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By default the input file index of the molecule is used as molecule ID. This parameter is only used if the output is in text table form (neither `-sdf-output` nor `-mrv-output` is specified).

The parameter `-id` parameter specifies the input SDF file tag that stores the molecule ID to be written in the output table.The display of table header and molecule ID column can be altered in the `-do-not-display` option. If neither `-sdf-output` nor `-mrv-output` are specified, then the calculation results are shown in text table form.Not every calculation has this decorated molecule output. Atomic results are written into atom labels, while molecular results are displayed as molecule properties. If the `-mrv-output` parameter is given, then the decorated result molecules are written in MRV format.If the `-sdf-output` parameter is given, then the input molecules are written in SDF format and the calculation results are added in SDF file tags.This option has no effect in `-sdf-output` and `-mrv-output` output modes. If the `-do-not-display` parameter is specified, then no molecule ID and/or table header is displayed.The command line parameter `-tag` specifies the SDF file tag name to be used when storing the calculation results in an SDF file.Some notes on the command line parameters: The syntax of commands can be different under various command line shells, e.g. `cxcalc totalchargedensity in.mol = ` `cxcalc totalChargeDensity in.mol`.`cxcalc logp in.mol = ` `cxcalc logP in.mol`.Plugin IDs are not case-sensitive, you can alter upper- and lower case letters if you like, e.g. If more plugins are given, then all calculations are performed for the input molecules. Input files can be given both on the general option side and on the plugin specific option side, in both cases these input files/strings give the input molecules for the calculations. You can also pass some JVM options to the Java Virtual Machine as command line arguments. Logging to file and SMILES when logging to Timelimit= only execution times above the specifiedДЇormat= log file format default is SDF when Time log calculation execution time calculation log-options list of logger options, separated by ',' Warning log warning and error level information

v, -verbose print calculation warnings to the console g, -ignore-error continue with next molecule on error

Plugin results are written in table form) M, -mrv-output result molecule output in MRV format S, -sdf-output SDF output with results in SDF tags i, -id the name of the existing SDFile tag that t, -tag name of the SDFile tag to store the o, -output output file path (default: standard output) The following general (that can be used for every calculation function) options are available: cxcalc -h, -help this help message,Д¬xcalc -h, -help plugin specific help message By default, results are written without the input molecule in a table form, but they can also written in an SDF file as an SDF tag by adding -sdf-output. Other output formats may be available for certain plugins, see the plugin specific options for the plugin. The order of the results corresponds to the order of the atoms determined by their atom indices. If the calculation gives a separate number for each atom in the molecule, it is written as a list of numbers separated by semicolons. If the result refers to the entire molecule, it is written as a single number. If no input file name or SMILES string is given in the command line, input molecules are read from the standard input.Д¬xcalc writes calculation results in a format that is based on the specified tags. Most molecular file formats are accepted (e.g. In this case calculations are run in the order of invocation.Д¬xcalc takes molecules from text files or from SMILES strings. Two or more plugins can also be invoked with its own parameters within one command. The command has the following syntax: cxcalc It can also be used to train some of the calculators.

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This manual gives a walk-through on how to use cxcalc command line tool:Д¬xcalcis the command line version of ChemAxon's Calculator Plugins.Д¬xcalc performs plugin calculations in a uniform way: it processes general input, output parameters and SDF file tag names and also plugin specific parameters that are different for each plugin.