mordred-ojmb 1.3.1

molecular descriptor calculator

🧬 mordred

A comprehensive, pure-Python molecular descriptor calculator built directly on RDKit — no external binaries, no JVM, nothing to install by hand beyond RDKit itself. Mordred computes molecular descriptors straight from an rdkit.Chem.Mol and hands results back as plain values or a ready-to-use pandas DataFrame.

✨ Features

• 🧬 1826 descriptors — 1613 2D and 213 3D descriptors covering constitutional, topological, geometrical, electronic, and other descriptor classes, computed directly through RDKit.
• ⚡ Fast & multiprocessing-ready — Calculator.map/Calculator.pandas spread work across CPU cores out of the box; hot numeric kernels (SASA, subgraph enumeration, atomic-ID trees, ...) are JIT-compiled with numba.
• 🧩 Composable — descriptors are plain Python classes; build new ones out of existing ones with ordinary arithmetic (descriptor_a + descriptor_b, descriptor_a * 2, ...).
• 📊 pandas-native output — Calculator.pandas() returns a tidy DataFrame, one row per molecule, with missing/undefined values handled for you.
• 🧯 Never silently misaligned — descriptors that fail to compute for a given molecule (missing 3D coordinates, disconnected fragments, zero-division, ...) come back as explicit, inspectable errors, never dropped without a trace.
• 💾 JSON-serializable — save and reload the exact descriptor set behind a calculation with Calculator.to_json/Calculator.from_json, for fully reproducible pipelines.
• 🖥️ Command-line interface — compute descriptors for .smi/.sdf/.mol files straight from the shell, no Python required.

✍️ Copyright and Citation Notice

This repository is Olivier J. M. Béquignon's actively maintained fork of the original mordred-descriptor/mordred by Hirotomo Moriwaki et al., modernized for current Python and dependency versions (Python 3.11+, NumPy 2.x, current RDKit/pandas/networkx), with additional bug fixes and performance work. Olivier J. M. Béquignon is not the original author of mordred.

Citing

If you use mordred in your research, please cite the original publication:

Moriwaki H, Tian Y-S, Kawashita N, Takagi T (2018) Mordred: a molecular descriptor calculator. Journal of Cheminformatics 10:4. DOI: 10.1186/s13321-018-0258-y

📦 Installation

pip install mordred-ojmb

Or from source:

git clone https://github.com/OlivierBeq/mordred.git
pip install ./mordred

🛠️ Requirements

• Python 3.11+
• RDKit

💡 Usage

Calculating descriptors

from rdkit import Chem
from mordred import Calculator, descriptors

# a calculator with every registered descriptor, 2D only
calc = Calculator(descriptors, ignore_3D=True)
print(len(calc.descriptors))  # 1613

# calculate for a single molecule
mol = Chem.MolFromSmiles("c1ccccc1")
result = calc(mol)
print(result["SLogP"])

# calculate for multiple molecules, as a pandas DataFrame
mols = [Chem.MolFromSmiles(smi) for smi in ["c1ccccc1Cl", "c1ccccc1O", "c1ccccc1N"]]
df = calc.pandas(mols)
print(df["SLogP"])

Selecting descriptor sets

Register individual descriptor modules — or individual descriptor classes/instances — instead of the full set:

from mordred import Calculator
from mordred import AtomCount, BondCount

calc = Calculator()
calc.register(AtomCount)
calc.register(BondCount)

3D descriptors

By default, ignore_3D=False, so 3D descriptors are included whenever the calculator is built from the full descriptors module — but they return missing values for any molecule without 3D coordinates. Embed a conformer first if you want them calculated:

from rdkit import Chem
from rdkit.Chem import AllChem
from mordred import Calculator, descriptors

mol = Chem.MolFromSmiles("c1ccccc1")
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)

calc = Calculator(descriptors, ignore_3D=False)
result = calc(mol)
print(result["GeomDiameter"])

