Module Overview

DART implements a list of commands (or modules) for the terminal which you can use to interact with the package. For the Assembler Module and the Ligand Filters Module, you will typically want to provide a configuration file in YAML format that specifies the options for the module. You can generate template configuration files using the configs module. You can use the dbinfo to get more information on the ligands in a ligand database file or the concat to concatenate multiple ligand database files into one.

usage: DARTassembler [-h] {assembler,ligandfilters,dbinfo,concat,configs} ...

Positional Arguments

module

Possible choices: assembler, ligandfilters, dbinfo, concat, configs

DART modules to choose from. See each module’s help for more information.

Sub-commands

assembler

Execute the assembler module using the provided configuration file.

Example: DARTassembler assembler --input assembler.yml

DARTassembler assembler [-h] --input INPUT [--n_max_ligands N_MAX_LIGANDS]

Named Arguments

--input

Path to a .yml file with assembler options.

--n_max_ligands

Maximum number of ligands to read in from the ligand databases. Useful for testing purposes. If None, all ligands are read in (default). When specified here, this argument overrides the value in the .yml file.

ligandfilters

Execute the ligandfilters module using the provided configuration file.

Example: DARTassembler ligandfilters --input ligandfilters.yml

DARTassembler ligandfilters [-h] --input INPUT [--n N]

Named Arguments

--input

Path to a .yml file with ligand filter options.

--n

Maximum number of ligands to read in from the database. Useful for testing purposes. If None, all ligands are read in (default). When specified here, this argument overrides the value in the .yml file.

dbinfo

Get info files (.csv & .xyz) from a .jsonlines ligand database. This can be used to browse the ligands in a database. The .csv file contains information about each ligand in the database such as stoichiometry, donors or formal charge. The concatenated .xyz file contains the 3D structures of all ligands in the database. To browse through the structures, you can use ase gui concat_LIGAND_DB.xyz.

Example: DARTassembler dbinfo --db ligand_db.jsonlines --outdir . --n 1000 --metal False

DARTassembler dbinfo [-h] [--db DB] [--outdir OUTDIR] [--n N]
                     [--metal [METAL]]

Named Arguments

--db

Path to a .jsonlines ligand database such as ligand_db.jsonlines. Use the string 'metalig' instead for the entire MetaLig database (default).

Default: 'metalig'

--outdir

Output directory for the .csv and .xyz files. By default, the current directory is used.

Default: .

--n

Maximum number of ligands to read in from the database. Useful for testing purposes. If None, all ligands are read in (default).

--metal

If True (default), a Hg pseudo metal center is included in the concatenated .xyz file. If False, only the ligand is included.

Default: True

concat

Concatenate multiple ligand databases into one.

Example: DARTassembler concat --dbs ligand_db1.jsonlines ligand_db2.jsonlines --outpath concat_ligand_db.jsonlines

DARTassembler concat [-h] --dbs DBS [DBS ...] --outpath OUTPATH [--n N]

Named Arguments

--dbs

List of paths to .jsonlines ligand databases to concatenate.

--outpath

Output filepath for the concatenated database .jsonlines file, e.g., concat_ligand_db.jsonlines.

--n

Maximum number of ligands to read in from each input ligand database. Useful for testing purposes. If None, all ligands are read in (default).

configs

Retrieve two .yml configuration files as useful templates for the assembler and ligandfilters module.

Example: DARTassembler configs --outdir .

DARTassembler configs [-h] [--outdir OUTDIR]

Named Arguments

--outdir

Directory to save the configuration files to. By default, the current directory is used.

Default: .