chem

chem subcommand [ options ] [ arguments ]
chem [ options ] input_file [ output_file ]

subcommand
    Specifies the operation to perform. Common subcommands might include convert (for format conversion), info (for displaying molecular information), calc (for calculating properties), or clean (for structural manipulation).

-h, --help
    Displays help information for the command or a specific subcommand.

-v, --version
    Prints the version of the chem utility.

-i format, --input-format=format
    Explicitly specifies the input file format (e.g., smi, sdf, mol2, pdb). If omitted, the command attempts to autodetect the format.

-o format, --output-format=format
    Explicitly specifies the output file format. This option is typically used with the convert subcommand or when writing results to a new file.

--add-hydrogens
    Adds implicit hydrogens to the molecular structure, making them explicit. Useful for certain calculations or conversions.

--remove-hydrogens
    Removes explicit hydrogens from the molecular structure, converting them back to implicit where appropriate.

--standardize
    Applies a set of standardization rules to the chemical structure (e.g., normalizing tautomers, representing salts consistently).

-p property, --property=property
    Used with the calc subcommand to specify a molecular property to calculate (e.g., mw for molecular weight, logp for octanol-water partition coefficient, tpsa for topological polar surface area).

-s SMILES_string, --smiles=SMILES_string
    Provides chemical input directly as a SMILES string, bypassing file input.

input_file
    The path to the input chemical file containing structures or data. Required for most operations.

output_file
    The path where the output chemical data or results should be written. If omitted, output typically goes to standard output (stdout).

The chem command, in this conceptual analysis, represents a hypothetical command-line utility designed for basic manipulation and analysis of chemical structures and data within a Linux environment. While not a standard or universally available command in most Linux distributions, its purpose would be to streamline common tasks encountered in computational chemistry, cheminformatics, and drug discovery workflows.

Such a utility would typically offer functionalities like converting between various chemical file formats (e.g., SMILES, SDF, Mol2, PDB), calculating fundamental molecular properties (e.g., molecular weight, exact mass, logP, TPSA), and performing basic structural modifications (e.g., adding or removing hydrogens, sanitizing structures, generating 2D coordinates).

Its primary value would lie in enabling quick, scriptable operations on chemical datasets, facilitating automation, batch processing, and integration with other command-line tools. It would serve as a convenient front-end for underlying cheminformatics libraries and toolkits, abstracting complex operations into simple, intuitive commands.

It is crucial to note that chem is not a standard, universally installed Linux command. This analysis describes a conceptual or hypothetical command that aggregates common cheminformatics functionalities. Actual implementations of such features are provided by specialized software packages and libraries like Open Babel (obabel command), RDKit (Python library), ChemAxon tools, or custom scripts utilizing these underlying frameworks. The behavior and exact options of any real chem-named command would depend entirely on its specific development and purpose.

Below are some examples of how a conceptual chem command might be used:

1. Convert SDF to SMILES:
chem convert -i sdf -o smi input.sdf output.smi
or simply:
chem input.sdf output.smi -o smi

2. Calculate Molecular Weight from SMILES:
chem calc --property=mw --smiles="CCO"

3. Add Hydrogens and Standardize a Molecule:
chem clean --add-hydrogens --standardize input.mol output_cleaned.mol

4. Get Information about a Molecule:
chem info molecule.mol

A real-world chem command would likely be a wrapper script or compiled program leveraging powerful open-source cheminformatics libraries such as:
- Open Babel: For extensive file format support and basic cheminformatics functionalities.
- RDKit: A robust toolkit for cheminformatics, machine learning, and property calculations.
- CDK (Chemistry Development Kit): Another comprehensive Java-based toolkit for cheminformatics.

The concept of a unified command-line tool for chemistry operations stems from the long-standing need for efficient data manipulation in computational chemistry. Historically, various tasks were handled by disparate, often specialized, programs from different research groups or software vendors. Tools like Open Babel emerged as comprehensive solutions for chemical file format interconversion and basic property calculation, effectively serving as the de facto 'chem' utility in many contexts. While no single command was formally named chem across Linux distributions, the underlying functionalities have evolved significantly with advancements in cheminformatics libraries and the increasing demand for automation in scientific workflows.

obabel(1), babel(1)