shepherd-score 1.2.2
3D scoring functions used for evaluation of ShEPhERD
License: MIT
Requires Python: >=3.9
Keywords: bioinformatics, molecular-modeling, 3d-scoring, drug-discovery, chemistry, bioisosteres

# *ShEPhERD* Scoring Functions

<div align="center">

[![PyPI version](https://img.shields.io/pypi/v/shepherd-score.svg)](https://pypi.org/project/shepherd-score/)
[![Python versions](https://img.shields.io/pypi/pyversions/shepherd-score.svg)](https://pypi.org/project/shepherd-score/)
[![Documentation Status](https://readthedocs.org/projects/shepherd-score/badge/?version=latest)](https://shepherd-score.readthedocs.io/en/latest/?badge=latest)

📄 **[Paper](https://arxiv.org/abs/2411.04130)** | 📚 **[Documentation](https://shepherd-score.readthedocs.io/en/latest/)** | 📦 **[PyPI](https://pypi.org/project/shepherd-score/)**

</div>


This repository contains the code for **generating/optimizing conformers**, **extracting interaction profiles**, **aligning interaction profiles**, and **differentiably scoring 3D similarity**. It also contains modules to evaluate conformers generated with *ShEPhERD*<sup>1</sup> and other generative models.

The formulation of the interaction profile representation, scoring, alignment, and evaluations are found in our preprint [*ShEPhERD*: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design](https://arxiv.org/abs/2411.04130). The diffusion model itself is found in a *separate* repository: [https://github.com/coleygroup/shepherd](https://github.com/coleygroup/shepherd).


<p align="center">
  <img width="200" src="./logo.svg">
</p>

<sub><sup>1</sup> *ShEPhERD*: **S**hape, **E**lectrostatics, and **Ph**armacophores **E**xplicit **R**epresentation **D**iffusion</sub>

## Table of Contents
1. [Documentation](#documentation)
2. [File Structure](#file-structure)
3. [Installation](#installation)
4. [Requirements](#requirements)
5. [Usage](#how-to-use)
6. [Scoring and Alignment Examples](#scoring-and-alignment-examples)
7. [Evaluation Examples and Scripts](#evaluation-examples-and-scripts)
8. [Data](#data)

## Documentation

Full documentation is available at [shepherd-score.readthedocs.io](https://shepherd-score.readthedocs.io/en/latest/).


## File Structure
```
.
├── shepherd_score/
│   ├── alignment_utils/                  # Alignment and rigid transformations tools
│   ├── evaluations/                      # Evaluation suite
│   │   ├── pdbs/                         # PDBQT files used in *ShEPhERD* manuscript
│   │   ├── utils/                        # Converting data types and others
│   │   ├── docking
│   │   │   ├── docking.py                # Docking classes
│   │   │   └── pipelines.py              # Docking evaluation pipelines
│   │   └── evaluate/                     # Generated conformer evaluation pipelines
│   │       ├── evals.py                  # Individual evaluation classes
│   │       └── pipelines.py              # Evaluation pipeline classes
│   ├── pharm_utils/                      # Pharmacophore definitions
│   ├── protonation/                      # Functions for protonation
│   ├── score/                            # Scoring related functions and constants
│   │   ├── constants.py
│   │   ├── electrostatic_scoring.py
│   │   ├── gaussian_overlap.py
│   │   └── pharmacophore_scoring.py
│   ├── alignment.py
│   ├── conformer_generation.py           # RDKit and xtb related functions for conformers
│   ├── container.py                      # Molecule and MoleculePair classes
│   ├── extract_profiles.py               # Functions to extract interaction profiles
│   ├── generate_point_cloud.py
│   ├── objective.py                      # Objective function used for REINVENT
│   └── visualize.py                      # Visualization tools
├── scripts/                              # Scripts for running evaluations
├── examples/                             # Jupyter notebook tutorials/examples 
├── tests/
└── README.md
```


## Installation

### Via PyPI
```bash
pip install shepherd-score
```

#### Install xTB
xTB will need to be installed manually since there are no PyPi bindings. This can be done in a conda environment, but since this approach has been reported to lead to conflicts, we suggest installing 
from [source](https://xtb-docs.readthedocs.io/en/latest/setup.html) and adding it to `PATH`.
### With optional dependencies
```bash
# JAX support (for faster scoring and alignment)
pip install "shepherd-score[jax]"

# Include docking evaluation tools
pip install "shepherd-score[docking]"

# Everything
pip install "shepherd-score[all]"
```

### For local development
```bash
git clone https://github.com/coleygroup/shepherd-score.git
cd shepherd-score
pip install -e ".[all]"
```

## Requirements

This package works where PyTorch, Open3D, RDKit, and xTB can be installed for Python >=3.9. **If you are coming from the *ShEPhERD* repository, you can use the same environment as described there.**
Core dependencies (installed automatically) which enables interaction profile extraction, scoring/alignment, and evaluations are listed below.
```
python>=3.9
numpy
torch>=1.12
open3d>=0.18
rdkit>=2023.03
pandas>=2.0
scipy>=1.10
```

> **Note**: If using `torch<=2.4`, ensure that `mkl==2024.0` with conda since there is a known [issue](https://github.com/pytorch/pytorch/issues/123097) that prevents importing torch.

