.
a_ambig	Ambiguous aromatization.
-a, -a_gen	General Dearomatization.
-a_huckel	Huckel dearomatization.
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure.
H, +H	Add explicit Hydrogen atoms.
-H	Remove explicit Hydrogen atoms.
0	Do not include chirality (parity) and double bond stereo (cis/trans) information	smiles:0 (not stereo) smiles:a0 (aromatic, not stereo)
q	Obsolete option. Atom equivalences are checked by default using graph invariants at double bonds.	smiles -s "C/C=C(/C)C" results CC=C(C)C
ri	Smiles export rigorousness (i with the following values): 1. Export the most information from the molecule to SMILES or SMARTS format. Don't check anything. 5. Atoms, bonds and the molecule is checked for SMILES, SMARTS compatibility (default). 7. In addition to the checks in case of value 5, double bonds in alternating single and double bond chain are checked for correct export.	Let molecule.mrv file contain the molecule CC=CC=CC=CC where the two side double bonds are in TRANS configuration but the middle one has no CIS, TRANS information (crossed double bond, or double bond with wiggly bond). molconvert smiles:r7 m.mrv drops the exception: "Nonstereo double bond between active CIS TRANS stereo bonds. Not possible to export it correctly to SMILES" molconvert smiles m.mrv results C\C=C\C=C\C=C\C (which is incorrect in the sense that the middle bond became TRANS configuration).
s	Write query smarts. (don't write explicit H in bracket) (See query SMARTS for details.)
u	Write unique smiles (considering chirality info also [2]). Note: Use this option if you want unique smiles export.
h	Convert explicit H atoms to query hydrogen count.
Tf1:f2:...	Export f1, f2 ... SDF fields. The fields are separated by tab character. If '-' is given before the T option like '-Tf1:f2:...' then no header line is written. '*' character is used to export all fields (and name also) in the molecules. 'name' field is used to export molecule name (if no 'name' field in the molecule exists).
t	Export terminal atom with single_or_aromatic bond.	Examples: instead of [#6]-c1ccccc1 export the molecule to [#6]c1ccccc1 instead of [#6]-[#6] export the molecule to [#6][#6]
n	Export molecule name (the first line of an MDL molfile).
Z	Use compressed format, and compress the SMILES string. Note that the compressed format is not recognized by the import, so it should be specified explicitly.
BOM	Write the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8.

peptide

Import options

--peptide <string>

The string is a valid one or three letter sequence.

convert a one-letter sequence to a molfile:

molconvert --peptide FFKMLL mol -o peptide.mol

Export options

peptide:3

three-letter sequence

convert SMILES representation to a three-letter sequence
```
molconvert peptide:3 -s "C[C@H](N)C(O)=O"
```

convert one-letter sequence to a three-letter sequence
```
molconvert --peptide GAG peptide:3
```

peptide:1

one-letter sequence

convert the SMILES string to a one-letter sequence

molconvert peptide:1 -s "C[C@H](N)C(O)=O"

PBD

Import Options

H or +H	Add explicit hydrogen atoms.	PDB:H
-H	Remove explicit hydrogen atoms.	PDB:-H
c	Omit CONECT records for hetero compounds. Bonds are detected by the PDB reader modul based on local geometry unless the `b` option is specified.	`pdb:c`
b	Do not recognize bond order. All bonds either defined by CONECT records or generated by PDB import are represented as ANY bonds.	`pdb:b`

Export Options

H or +H	Add explicit hydrogen atoms.	`PDB:H`
-H	Remove explicit Hydrogen atoms.	`PDB:-H`

Export options

Codename	Explanation
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

Codename	Explanation
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

Export options

Codename	Explanation
t	converts to traditional name. This option generates a common name if one is known for the structure. Otherwise, it generates a systematic name, but sometimes uses some traditionally accepted rules instead of the strict application of the IUPAC rules, when that generates a simpler name.
i	converts to IUPAC name (default).
common	generates the most popular common name of a structure. (It fails if none is known.)
common,all	generates all common names of a structure.
source	outputs the name present in the source data (no generation).
CAS#	Fetches the CAS Registry Number(s) of the structure, using a public internet webservice. In case the structure corresponds to several CAS Registry Numbers, they are all returned, separated by commas.
singleCAS#	Fetches the CAS Registry Number of the structure, using a public internet webservice. In case the structure corresponds to several CAS Registry Numbers, the lowest one (historically assigned earlier) is returned.
ascii	Use only ASCII characters to encode the name.
timeout=<N>	Use at most N seconds for the name to be computed. The default timeout is currently 20 seconds (which should normally be reached exceptionally, for very large structures). A value of 0 means no timeout.

