dProperties Command Line Interface

The dProperties command-line interface (CLI for short) allows the execution of dProperties as a background application. This mode can be very useful when dProperties is used into a calculation pipeline together with other software, or when processing very large datasets. The dProperties CLI recalls the same calculation engine of dProperties graphical user interface, thus all information and limitations about properties calculation are the same as reported in other sections of this help.

 

dProperties CLI can be run by invoking its executable dProperties_shell from a command-line environment, i.e. command prompt under Windows or any shell (like sh, bash etc.) under Linux. dProperties_shell CLI accepts the following parameters:

 

Usage: dProperties_shell <input_type_options> [molecule_file_name] <output_type_options> [output_file_name]

 

Input type options:

-m <molecule_file_name>/--molecule<=molecule_file_name>: calculates properties on <molecule_file_name>

--msmi[=molecule_file_name]: calculates properties on [molecule_file_name] if specified, otherwise gets the molecules from the standard input (SMILES file format)

--mmdl[=molecule_file_name]: calculates properties on [molecule_file_name] if specified, otherwise gets the molecules from the standard input (MDL/SDF file format)

--mhin[=molecule_file_name]: calculates properties on [molecule_file_name] if specified, otherwise gets the molecules from the standard input (HYPERCHEM file format)

--mmacromodel[=molecule_file_name]: calculates properties on [molecule_file_name] if specified, otherwise gets the molecules from the standard input (MACROMODEL file format)

--msybyl[=molecule_file_name]: calculates properties on [molecule_file_name] if specified, otherwise gets the molecules from the standard input (SYBYL file format)

-a/--add_hydrogens: adds missing 2D hydrogens to the molecules

 

Output type options:

-t [output_file_name]/--text[=output_file_name]: saves the calculated properties on a TABBED text file [output_file_name] if specified, otherwise sends the results to the standard output

-s [output_file_name]/--sdf[=output_file_name]: saves the calculated properties on a SD file [output_file_name] if specified, otherwise sends the results to the standard output

-d [output_file_name]/--dragon_sdf[=output_file_name]: saves the calculated properties on a SD file using Dragon Bond Orders [output_file_name] if specified, otherwise sends the results to the standard output

--xc[=output_file_name_calculated]: saves the properties for 'calculated' molecules on [output_file_name_calculated] if specified, otherwise omits to save properties for 'calculated' molecules

--xw[=output_file_name_warned]: saves the properties for 'warned' molecules on [output_file_name_warned] if specified, otherwise omits to save properties for 'warned' molecules

--xr[=output_file_name_rejected]: saves the properties for 'rejected' molecules on [output_file_name_rejected] if specified, otherwise omits to save properties for 'rejected' molecules

-o/--omit_labels: omits molecule and property labels when saving the properties as TABBED text file. Can be used only if -t/--text options has been selected

--add_status: adds a column including the molecule status (0-calculated, 1-rejected, 2-warned) when saving the properties as TABBED text file. Can be used only if -t/--text options has been selected

--logsdf: saves log messages in the SD file as <DRAGON_LOG> tag. Can be used only if -s/--sdf or -d/--dragon_sdf options have been selected

 

Additional options:

-i <license_file_name>/--install_license<=license_file_name>:  install <license_file_name>

-g/--global:  license is installed for global usage rather than only for local user

-l [license_file_name]/--license[=license_file_name]:  shows complete information of the given license file or of current license if no file is given

-c/--cite:  shows how to cite dProperties

-h/--help:  shows this help