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https://github.com/simonboothroyd/mdtop
A simple package for storing topological information about a system to simulate.
https://github.com/simonboothroyd/mdtop
Last synced: 29 days ago
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A simple package for storing topological information about a system to simulate.
- Host: GitHub
- URL: https://github.com/simonboothroyd/mdtop
- Owner: SimonBoothroyd
- License: mit
- Created: 2024-12-02T12:26:52.000Z (about 1 month ago)
- Default Branch: main
- Last Pushed: 2024-12-03T04:32:02.000Z (about 1 month ago)
- Last Synced: 2024-12-03T05:26:56.119Z (about 1 month ago)
- Language: Python
- Homepage: https://simonboothroyd.github.io/mdtop/
- Size: 679 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
mdtop
A simple package for storing topological information about a system to simulate.
---
The `mdtop` framework aims to provide a simple, modern, and flexible way to store
topological information about a system to simulate. While this may be 'yet another
`Topology` object', it is designed to take the best of all worlds from the fantastic
`mdtraj`, `parmed`, and `openmm` packages, and provide a clean way to store atom
data, merge multiple topologies, and also select subsets using the ubiquitous `PyMol`
atom selection language.
## Installation
This package can be installed using `conda` (or `mamba`, a faster version of `conda`):
```shell
mamba install -c conda-forge mdtop
```
## Getting Started
### Creating a Topology
Topologies can be created from a variety of sources. However, the most robust workflows
typically involve:
* **Creating a topology from OpenMM**: Use the `Topology.from_openmm()` method to import
an existing OpenMM topology containing, for example, a protein structure.
* **Creating a topology from an RDKit molecule**: Use the `Topology.from_rdkit()` method
to create a topology from an RDKit molecule representation.
* **Loading a topology from a file**: Use the `Topology.from_file()` method to import
an existing PDB, SDF, or MOL2 file.
```python
from openmm.app import PDBFile
from rdkit import Chem
from mdtop import Topology
# Load a protein topology from OpenMM
protein_top_omm = PDBFile("protein.pdb").topology
protein_top = Topology.from_openmm(protein_top_omm)
# OR
protein_top = Topology.from_file("protein.pdb")
# Load a ligand using RDKit
ligand_rd = Chem.MolFromMolFile("ligand.sdf")
ligand_top = Topology.from_rdkit(ligand_rd)
# OR
ligand_top = Topology.from_file("ligand.sdf")
# Merge the protein and ligand topologies
system_top = Topology.merge(protein_top, ligand_top)
# OR
system_top = protein_top + ligand_top
```
### Atom Selection
Subsets of atoms can be selected using a (for now) subset of the
[PyMol atom selection language]((https://pymolwiki.org/index.php/Selection_Algebra)).
For example, to select all atoms in chain A:
```python
selection = system_top.select("chain A")
```
or all atoms within 5 Å of the ligand:
```python
atom_idxs = system_top.select("all within 5. of resn LIG")
```
A subset of the topology can then be created using the `subset()` method:
```python
subset = system_top.subset(atom_idxs)
```
or by indexing directly:
```python
subset = system_top["chain A"]
# OR
subset = system_top[atom_idxs]
```
### Exporting Topologies
Topologies can be converted back into OpenMM or RDKit formats for further analysis or
simulation.
```python
# Export to OpenMM topology
system_top_omm = system_top.to_openmm()
# Export to RDKit molecule - this currently only works for topologies that contain
# full formal charge and bond order information.
mol_rd = ligand_top.to_rdkit()
```
They can also be directly written to a file:
```python
system_top.to_file("system.pdb")
```