Molconvert

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

    Syntax

    Options

    Examples

    Syntax

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

    The outformat stands for one of the supported formats.

    Formats

    Format type Outformat
    Document formatsMRV ChemAxon Marvin DocumentChemDraw sketch file (CDX)ISIS/Draw sketch file (SKC) mrvcdxskc
    Molecule file formatsMDL MOLRG fileRxn fileSD fileRD fileChemAxon Compressed MolfileChemaxon Compressed Rxn fileChemAxon Compressed SDfileChemAxon Compressed RDfileSMARTSChemAxon Extended SMARTSSMILESChemAxon Extended SMILESChemAxon SMILES Abbreviated Groups1-letter Peptide Sequence3-letter Peptide SequenceTripos SYBYL molfileTripos Mol2Protein Data BankMSC XYZIUPAC InChIIUPAC InChIKeyIUPAC NameCSVGaussian cubeGaussian input output molrgfrxnsdfrdfcsmolcsrxncssdfcsrdfsmartscxsmartssmilescxsmilesabbrevgrouppeptide:1peptide:3sybylmol2pdbxyzinchiinchikeynamecsvcubegjf
    Graphics formatsjpegmsbmppngpovsvgemftiffeps jpegmsbmppngpovsvgemftiffeps
    Compression and EncodinggzipBase64 gzipbase64

    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

    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 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)
    -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

    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

    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 MDL MOL Import and Export Options

    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
    strict When it is applied, the output strictly follows the CTFile format specification (i.e. names longer than 80 characters are omitted) mol:strict
    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 {f FIELD1 ,f FIELD2 , ... } 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 [H] (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.
    x Do not import any stereochemical information. molconvert smiles "C/C=C/[C@@H]1CCC@HCC1{smiles:x}" CC=CC1CCC(C)CC1
    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]c1ccccc1instead 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.
    x
    BOM Write the UTF-8 byte order mark (BOM), if the given or the system's encoding is UTF-8.

    peptide

    Import options

    --peptide 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 sequencemolconvert peptide:3 -s "CC@HC(O)=O" convert one-letter sequence to a three-letter sequencemolconvert --peptide GAG peptide:3
    peptide:1 one-letter sequence convert the SMILES string to a one-letter sequencemolconvert peptide:1 -s "CC@HC(O)=O"

    PBD PDB import and export options

    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

    InChI

    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

    Import options

    Codename Explanation
    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
    -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.

    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® of the structure. This option uses a public internet webservice, so do not use it with confidential structures. ChemAxon assumes no liability whatsoever. Read the notice about CAS Registry Numbers® for more information. 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. This option uses a public internet webservice, so do not use it with confidential structures. ChemAxon assumes no liability whatsoever. Read the notice about CAS Registry Numbers® for more information. 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= Use at most N seconds for the name to be computed. The default timeout is currently 20 seconds (which should normally only be reached exceptionally, for very large structures). A value of 0 means no timeout.

    CSV

    Basic information about the format

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

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

    In this file we have 3 molecules, and each 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:

    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 recognizes 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,amphetamine
    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 override column names. For this he has to set the names in order. (Every definition starts with an " f " and separated by comma".) 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 column. 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 column with the " format " keyword. For example for names / smiles / smarts, etc use:

    csv:formatname
    or:
    csv:formatsmiles
    or:
    csv:formtsmarts
    etc...

    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 " f " like:

    csv:fname,fmol,fuser

    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
    MP_LABEL_VISIBLE Show M/P for any molecule. XXX:mp
    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
    <a name="src-1806960-molconvert-scale"></a>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: 0.4Note: atsiz 1.54 Å = atsiz scale points
    atomFont... Atom label font type and size in pt. atomFont:SansSerif-ITALIC-10atomFont:Times New Roman-PLAIN-10
    bondl... Bond length in pt. Default: 28 bondl42.0
    bondw... Bond spacing in C-C bond length units. Default: 0.18Note: bondw 1.54 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).
    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 "a k :#rrggbb" for atom set k , " b k :#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 Absolute 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

    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