#### Docking with Autodock Vina
Installing `shepherd-score[docking]` will automatically install the python bindings for Autodock Vina for the python interface. However, a manual installation of the executable of Autodock Vina v1.2.5 is required and can be found here: [https://vina.scripps.edu/downloads/](https://vina.scripps.edu/downloads/).

## Usage
The package has base functions and convenience wrappers. Scoring can be done with either NumPy or Torch, but alignment requires Torch. There are also Jax implementations for both scoring and alignment of gaussian overlap, ESP similarity, and pharmacophore similarity.

**Update 8/20/25**: Applicable xTB functions and evaluation pipeline evaluations are now parallelizable through the `num_workers` argument in the `.evaluate` method.

### Base functions
#### Conformer generation
Useful conformer generation functions are found in the `shepherd_score.conformer_generation` module.

#### Interaction profile extraction
| Interaction profile | Function |
| :------- | :------- |
| shape | `shepherd_score.extract_profiles.get_molecular_surface()` |
| electrostatics | `shepherd_score.extract_profiles.get_electrostatic_potential()` |
| pharmacophores | `shepherd_score.extract_profiles.get_pharmacophores()` |

#### Scoring
```shepherd_score.score``` contains the base scoring functions with seperate modules for those dependent on PyTorch (`*.py`), NumPy (`*_np.py`), and Jax (`*_jax.py`).

| Similarity | Function |
| :------- | :------- |
| shape | `shepherd_score.score.gaussian_overlap.get_overlap()` |
| electrostatics | `shepherd_score.score.electrostatic_scoring.get_overlap_esp()` |
| pharmacophores | `shepherd_score.score.pharmacophore_scoring.get_overlap_pharm()` |

### Convenience wrappers
- `Molecule` class
    - `shepherd_score.container.Molecule` accepts an RDKit `Mol` object (with an associated conformer) and generates user-specified interaction profiles
- `MoleculePair` class
    - `shepherd_score.container.MoleculePair` operates on `Molecule` objects and prepares them for scoring and alignment


## Scoring and Alignment Examples

Full jupyter notebook tutorials/examples for extraction, scoring, and alignments are found in the [`examples`](./examples/) folder. Some minimal examples are below.

### Extraction
Extraction of interaction profiles.

```python
from shepherd_score.conformer_generation import embed_conformer_from_smiles
from shepherd_score.conformer_generation import charges_from_single_point_conformer_with_xtb
from shepherd_score.extract_profiles import get_atomic_vdw_radii, get_molecular_surface
from shepherd_score.extract_profiles import get_pharmacophores, get_electrostatic_potential
from shepherd_score.extract_profiles import get_electrostatic_potential

# Embed conformer with RDKit and partial charges from xTB
ref_mol = embed_conformer_from_smiles('Oc1ccc(CC=C)cc1', MMFF_optimize=True)
partial_charges = charges_from_single_point_conformer_with_xtb(ref_mol)

# Radii are needed for surface extraction
radii = get_atomic_vdw_radii(ref_mol)
# `surface` is an np.array with shape (200, 3)
surface = get_molecular_surface(ref_mol.GetConformer().GetPositions(), radii, num_points=200)

# Get electrostatic potential at each point on the surface
# `esp`: np.array (200,)
esp = get_electrostatic_potential(ref_mol, partial_charges, surface)

# Pharmacophores as arrays with averaged vectors
# pharm_types: np.array (P,)
# pharm_{pos/vecs}: np.array (P,3)
pharm_types, pharm_pos, pharm_vecs = get_pharmacophores(ref_mol, multi_vector=False)
```

### 3D similarity scoring
An example of scoring the similarity of two different molecules using 3D surface, ESP, and pharmacophore similarity metrics.

```python
from shepherd_score.score.constants import ALPHA
from shepherd_score.conformer_generation import embed_conformer_from_smiles
from shepherd_score.conformer_generation import optimize_conformer_with_xtb
from shepherd_score.container import Molecule, MoleculePair

# Embed a random conformer with RDKit
ref_mol_rdkit = embed_conformer_from_smiles('Oc1ccc(CC=C)cc1', MMFF_optimize=True)
fit_mol_rdkit = embed_conformer_from_smiles('O=CCc1ccccc1', MMFF_optimize=True)
# Local relaxation with xTB
ref_mol, _, ref_charges = optimize_conformer_with_xtb(ref_mol_rdkit)
fit_mol, _, fit_charges = optimize_conformer_with_xtb(fit_mol_rdkit)

