Molecular Descriptor Calculator

A fast JavaScript-based tool for calculating molecular descriptors from SMILES strings. This tool was created as an alternative to the Python/CDK-based descriptor calculator.

Features

• Process CSV files containing SMILES strings
• Calculate common molecular descriptors
• Process in chunks for efficient memory usage
• Parallel processing support
• Configurable descriptor types
• CSV output with original columns preserved (optional)

Installation

1. Make sure you have Node.js installed (v14 or higher)
2. Clone this repository
3. Install dependencies:

npm install

Usage

Basic usage:

node process-molecules.js --input data/raw/test.csv --output data/raw/output-test.csv

Full options:

node process-molecules.js --input data/raw/test.csv --output data/raw/output-test.csv --smiles-col SMILES --keep-original-cols --chunk-size 1000 --processes 4 --descriptor-type all --verbose

Command Line Options

Option	Description
--input FILE	Input file (CSV)
--output FILE	Output file
--smiles-col NAME	SMILES column name or index (for CSV)
--keep-original-cols	Keep original columns in output (for CSV)
--no-header	Input CSV has no header row
--delimiter CHAR	CSV delimiter (default: ,)
--chunk-size NUM	Number of molecules per chunk (default: 1000)
--processes NUM	Number of processes (default: number of CPU cores - 1)
--skip-errors	Skip rows with calculation errors instead of marking them
--verbose	Print verbose output
--descriptor-type TYPE	Type of descriptors to calculate (all, basic, extended)
--help	Show help message

Available Descriptors

Basic Descriptors

• logP
• molWt
• numAtoms
• numHeavyAtoms
• numBonds
• numRotatableBonds
• TPSA
• numHBondDonors
• numHBondAcceptors

Extended Descriptors (all)

• All basic descriptors plus:
• exactMolWt
• numHeteroatoms
• numRings
• numAromaticRings
• Fsp3 (fraction of sp3 hybridized carbon atoms)
• lipinskiRuleOfFive (count of violations)

Requirements

• Node.js v14+
• NPM or Yarn for dependency management

License

MIT