There are some built-in calculations such as charge, pKa, logP and logD computations that can be evaluated in demo mode or purchased from ChemAxon. See the Calculator Plugins guide for the details of these calculations.
Other calculations can be added by writing custom plugins as described in the Plugin Developer's Guide.
- Download and launch platform specific installer by following the installation instructions.
cxcalc [general options] [input files] <plugin> [plugin options] [input files]
cxcalc [general options] [input files] <plugin1> [plugin1 options] [input files] <plugin2> [plugin2 options] [input files] ...
cxcalc -h, --help this help message cxcalc <plugin> -h, --help plugin specific help message -o, --output <filepath> output file path (default: stdout) -t, --tag name of the SDFile tag to store the calculation results default tag name: see plugin help -i, --id SDFile tag that stores the molecule ID in the input SDF (default: molecule index) -N, --no-header do not display table header (in text mode) -S, --sdf-output SDF output (otherwise only plugin result) -g, --ignore-error continue with next molecule on error -v, --verbose print calculation warnings to the console
Input files can be given both on the general option side and on the plugin specific option side, in either case these input files give the input molecules for the calculations. If more plugins are given then all plugin calculations are performed for all input molecules.
The available plugins are configured in one or more configuration files.
First the chemaxon/marvin/calculations/calc.properties
configuration file is read.
User-defined plugins may be configured
in this file or in separate files, listed in the rcfiles
property.
The built-in plugin configuration file is
chemaxon/marvin/calculations/calc.properties
which contains data for the built-in plugins that can be purchased from
ChemAxon. This file path is the default value of the
rcfiles
property.
The configuration file path is taken relative to the directories specified in the
CLASSPATH
environment variable.
A detailed description of the configuration file is given below.
The command line parameter --tag
specifies the SDF file tag name to be used
when storing the calculation results in an SDF file.
If the --no-header
parameter is specified then no table header is displayed.
This option has no effect in --sdf-output
mode.
If the --sdf-output
parameter is given, then the input molecules are
written in SDF format and the calculation result is added as an SDF file tag, otherwise
only the calculation result is shown in table form.
The parameter --id
parameter specifies the input SDF file tag that stores the
molecule ID to be written in the output table. This parameter is only used if output is in
table form (--sdf-output
parameter is not given). If not specified then the input
file index of the molecule is used as molecule ID.
The plugin specific help message is printed if the user types:
cxcalc <plugin> -hHere
plugin
is the plugin key from the configuration file.
Example
Typing
cxcalc logp -hproduces the help string
Calculator plugin: logp. logP calculation Usage: cxcalc [general options] [input files] logp [logp options] [input files] logp options: -h, --help this help message -p, --precision <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) -t, --type [increments|implh|logP] (default: logP) -i, --implh [true|false] implicit H logP sum shown in brackets (for incremental logP only) (default: false) Multiple parameter values should be separated by ',' characters.
The command line parameter --precision
specifies the required floating point
precision, that is, the number of required decimal digits in the output.
The command line parameter --type
specifies the result type:
increments
gives the atomic logp increment values for each atom in the molecule
while molecule
gives the overall logp value for the molecule. Both results can be
queried by specifying both types separated by a comma: -t increments,implh,logP
.
The software may take molecules from a text file. Most molecular file formats are accepted (for instance MDL molfile, Compressed molfile, SDfile, Compressed SDfile, SMILES).
If no input file name is given in the command line, then the standard input is read.
Calculator writes calculation results in a format based on the specified tags.
If the result
refers to the entire molecule, it is written as a single number.
If the calculation gives a separate number for each atom in the molecule, it is written
as a list of numbers separated by semicolons. The order of the results
corresponds to the order of the atoms determined by their atom indices. Other output formats
may be available for certain plugins, see the plugin specific options
for the specific plugin. By default, results are written without the input
molecule in a table form, but Calculation results can be written in an SDF file as an SDF tag
if the --sdf-output
parameter is specified.
The available plugins are configured in a java property file for the command line tool
calc
.
The main calculator configuration file is chemaxon/marvin/calculations/calc.properties
whose path is taken relative to the directories in the CLASSPATH
environment variable. The configuration for user plugins can either be added to this file or
can be put in separate ones. In the latter case the value of the
rcfiles
property
has to be modified to include the additional configuration file names (again, relative to the
CLASSPATH
). By default, the rcfiles
property
value contains only the configuration file path for the built-in plugins that can be purchased
from ChemAxon which is
chemaxon/marvin/calculations/calc.properties
.
The configuration file is a java property file. The format of the configuration file is best shown by an example:
rcfiles=chemaxon/marvin/calculations/calc.properties,pluginconf/plugins.properties chg=org.charge.ChargePlugin\ $p=precision:2;t=type:total;i=implh:false\ $CHARGE\ $partial charge calculation\ $-p, --precision=<floating point precision as number of\n\ fractional digits: 0-8 or inf> (default: 2);\ -t, --type=[sigma|pi|total|implh] (default: total);\ -i, --implh=[true|false] implicit H charge sum shown in brackets\n\ (for sigma and total charge only) (default: false)\ $cxcalc -S -o result.sdf -t myCHARGE charge -t pi,total -p 3 test.mol
The property rcfiles
specifies the additional configuration files that contain
plugin configurations as a comma-separated file path list, each item is taken relative to
directories in the CLASSPATH
environment variable. In this example it contains the
built-in plugin configuration file and a user defined plugin configuration file.
The key chg
is the plugin name that the plugin is
referenced by in the calc
command line tool.
The value contains the configuration for a custom (user defined) charge
plugin:
configuration items are separated by '$' characters. The '\' characters allows property values
to be expanded to multiple lines: the '\' character itself as well as leading white spaces in
the next line are ignored.
The configuration items:
<short name>=<long name>:<default value>separated by semicolons
Important: the long parameter names in the "plugin specific parameters" section must correspond to the
parameter property keys used in the plugin class in the
setParameters(Properties params)
method!
cxcalc mols.sdf pka
ID
tag of the input SDF file,
writing three significant values from each pKa type:
cxcalc mols.sdf -i ID pka -a 3 -b 3
-5
,
maximum acidic pKa to 15
:
cxcalc mols.sdf -i ID pka -a 3 -b 3 -i -5 -m 15
mols.sdf
file,
uses the default configuraion file, writes results to the standard output in SDF format
using the default SDF charge tag for storing the calculation results:
cxcalc -S charge mols.sdf
molcharges.sdf
file to be created in the
same directory:
cxcalc -S -o molcharges.sdf charge mols.sdf
cxcalc mols.sdf -S -o molcharges.sdf charge
cxcalc -S mols.sdf -o molcharges.sdf charge -t sigma,pi,total mview molcharges.sdfBy setting the
Table / Show Fields
option in MarvinView the SDF file tags
will be shown in the table cells and in this way the charge values can be seen.
cxcalc -S mols.sdf -t LOGP_BOTH logp -t increments,logP | mview -
Note, that such piping does not work in Windows.
ID
tag of the input SDF file,
output written to text file elemanal.txt
:
cxcalc -o elemanal.txt -i ID elemanal mols.sdf
mols.smiles
and output written as SDF
to elemanal.sdf
with ELEMANAL
tag name:
cxcalc -S -t ELEMANAL -o elemanal.sdf elemanal mols.smiles