# Extract interaction profiles
ref_molec = Molecule(ref_mol,
                     num_surf_points=200,
                     partial_charges=ref_charges,
                     pharm_multi_vector=False)
fit_molec = Molecule(fit_mol,
                     num_surf_points=200,
                     partial_charges=fit_charges,
                     pharm_multi_vector=False)

# Centers the two molecules' COM's to the origin
mp = MoleculePair(ref_molec, fit_molec, num_surf_points=200, do_center=True)

# Compute the similarity score for each interaction profile
shape_score = mp.score_with_surf(ALPHA(mp.num_surf_points))
esp_score = mp.score_with_esp(ALPHA(mp.num_surf_points), lam=0.3)
pharm_score = mp.score_with_pharm()
```

### Alignment
Next we show alignment using the same MoleculePair class.

```python
# Centers the two molecules' COM's to the origin
mp = MoleculePair(ref_molec, fit_molec, num_surf_points=200, do_center=True)

# Align fit_molec to ref_molec with your preferred objective function
# By default we use automatic differentiation via pytorch
surf_points_aligned = mp.align_with_surf(ALPHA(mp.num_surf_points),
                                         num_repeats=50)
surf_points_esp_aligned = mp.align_with_esp(ALPHA(mp.num_surf_points),
                                            lam=0.3,
                                            num_repeats=50)
pharm_pos_aligned, pharm_vec_aligned = mp.align_with_pharm(num_repeats=50)

# Optimal scores and SE(3) transformation matrices are stored as attributes
mp.sim_aligned_{surf/esp/pharm}
mp.transform_{surf/esp/pharm}

# Get a copy of the optimally aligned fit Molecule object
transformed_fit_molec = mp.get_transformed_molecule(
    se3_transform=mp.transform_{surf/esp/pharm}
)
```

## Evaluation Examples and Scripts

We implement three evaluations of generated 3D conformers. Evaluations can be done on an individual basis or in a pipeline. Here we show the most basic use case in the unconditional setting.


- `ConfEval`
    - Checks validity, pre-/post-xTB relaxation
    - Calculates 2D graph properties
- `ConsistencyEval`
    - Inherits from `ConfEval` and evaluates the consistency of the molecule's jointly generated interaction profiles with the true interaction profiles using 3D similarity scoring functions
- `ConditionalEval`
    - Inherits from `ConfEval` and evaluates the 3D similarity between generated molecules and the target molecule

**Note**: Evaluations can be run from any molecule's atomic numbers and positions with explicit hydrogens (i.e., straight from an xyz file).

### Examples

Full jupyter notebook tutorials/examples for evaluations are found in the [`examples`](./examples/) folder. Some minimal examples are below.

```python
from shepherd_score.evaluations.evalutate import ConfEval
from shepherd_score.evaluations.evalutate import UnconditionalEvalPipeline

# ConfEval evaluates the validity of a given molecule, optimizes it with xTB,
#   and also computes various 2D graph properties
# `atom_array` np.ndarray (N,) atomic numbers of the molecule (with explicit H)
# `position_array` np.ndarray (N,3) atom coordinates for the molecule
conf_eval = ConfEval(atoms=atom_array, positions=position_array)

# Alternatively, if you have a list of molecules you want to test:
uncond_pipe = UnconditionalEvalPipeline(
    generated_mols = [(a, p) for a, p in zip(atom_arrays, position_arrays)]
)
uncond_pipe.evaluate(num_workers=4)

# Properties are stored as attributes and can be converted into pandas df's
sample_df, global_series = uncond_pipe.to_pandas()
```

### Scripts
Scripts to evaluate *ShEPhERD*-generated samples can be found in the `scripts` directory.

## Data
We provide the data used for model training, benchmarking, and all *ShEPhERD*-generated samples reported in the paper at this [Dropbox link](https://www.dropbox.com/scl/fo/rgn33g9kwthnjt27bsc3m/ADGt-CplyEXSU7u5MKc0aTo?rlkey=fhi74vkktpoj1irl84ehnw95h&e=1&st=wn46d6o2&dl=0). There are comprehensive READMEs in the Dropbox describing the different folders.

## License

This project is licensed under the MIT License -- see [LICENSE](./LICENSE) file for details.

## Citation
If you use or adapt `shepherd_score` or [*ShEPhERD*](https://github.com/coleygroup/shepherd) in your work, please cite us:

```bibtex
@misc{adamsShEPhERD2024,
  title = {{{ShEPhERD}}: {{Diffusing}} Shape, Electrostatics, and Pharmacophores for Bioisosteric Drug Design},
  author = {Adams, Keir and Abeywardane, Kento and Fromer, Jenna and Coley, Connor W.},
  year = {2024},
  number = {arXiv:2411.04130},
  eprint = {2411.04130},
  publisher = {arXiv},
  doi = {10.48550/arXiv.2411.04130},
  archiveprefix = {arXiv}
}
```