Created
October 31, 2017 23:07
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MDAnalysis Reader performance
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{ | |
"cells": [ | |
{ | |
"cell_type": "code", | |
"execution_count": 1, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"import MDAnalysis as mda\n", | |
"from MDAnalysisTests.datafiles import PSF, DCD" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 2, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"u = mda.Universe(PSF, DCD)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 3, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"11.2 ms ± 360 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n" | |
] | |
} | |
], | |
"source": [ | |
"%%timeit\n", | |
"for ts in u.trajectory:\n", | |
" pass" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 4, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"reader = mda.coordinates.DCD.DCDReader(DCD)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 5, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"11.3 ms ± 242 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n" | |
] | |
} | |
], | |
"source": [ | |
"%%timeit\n", | |
"for ts in reader:\n", | |
" pass" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 6, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"dcd = mda.lib.formats.libdcd.DCDFile(DCD)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 7, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"1.63 ms ± 77.9 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)\n" | |
] | |
} | |
], | |
"source": [ | |
"%%timeit\n", | |
"for frame in dcd:\n", | |
" pass" | |
] | |
} | |
], | |
"metadata": { | |
"kernelspec": { | |
"display_name": "Python [default]", | |
"language": "python", | |
"name": "python3" | |
}, | |
"language_info": { | |
"codemirror_mode": { | |
"name": "ipython", | |
"version": 3 | |
}, | |
"file_extension": ".py", | |
"mimetype": "text/x-python", | |
"name": "python", | |
"nbconvert_exporter": "python", | |
"pygments_lexer": "ipython3", | |
"version": "3.6.3" | |
}, | |
"toc": { | |
"nav_menu": {}, | |
"number_sections": true, | |
"sideBar": true, | |
"skip_h1_title": false, | |
"toc_cell": false, | |
"toc_position": {}, | |
"toc_section_display": "block", | |
"toc_window_display": false | |
} | |
}, | |
"nbformat": 4, | |
"nbformat_minor": 2 | |
} |
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