MolVoxel: Molecular Voxelization Tool

MolVoxel is an Easy-to-Use Molecular Voxelization Tool implemented in Python.

It requires minimal dependencies, so it's very simple to install and use. If you want to use numba version, just install numba additionally.

Dependencies

• Required
  • Numpy, SciPy
• Optional
  • Numba
  • PyTorch, CUDA Available
  • RDKit, pymol-open-source

Citation

@article{seo2023pharmaconet,
  title = {PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling},
  author = {Seo, Seonghwan and Kim, Woo Youn},
  journal = {arXiv preprint arXiv:2310.00681},
  year = {2023},
  url = {https://arxiv.org/abs/2310.00681},
}

Quick Start

Installation

pip install molvoxel
pip install molvoxel[numba, torch, rdkit]	# Optional Dependencies

Configuring Voxelizer Object

import molvoxel
# Default (Resolution: 0.5, dimension: 64, density_type: gaussian, sigma: 0.5, library='numpy')
voxelizer = molvoxel.create_voxelizer()
# Set gaussian sigma = 1.0, spatial dimension = (48, 48, 48) with numba library
voxelizer = molvoxel.create_voxelizer(dimension=48, density_type='gaussian', sigma=1.0, library='numba')
# Set binary density with torch library
voxelizer = molvoxel.create_voxelizer(density_type='binary', library='torch')
# CUDA
voxelizer = molvoxel.create_voxelizer(library='torch', device='cuda')

Voxelization

Numpy, Numba

from rdkit import Chem  # rdkit is not required packages
import numpy as np

def get_atom_features(atom):
    symbol, aromatic = atom.GetSymbol(), atom.GetIsAromatic()
    return [symbol == 'C', symbol == 'N', symbol == 'O', symbol == 'S', aromatic]

mol = Chem.SDMolSupplier('./test/10gs/10gs_ligand.sdf')[0]
channels = {'C': 0, 'N': 1, 'O': 2, 'S': 3}
coords = mol.GetConformer().GetPositions()                                      # (V, 3)
center = coords.mean(axis=0)                                                    # (3,)
atom_types = np.array([channels[atom.GetSymbol()] for atom in mol.GetAtoms()])  # (V,)
atom_features = np.array([get_atom_features(atom) for atom in mol.GetAtoms()])  # (V, 5)
atom_radius = 1.0                                                               # scalar

image = voxelizer.forward_single(coords, center, atom_radius)                   # (1, 64, 64, 64)
image = voxelizer.forward_types(coords, center, atom_types, atom_radius)        # (4, 64, 64, 64)
image = voxelizer.forward_features(coords, center, atom_features, atom_radius)  # (5, 64, 64, 64)

PyTorch - Cuda Available

# PyTorch is required
import torch

device = 'cuda' # or 'cpu'
coords = torch.FloatTensor(coords).to(device)               # (V, 3)
center = torch.FloatTensor(center).to(device)               # (3,)
atom_types = torch.LongTensor(atom_types).to(device)        # (V,)
atom_features = torch.FloatTensor(atom_features).to(device) # (V, 5)

image = voxelizer.forward_single(coords, center, atom_radius)                   # (1, 64, 64, 64)
image = voxelizer.forward_types(coords, center, atom_types, atom_radius)        # (4, 32, 32, 32)
image = voxelizer.forward_features(coords, center, atom_features, atom_radius)  # (5, 32, 32, 32)

Voxelization

Input

• $X \in \mathbb{R}^{N\times3}$ : Coordinates of $N$ atoms
• $R \in \mathbb{R}^N$ : Radii of $N$ atoms
• $F \in \mathbb{R}^{N\times C}$ : Atomic Features of $N$ atoms - $C$ channels.

Kernel

$d$: distance, $r$: atom radius

Gaussian Kernel

$\sigma$: gaussian sigma (default=0.5)

$$ f(d, r, \sigma) = \begin{cases} \exp \left( -0.5(\frac{d/r}{\sigma})^2 \right) & \text{if}~d \leq r \ 0 & \text{else} \end{cases} $$

Binary Kernel

$$ f(d, r) = \begin{cases} 1 & \text{if}~d \leq r \ 0 & \text{else} \end{cases} $$

Output

• $I \in \mathbb{R}^{D \times H \times W \times C}$ : Output Image with $C$ channels.
• $G \in \mathbb{R}^{D\times H\times W \times 3}$ : 3D Grid of $I$.

$$ I_{d,h,w,:} = \sum_{n}^{N} F_n \times f(||X_n - G_{d,h,w}||,R_n,\sigma) $$

RDKit Wrapper

# RDKit is required
from molvoxel.rdkit import AtomTypeGetter, BondTypeGetter, MolPointCloudMaker, MolWrapper
atom_getter = AtomTypeGetter(['C', 'N', 'O', 'S'])
bond_getter = BondTypeGetter.default()		# (SINGLE, DOUBLE, TRIPLE, AROMATIC)

pointcloudmaker = MolPointCloudMaker(atom_getter, bond_getter, channel_type='types')
wrapper = MolWrapper(pointcloudmaker, voxelizer, visualizer)
image = wrapper.run(rdmol, center, radii=1.0)