Import options

Codename	Explanation
ocr	converts names containig 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
-common	disable conversion of common names (such as aspirin)
-elements	disable 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.
-ions	disable conversion of atomic ion syntax, for instance "Ca2+".
-groups	disable conversion of groups and fragments, such as "oxo" or "methyl".
-cas	disable the conversion of CAS registry numbers
-casNames	disable the conversion of CAS names
nameField=FIELD	sets 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.

CSV

Basic information about the format
Import options
Export options

code:csv

Basic information about the format

CSV stands for "coma separated value" and it is very simple molecule format.

id,mol,registeting_user,note
1,C,[email protected],this is a rather common element
2,[H],[email protected],"I bet this is more common, how could you miss it?"
3,[He],[email protected],This is boring il ne reagit pas avec quoi que ce soit!

In this file we have 3 molecules, and every of them has the following information:

ID
registering_user
note

The molecule sources are in smiles. After import we get the following structures and properties:

A simple Carbon, with:
- ID = 1
- registering_user = [email protected]
- note = this is a rather common element
A simple Hydrogen, with:
- ID = 2
- registering_user = [email protected]
- note = I bet this is more common, how could you miss it?
A simple Helium, with:
- ID = 3
- registering_user = [email protected]
- note = This is boring il ne reagit pas avec quoi que ce soit!

But the user can specify molecule during import which header to use. For example this file:

id,CHEMICAL_DATA,name
1,c1ccccc1CC(N)C,amphetamin
2,c1ccccc1,benzene

Can be imported with the following settings:

csv:strucCHEMICAL_DATA

With this MolImporter recognise that CHEMICAL_DATA filed holds the structure.

Import options

Headers

Automatically recognized molecule headers

Molecule can have any ChemAxon supported formats, but they must be written in one line. The recognized molecule headers are:

mol
molecule
structure
struc
smiles
cxsmiles
smarts
cxsmarts
inchi

User defined header

User can define which header to use as identifier of the molecule column when importing structure. This can be done with the "struc" parameter.

For example this file:

id,CHEMICAL_DATA,name
1,c1ccccc1CC(N)C,amphetamin
2,c1ccccc1,benzene

Can be imported with the following settings:

csv:strucCHEMICAL_DATA

With this MolImporter recognise that CHEMICAL_DATA filed holds the structure.

Headless import

User can import CSV molecules without header, in this case csv importer must be informed that all rows are data (for this use "headless" keyword), and the which colum has the chemical structure. This can be done by defining the zero-based index of the structure column. For example the following file

7,12,4,ccCCcc,rt,gh,jk
23,1,56,COO,rf,gg,kk

Can be imported as:

csv:headless,struc3

This would import the following structure:

ccCCcc (as smiles) with the following properties:
- column_0 = 7
- column_1 = 12
- column_2 = 4
- column_3 = rt
- column_4 = gh
- column_5 = jk
COO (as smiles) with the following properties:
- column_0 = 23
- column_1 = 1
- column_2 = 56
- column_3 = rf
- column_4 = gg
- column_5 = kk

Override column names

During import user can dynamically ovverride column names. For this he has to set the names in order. (Every definition starts with an "f" and spearated by coma".) For example this file:

result,hour
S.[He],11:15:00
[He],11:10:00

can be imported as:

S.[He]
- TIME = 11:15:00
[He]
- TIME = 11:10:00

With the following params:

csv:fMOL,fTIME

In the above example the renamed headers contained an autoreconizable header name, so we did not have to specifiy molecule colum. But this can be than as it is described in Header section with the "struc" keyword.?

