semvec/pypi-packages huggingface dataset:
qmrun 0.1.5
Orca6 input file generator from SDF files
License: MIT

<h1 align="center"> qmrun </h1>

qmrun is a small python utility for running Orca6 computations all over the structures in a V2000 SDF file


<h2>Requirements </h2>
python3
rdkit

<h2>Installation  </h2>
pip install qmrun

<h2>Running qmrun </h2>
In windows qmrun must be run inside a powershell console. The orca.exe file should be in the path
In MacOS and Linux the orca executable file should be installed in $HOME/software/orca_6/orca
sc-simvar 0.3.1
A re-implementation of the hotspotsc package using wrappers around Rust code.
License: MIT
Requires Python: >=3.10

# sc_simvar

A re-implementation of the [hotspotsc](https://github.com/YosefLab/Hotspot) v1.1.1 Python package using Rust for the computationally intensive portions.

Not all code from `hotspotsc` has been translated to Rust, but all code has been localized.

All functions (Rust and Python) are tested to have the exact same output as Hotspotsc for the same input data.

Full Docs: https://genentech.github.io/sc_simvar/

## Performance

Using simulated data that varied in the number of genes, cells, and dimensions I ran the pipeline varying whether approx_neighbors or the weighted_graph were used when calculating the knn graph. For the local correlations I used half the number of genes to calculate the correlations on.

Across the 108 total simulations performed the mean speed up of `SCSimVar` over `Hotspot` was: **3x**.

Summary of benchmarking results:

![image](https://raw.githubusercontent.com/Genentech/sc_simvar/main/benchmark_results.png)

Machine specs:

    Model Identifier: MacBookPro18,3
    Total Number of Cores: 8 (6 performance and 2 efficiency)
    Memory: 16 GB
    System Version: macOS 14.7.4 (23H420)
    Kernel Version: Darwin 23.6.0
    Secure Virtual Memory: Enabled
    Memory: 16 GB

    rustc: 1.85.0 (4d91de4e4 2025-02-17)
    Python: 3.10.14

## Usage

The ``SCSimVar`` class of this package is a direct replacement for the ``Hotspot`` class of ``hotspotsc``.

```python
from sc_simvar import SCSimVar as Hotspot

# Your old code here, no changes needed.
```

If you run into a problem with ``SCSimVar`` compared to ``Hotspot`` please let me know!