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 specifiedįormat= 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,Ĭxcalc -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.Ĭxcalc 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.Ĭxcalc 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.
This manual gives a walk-through on how to use cxcalc command line tool:Ĭxcalcis the command line version of ChemAxon's Calculator Plugins.Ĭxcalc 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.
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