Molecule format

User can specify what is the format of the molecules in the molecule comulmn with the "input" keyword. For example fro names use:

csv:inputname

Export options

Define Molecule column name:

User can set the name of the molecule column with "struc" keyword, like:

csv:strucMY_MOL_COLUMN

Define headless export

User can export molecules without headers with the "headless" keyword, like:

csv:headless

Define export format

User can define which format to use when export molecule with the "format" keyword, like:

csv:formatsmarts

Define exported column header names

It is possible to define the name of the exported clumns every name must start with an "s" like:

csv:sname,smol,suser

Graphic formats

a, +a, +a_gen	General aromatization	XXX:a
a_loose	Loose aromatization	XXX:a_loose
a_ambig	Ambiguous aromatization	XXX:a_ambig
-a, -a_gen	General Dearomatization	XXX:-a
-a_huckel	Huckel dearomatization	XXX:-a_huckel
-a_huckel_ex	Huckel dearomatization, throwing exception in case of failure	XXX:-a_huckel_ex
H, +H	Add explicit Hydrogen atoms	XXX:H
-H	Remove explicit Hydrogen atoms	XXX:-H
+numbering	assigns atom numberings corresponding to the IUPAC name	XXX:+numbering
`H_off`	Do not show implicit Hydrogen labels.	XXX:`H_off`
`H_hetero`	Implicit Hydrogen labels on heteroatoms only.	XXX:H_hetero
`H_heteroterm`	Implicit Hydrogen labels on hetero- and terminal atoms (default).	XXX:H_heteroterm
`H_all`	Implicit Hydrogen labels on all atoms.	XXX:H_all
`chiral_off`	Switch off chirality support, do not show R/S labels (default).	XXX:chiral_off
`chiral_selected`	Show R/S if the chiral flag is set for the molecule.	XXX:chiral_selected
`chiral_all`	Show R/S for any molecule.	XXX:chiral_all
`noRGroups`	Do not show R-groups.	XXX:noRgroups
`noRLogic`	Do not show R-logic.	XXX:noRLogic
`w...` `h...`	Image width and height in pixels. If only one from w and h is specified, then the other will have the same value. If none of them is specified, then their values are calculated from scale. If scale is not specified, then the default size is 200x200.	`XXX:w200,h200`
`scale...`	Magnification. 1.54Å (C-C bond length) is scale pixels.
`maxscale...`	Maximizes the magnification to prevent overscaling of small molecules. It is usually set to 28, which is the scale factor for 100% magnification.
`atsiz...`	Atom label font size in C-C bond length units. Default: 0.4 Note: atsiz1.54 Å = atsiz**scale points
atomFont...	Atom label font type and size in pt.	atomFont:SansSerif-ITALIC-10 atomFont:Times New Roman-PLAIN-10
`bondl...`	Bond length in pt. Default: 28	bondl42.0
`bondw...`	Bond spacing in C-C bond length units. Default: 0.18 Note: bondw1.54 Å = bondw**scale pixels
`boldbondw...`	Width of bold bond in pt. Default: 6
bondHashSpacing...	The spacing of the hash in hashed bonds in C-C bond length units.
`wireThickness...`	Bond thickness in wireframe mode. Default: 0.064
`stickThickness...`	The stick diameter for ball and stick mode. Default: 0.1
`ballRadius...`	Ball radius for ball and stick mode. Default: 0.5
`#rrggbb`	Background color. It also determines the brightness of the CPK palette (for atoms and bonds); lighter colors are choosen automatically for dark background and conversely. Default: "#ffffff"
`#aarrggbb`	Background color with alpha value. Use alpha=0 for transparent background, e.g. "#00ffffff". Note that the alpha channel is not supported by all image formats. Default: "#ffffffff"
`transbg`	Sets the image background to transparent.
`mono`	Black & white.
`cpk`	Use CPK colors (default).
`shapely`	Use the shapely color scheme.
`group`	Use coloring based on residue sequence numbers.
`setcolors:`...	Use atom/bond set colors. Colors can be specified as a colon separated list of values. Use "ak:#rrggbb" for atom set k, "bk:#rrggbb" for bond set k. The hashmark "#" can be omitted. Human-readable color names like "red", "green", "blue" can also be used.
`wireframe`	Wireframe rendering style (default for 2D).
`wireknobs`	Wireframe with knobs - used til version 17.9. Later versions fall back to `wireframe`
`ballstick`	"Ball & stick" rendering style (default for 3D).
`spacefill`	Spacefill rendering style.
`noantialias`	Switch off antialiasing.
`amap`	Displays atom mapping.
`anum`	Displays atom numbers.
`atomNumberingType...`	Sets the type of atom numbering. Implies anum parameter. Possible values: 1 (Atom numbers) 2 (IUPAC numbering)
`lp`	Displays lone pairs.
`lpexpl`	Display the explicit lone pairs instead of the implicit lone pairs if lone pair displaying is switched on. See the `lp` parameter.
`lonePairsAsLine`	Display lone pairs as a line instead of the default two dots. This parameter has effect only if the `lp` parameter is also specified.
`downwedge_mdl`	Down wedge orientation points downward (MDL). (default)
`downwedge_daylight`	Down wedge orientation points upward (Daylight).
`anybond_auto`	Draw any bonds with dashed lines in most cases. If all bonds are generated from atom coordinates, any bonds are displayed with solid lines. (default)
`anybond_dashed`	Draw any bonds with dashed lines.
`anybond_solid`	Draw any bond with solid lines.
`noatsym`	Hide atom symbols in 3D mode.
`valprop`	Show valence property on atoms that have the valence property explicitly set.
`ez`	Show E/Z labels.
`cv_on`	Always show the atom labels of carbon atoms.
`cv_off`	Never show the atom labels of carbon atoms.
`cv_inChain`	Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.
`bondLengthVisible`	Display the length of bonds in Angstroms.
`valenceErrorVisible`	Display valence errors.
`absLabelVisible`	Set the Abolute label visibility to true.
`ligandOrderVisibility_withDef`	Active by default. Show ligand order on images only when the R-group definition is present.
`ligandOrderVisibility_on`	Show all ligand order on images for R-groups.
`ligandOrderVisibility_off`	Never show ligand order on images for R-groups.
`aprop`	Show explicitly set properties on atoms.
`liganderr`	Show ligand errors on R-groups.
`coordBondStyle_solid`	Display coordinate bond as a single bond.
`coordBondStyle_arrow`	Display coordinate bond as an arrow.
`coordBondStyleAtMulticenter_hashed`	Display coordinate bond as a dashed bond when it connects to a multicenter atom.
`coordBondStyleAtMulticenter_solid`	Display coordinate bond as a single bond when it connects to a multicenter atom.
`chargeWithCircle`	Display charge symbols in a circle.
`oneLetterPeptideDisplay`	Display peptides with their one letter abbreviation instead of the three letter abbreviation which is the default.
disableAminoAcidBondColoring	Disable the amino acid bond coloring.
`fogFactor...`	Set the fog factor scale value (integer). Default value: 0, range: 0..100.
`marginSize...`	Set the margin width in pt. Default: 10