Descriptor arithmetic

Descriptors are ordinary Python objects and compose with +, -, *, /, and more:

from rdkit import Chem
from mordred import ABCIndex, Chi

benzene = Chem.MolFromSmiles("c1ccccc1")

abci = ABCIndex.ABCIndex()
chi_p2 = Chi.Chi(type="path", order=2)

abci_x_chi_p2 = abci * chi_p2
print(abci_x_chi_p2, abci_x_chi_p2(benzene))

JSON serialization

Save the exact descriptor set behind a calculation, and reload it later for a fully reproducible pipeline:

import json
from mordred import Calculator, descriptors

calc = Calculator(descriptors)
serialized = json.dumps(calc.to_json())

calc2 = Calculator.from_json(json.loads(serialized))
assert calc.descriptors == calc2.descriptors

Command line

python -m mordred molecules.smi -o descriptors.csv

Accepts .smi, .sdf, and .mol input (auto-detected from the extension, or set explicitly with -t); run python -m mordred -h for the full option list.

📄 License

This project is licensed under the BSD-3-Clause License - see the LICENSE file for details. Original work Copyright (c) 2015-2017, Hirotomo Moriwaki.

📚 API Documentation

Calculator(descs=None, version=None, ignore_3D=False, config=None)

The main entry point: a registry of descriptors bound to computation logic.

Parameters

• descs : Descriptor-like, optional Descriptors to register on construction — anything accepted by register below.
• version : str, optional Mordred version to register descriptor presets for; defaults to the installed version.
• ignore_3D : bool Skip descriptors that require 3D coordinates.
• config : dict, optional Global configuration dictionary, shared by all registered descriptors.

Attributes

• descriptors : tuple[Descriptor, ...] All currently registered descriptors, in registration order. Settable and deletable.

Methods

• register(desc, version=None, ignore_3D=False) Register a descriptor, descriptor class, module, or any iterable of the above. A descriptor class is expanded via its .preset() method (e.g. AtomCount registers one instance per atom type); a module registers every descriptor-like object it exposes.
• __call__(mol, id=-1) → Result Calculate every registered descriptor for a single rdkit.Chem.Mol. id selects the conformer used for 3D descriptors. Returns a Result, a dict-and-sequence-like mapping from descriptor to value (or to an Error if that descriptor failed for this molecule).
• map(mols, nproc=None, quiet=False, id=-1, **kwargs) → Iterator[Result] Calculate over an iterable of molecules, optionally in parallel (nproc processes; defaults to all available CPU cores). kwargs are forwarded to the tqdm progress bar.
• pandas(mols, conf_id=-1, decimals=3, fill_na=0, nproc=None, quiet=False, dtype=np.float32, **kwargs) → pd.DataFrame Calculate over an iterable of molecules and return a tidy DataFrame, one row per molecule, with missing/undefined/absurdly-large values replaced by fill_na and results rounded to decimals places.
• to_json() → list[dict] Serialize the registered descriptor set to a JSON-compatible structure.
• Calculator.from_json(obj) (classmethod) → Calculator Build a Calculator back from the output of to_json.

---

Descriptor

Base class for every descriptor family (AtomCount, Chi, SLogP, ...). Concrete descriptors are plain Python objects: instantiate them directly (Chi.Chi(type="path", order=2)), or call SomeDescriptor.preset(version) to get every parametrization mordred registers by default for that family. Descriptor instances are directly callable on a single molecule (descriptor(mol)), comparable/hashable, and composable with standard arithmetic operators.

Notable attributes

• explicit_hydrogens : bool Whether this descriptor needs explicit hydrogens on the input molecule.
• require_3D : bool Whether this descriptor needs 3D coordinates.
• description() → str Human-readable description of this specific descriptor instance.

---

Result

A dict-and-sequence-like mapping from descriptor to value (or Error), returned by Calculator.__call__/map. Index by descriptor name (result["SLogP"]), by position, or iterate with .items()/.keys()/.values().

Methods

• fill_missing(value=nan) → Result Replace missing/errored values with value.
• drop_missing() → Result Drop missing/errored values entirely.