digichem convert

usage: digichem convert [-h] [-I] [-V] [--log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL,OFF}] [-S [SETTING ...]] [--config_files [CONFIG_FILES ...]] [-i INPUT_FORMAT] [-o OUTPUT_FORMAT] [-O OUTPUT_FILE] [-C CHARGE] [-M MULTIPLICITY]
                        [--gen3D GEN3D] [--readable] [--writable] [--json]
                        [input_file]

Positional Arguments

input_file

Input file to read and convert.

Named Arguments

-i, --input_format

Input format (.com, .xyz, .tmol etc)

-o, --output_format

Output format (.com, .xyz, .tmol etc)

-O, --output_file

Output file

Default: “-”

-C, --charge

The molecular charge to set in the output format. Note that not all formats support a charge

-M, --multiplicity

The multiplicity to set in the output format. Note that not all formats support a multiplicity

--gen3D

Whether to generate 3D coordinates (this will scramble existing atom coordinates). The default is yes, but only if it can be safely determined that the loaded coordinates are not already in 3D)

--readable

List readable (input) formats

Default: False

--writable

List writable (output) formats

Default: False

--json

Dump the list of readable and/or writable formats in JSON

Default: False

General Options

General options that control various aspects of silico

-I, --interactive

Run this command interactively

Default: False

-V, --verbose

Increase verbosity, stack with itself to further increase verbosity (each time this option is given, log_level is increased by one stage)

--log_level

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, OFF

The level of messages to print

-S, --setting

Set a config option to a value. Options of this type are parsed as if they were a config file (in yaml format) and are then used to set corresponding options, eg -S “absorption_graph: {fwhm: 100}”

Default: []

--config_files

An additional config file to read from. See the master config file for possible config options. Note that the master config file (at silico/data/config/silico.yaml) and user config file (at ~/.config/silico/silico.yaml) are always read automatically and do not need to be specified here. Multiple files may be given and will be processed in the order specified (the last having highest priority)

Default: []