https://github.com/mdanalysis/rdkitconverter-benchmark
Benchmark for the RDKitConverter's inferring of bond orders and charges
https://github.com/mdanalysis/rdkitconverter-benchmark
Last synced: 5 months ago
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Benchmark for the RDKitConverter's inferring of bond orders and charges
- Host: GitHub
- URL: https://github.com/mdanalysis/rdkitconverter-benchmark
- Owner: MDAnalysis
- License: gpl-2.0
- Created: 2022-03-19T21:29:47.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-08-07T18:17:13.000Z (almost 2 years ago)
- Last Synced: 2024-10-29T17:32:42.677Z (over 1 year ago)
- Language: HTML
- Size: 75.1 MB
- Stars: 3
- Watchers: 10
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# RDKitConverter benchmark
This repository benchmarks the ability of MDAnalysis' `RDKitConverter` to infer bond orders and charges from molecules with all hydrogens explicit.
To cite this repository, please use the following DOI:
[](https://zenodo.org/badge/latestdoi/471816709)
## Results
| Description | Value |
| --- | --- |
| **MDAnalysis version** | 2.4.3 |
| **Accuracy** | 99.19% |
| **Number of molecules fetched** | 2,372,174 |
| **Number of molecules processed** | 2,166,327 |
| **Number of molecules failed** | 17,577 |
Details on the benchmark can also be found [here](results/results.json).
The **interactive list of molecules** currently failing can be accessed [here](https://raw.githack.com/MDAnalysis/RDKitConverter-benchmark/main/results/failed_molecules.html) (click on a molecule's image to zoom in).
Failing **scaffolds** can be accessed [here](https://raw.githack.com/MDAnalysis/RDKitConverter-benchmark/main/results/failed_scaffolds.html). The scaffold network used to
create this file can be viewed [here](https://raw.githack.com/MDAnalysis/RDKitConverter-benchmark/main/results/scaffold_network.html).
## Instructions
Running the benchmark requires conda (or mamba) on a Linux machine.
Start by cloning this repository:
```shell
git clone https://github.com/MDAnalysis/RDKitConverter-benchmark.git
cd RDKitConverter-benchmark
```
Then install the python dependencies with `make install`:
```shell
# to speed things up you can use mamba:
make install CONDA=mamba
```
This will create a separate conda environment called `rdkitconverter`.
Finally, run the benchmark:
```shell
make
```
Run `make help` to get a list of available commands.
The results are available in the `results/` directory:
- `results.json`, a JSON file listing all the necessary information
- `failed_molecules.smi`, a SMILES file containing the molecules that failed the test
- `failed_molecules.html`, an interactive table displaying the failed molecules
## Methods
The benchmark will fetch ChEMBL 33 as an SDF file and process the molecules the following way:
- Discard molecules that could not be read or sanitized by RDKit
- Keep only the largest fragment
- Keep only molecules with 2 to 50 heavy atoms
- Discard molecules with radicals
- Drop duplicate molecules based on their InchiKey
Once the data is fetched and standardized, the benchmark can be run. The benchmark will start by preparing a "reduced" version of the molecule by adding explicit hydrogen atoms and removing bond orders and formal charges. This is done to mimic the minimal information available in most topology files for MD simulations.
The RDKitConverter might give different results depending on the order of atoms in the molecule. For that reason, the benchmark will enumerate reordered version of the molecule so that each atom appears in the first position once.
This is done by reading a SMILES of the molecule rooted at the given atom, so that the other atoms of the molecule are reordered in a realistic way.
Finally, the reordered "reduced" molecule goes through the MDAnalysis code responsible for inferring bond orders and formal charges.
During the enumeration of reordered molecules, if any of the inferred molecules fails to match with the original molecule or one of its resonance structures, the whole test fails for that molecule.
Prototype code:
```python
def benchmark_mol(reference_mol):
reduced_mol = remove_bond_orders_and_charges(reference_mol)
for mol in enumerate_reordered_mol(reduced_mol):
mol = infer_bond_orders_and_charges(mol)
valid = is_same_mol_or_resonance_structure(mol, reference_mol)
if not valid:
return "FAILED"
return "SUCCESS"
```