2D defaults: H_heteroterm,w200,h200,#ffffffff,cpk,wireframe

3D defaults: H_heteroterm,w200,h200,#ff000000,cpk,ballstick

Examples:

`jpeg`	Default settings: 200x200 pixels, white background (or black in 3D).
`jpeg:w100,#ffff00`	100x100 JPEG with yellow background.
`jpeg:w100,h150`	100x150 JPEG with default background.
`png:aprop -s "C1-C10 alkyl" -o alkyl.png`	PNG showing "C1-C10 alkyl".

Examples

Example

Printing the SMILES string of a molecule in a molfile

molconvert smiles caffeine.mol
Dearomatizing an aromatic molecule:

molconvert smiles:-a -s "c1ccccc1"
Aromatizing a molecule:

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

(The default general aromatization is used.)
Aromatizing a molecule using the basic algorithm:

molconvert smiles:a_bas -s "CN1C=NC2=C1C(=O)N(C)C(=O)N2C"
Converting a SMILES file to MDL Molfile

molconvert mol caffeine.smiles -o caffeine.mol
Making an SDF from molfiles:

molconvert sdf *.mol -o molecules.sdf
Printing the encodings of SDfiles in the working directory:

molconvert query-encoding *.sdf
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
2D coordinate calculation with optimization and fixed atom coordinates for atoms 1, 5, 6:

molconvert -2:2:F1,5,6 mol caffeine.mol
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.
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}"
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}"
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}"
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
Fuse R2 definition from file, filter fragments with 1 attachment point:

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):

molconvert mrv in.mrv -R frags.mrv
Generate all common names for a structure:

molconvert "name:common,all" -s tylenol
Generate the most popular common name for a structure (It fails if none is known.):

molconvert name:common -s viagra
Generate SMILES from those molecules that names are mentioned in a file foo.html:

molconvert smiles foo.html

Molecule File Conversion with MolConverter

Syntax

Options

Options for file formats:

Export options

Import options

Export options

Import options

Export options

Import options

Export options

Import Options

Export Options

Export options

Export options

Export options

Import options

Basic information about the format

Import options

Headers

Automatically recognized molecule headers

User defined header

Headless import

Override column names

Molecule format

Export options

Define Molecule column name:

Define headless export

Define export format

Define exported column header names

Examples

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