Oliver Beckstein orbeckst
orbeckst
/ secondary_structure_TopologyAttribute.py
Last active
November 10, 2025 08:20
Example for how to add a custom TopologyAttribute (for secondary structure) in MDAnalysis
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| import numpy as np | |
| import MDAnalysis as mda | |
| # (1) define the custom SecondaryStructure attribute | |
| from MDAnalysis.core.topologyattrs import ResidueAttr | |
| # Just *defining* this class registers it with MDAnalysis | |
| # and makes "ss" available for Universe.add_TopologyAttr() |
orbeckst
/ mda_universe_from_array.py
Created
January 9, 2025 00:20
Create a MDAnalysis Universe for a "trajectory" in a numpy array.
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| import MDAnalysis as mda | |
| import numpy as np | |
| n_atoms = 6 | |
| n_steps = 4 | |
| # create empty Universe with one atom per residue | |
| u = mda.Universe.empty(n_atoms, n_residues=n_atoms, atom_resindex=np.arange(n_atoms), trajectory=True) | |
| # optional: name each atom CA |
orbeckst
/ distances-legacy-0.ipynb
Last active
June 12, 2021 05:00
Analysis of moving across the board in the game Pandemic Legacy Season 0.
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orbeckst
/ polymer_rdf_COM.ipynb
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August 31, 2025 03:41
Radial distribution function (RDF) calculation of the centers of mass of molecules with MDAnalysis.
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orbeckst
/ regularized_function_example.ipynb
Last active
March 7, 2025 23:13
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orbeckst
/ pmda-rmsf-example.ipynb
Last active
October 19, 2020 10:36
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orbeckst
/ xtc_vs_memreader.py
Created
June 12, 2019 17:58
Testing memory consumption of the MDAnalysis XTCReader vs MemoryReader. See https://github.com/MDAnalysis/mdanalysis/wiki/memory-profiling
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| # -*- coding: utf-8 -*- | |
| # load trajectory and iterate | |
| import numpy as np | |
| import tqdm | |
| import MDAnalysis as mda | |
| import gc | |
orbeckst
/ dihedral_benchmark.ipynb
Last active
August 27, 2018 16:59
benchmarking dihedral featurization in MDAnalysis
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