https://github.com/rmeli/densitymatch
Match libmolgrid densities
https://github.com/rmeli/densitymatch
Last synced: 3 months ago
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Match libmolgrid densities
- Host: GitHub
- URL: https://github.com/rmeli/densitymatch
- Owner: RMeli
- Created: 2021-06-24T13:23:59.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2022-06-28T10:58:08.000Z (almost 3 years ago)
- Last Synced: 2025-02-01T05:26:02.726Z (4 months ago)
- Language: Jupyter Notebook
- Size: 76.6 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: licenses/sensaas.txt
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README
# Density Match
Match [libmolgrid](https://github.com/gnina/libmolgrid)-generated densities using [sensaas](https://github.com/SENSAAS/sensaas).
## Pipeline
The goal is to align a molecule (or fragment) to a given `libmolgrid` density. This is achieved by transforming both the density and the given molecule into point clouds and aligning those.
### Fragment/Scaffold Placement and Molecular Growth
* [`libmolgrid`] Compute density for the molecule
* Compute point clouds from the densities (isosurfaces)
* [`SENSAAS`] Align point clouds
* Apply transformation to the molecule
* [`libmolgrid`] Re-compute density for the (aligned) molecule
* Compute difference between two densities
* [`liGAN`] Fit remaining density with atom
* [`liGAN`] Reconstruct full molecule
### Scripts
* [molgrid_to_pcd.py]: convert molecule into atomic density grid and subsequently convert the grid into a point cloud
* [score_pcd.py]: score alignment between point clouds and provide rototranslation for the optimal alignment
* [molgrid_diff.py]: compute difference between atomic density grids
* [fit_to_grid.py]: fit atoms to density grid (difference)
## Tools
### Convert SDF File to Point Cloud
A SDF file can be converted to a point cloud (`.pcd`, `.xyzrgb`, ...) using `molgrid_to_pcd.py`.
### View Point Cloud
One or multiple point clouds can be visualized with `view_pcd.py`.
### Convert Binary Point Cloud File to ASCII
A binary point cloud file can be converted into an ASCII file using `pcd_to_ascii.py`.
## Notes
### Running Experiments
Given [libmolgrid/#62](https://github.com/gnina/libmolgrid/issues/62) most scripts need to run within a Singularity container, where `libmolgrid` has been compiled from scratch. This extends to Jupyter Notebooks that require `libmolgrid`.
The `development/densitymatch.def` container allows to build a minimal Singularity container. The reconstruction (fitting) of atoms from atomic densities requires [liGAN](https://github.com/mattragoza/liGAN), which can be run within the full Singularity container built from `development/ligan.def`.