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| 250 | <div·class="jupyter·output"> | 250 | <div·class="jupyter·output"> |
| 251 | <div·class="jupyter·output_area"><div·class="jupyter·prompt·output_prompt">Out[2]:</div> | 251 | <div·class="jupyter·output_area"><div·class="jupyter·prompt·output_prompt">Out[2]:</div> |
| 252 | <div·class="jupyter·output_text·output_subarea·output_execute_result"> | 252 | <div·class="jupyter·output_text·output_subarea·output_execute_result"> |
| 253 | <pre><mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at·0xffff9 | 253 | <pre><mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at·0xffff951213d0></pre> |
| 254 | </div> | 254 | </div> |
| 255 | </div> | 255 | </div> |
| 256 | </div> | 256 | </div> |
| 257 | </div> | 257 | </div> |
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| 292 | <div·class="jupyter·output"> | 292 | <div·class="jupyter·output"> |
| 293 | <div·class="jupyter·output_area"><div·class="jupyter·prompt·output_prompt">Out[3]:</div> | 293 | <div·class="jupyter·output_area"><div·class="jupyter·prompt·output_prompt">Out[3]:</div> |
| 294 | <div·class="jupyter·output_text·output_subarea·output_execute_result"> | 294 | <div·class="jupyter·output_text·output_subarea·output_execute_result"> |
| 295 | <pre><mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at·0xffff9 | 295 | <pre><mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at·0xffff951213d0></pre> |
| 296 | </div> | 296 | </div> |
| 297 | </div> | 297 | </div> |
| 298 | </div> | 298 | </div> |
| 299 | </div> | 299 | </div> |
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| 52 | Lets·load·up·our·trajectory.·This·is·the·trajectory·that·we·generated·in·the | 52 | Lets·load·up·our·trajectory.·This·is·the·trajectory·that·we·generated·in·the |
| 53 | "Running·a·simulation·in·OpenMM·and·analyzing·the·results·with·mdtraj"·example. | 53 | "Running·a·simulation·in·OpenMM·and·analyzing·the·results·with·mdtraj"·example. |
| 54 | In [2]: | 54 | In [2]: |
| 55 | traj·=·md.load('ala2.h5') | 55 | traj·=·md.load('ala2.h5') |
| 56 | traj | 56 | traj |
| 57 | Out[2]: | 57 | Out[2]: |
| 58 | <mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at | 58 | <mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at |
| 59 | 0xffff9 | 59 | 0xffff951213d0> |
| 60 | Create·a·two·component·PCA·model,·and·project·our·data·down·into·this·reduced | 60 | Create·a·two·component·PCA·model,·and·project·our·data·down·into·this·reduced |
| 61 | dimensional·space.·Using·just·the·cartesian·coordinates·as·input·to·PCA,·it's | 61 | dimensional·space.·Using·just·the·cartesian·coordinates·as·input·to·PCA,·it's |
| 62 | important·to·start·with·some·kind·of·alignment. | 62 | important·to·start·with·some·kind·of·alignment. |
| 63 | In [3]: | 63 | In [3]: |
| 64 | pca1·=·PCA(n_components=2) | 64 | pca1·=·PCA(n_components=2) |
| 65 | traj.superpose(traj,·0) | 65 | traj.superpose(traj,·0) |
| 66 | Out[3]: | 66 | Out[3]: |
| 67 | <mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at | 67 | <mdtraj.Trajectory·with·100·frames,·22·atoms,·3·residues,·without·unitcells·at |
| 68 | 0xffff9 | 68 | 0xffff951213d0> |
| 69 | In [4]: | 69 | In [4]: |
| 70 | reduced_cartesian·=·pca1.fit_transform(traj.xyz.reshape(traj.n_frames, | 70 | reduced_cartesian·=·pca1.fit_transform(traj.xyz.reshape(traj.n_frames, |
| 71 | traj.n_atoms·*·3)) | 71 | traj.n_atoms·*·3)) |
| 72 | print(reduced_cartesian.shape) | 72 | print(reduced_cartesian.shape) |
| 73 | (100,·2) | 73 | (100,·2) |
| 74 | Now·we·can·plot·the·data·on·this·projection. | 74 | Now·we·can·plot·the·data·on·this·projection. |
| 75 | In [5]: | 75 | In [5]: |
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| 281 | <div·class="jupyter·output_wrapper"> | 281 | <div·class="jupyter·output_wrapper"> |
| 282 | <div·class="jupyter·output"> | 282 | <div·class="jupyter·output"> |
| 283 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> | 283 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> |
| 284 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> | 284 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> |
| 285 | <pre>md.rmsd():· | 285 | <pre>md.rmsd():·30880.44·rmsds·/·s |
| 286 | </pre> | 286 | </pre> |
| 287 | </div> | 287 | </div> |
| 288 | </div> | 288 | </div> |
| 289 | </div> | 289 | </div> |
| 290 | </div> | 290 | </div> |
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| 330 | <div·class="jupyter·output_wrapper"> | 330 | <div·class="jupyter·output_wrapper"> |
| 331 | <div·class="jupyter·output"> | 331 | <div·class="jupyter·output"> |
| 332 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> | 332 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> |
| 333 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> | 333 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> |
| 334 | <pre>md.rmsd(precentered=True):· | 334 | <pre>md.rmsd(precentered=True):·61870.09·rmsds·/·s |
| 335 | </pre> | 335 | </pre> |
| 336 | </div> | 336 | </div> |
| 337 | </div> | 337 | </div> |
| 338 | </div> | 338 | </div> |
| 339 | </div> | 339 | </div> |
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| 375 | <div·class="jupyter·output_wrapper"> | 375 | <div·class="jupyter·output_wrapper"> |
| 376 | <div·class="jupyter·output"> | 376 | <div·class="jupyter·output"> |
| 377 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> | 377 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> |
| 378 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> | 378 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> |
| 379 | <pre>pure·numpy·rmsd_qcp():· | 379 | <pre>pure·numpy·rmsd_qcp():·815.07·rmsds·/·s |
| 380 | </pre> | 380 | </pre> |
| 381 | </div> | 381 | </div> |
| 382 | </div> | 382 | </div> |
| 383 | </div> | 383 | </div> |
| 384 | </div> | 384 | </div> |
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| 59 | start·=·time.time() | 59 | start·=·time.time() |
| 60 | for·i·in·range(100): | 60 | for·i·in·range(100): |
| 61 | ····md.rmsd(t,·t,·0) | 61 | ····md.rmsd(t,·t,·0) |
| 62 | print('md.rmsd():·%.2f·rmsds·/·s'·%·((t.n_frames·*·100)·/·(time.time()·- | 62 | print('md.rmsd():·%.2f·rmsds·/·s'·%·((t.n_frames·*·100)·/·(time.time()·- |
| 63 | start))) | 63 | start))) |
| 64 | md.rmsd():· | 64 | md.rmsd():·30880.44·rmsds·/·s |
| 65 | But·for·some·applications·like·clustering,·we·want·to·run·many·rmsd() | 65 | But·for·some·applications·like·clustering,·we·want·to·run·many·rmsd() |
| 66 | calculations·per·trajectory·frame.·Under·these·circumstances,·the·centering·of | 66 | calculations·per·trajectory·frame.·Under·these·circumstances,·the·centering·of |
| 67 | the·trajectories·is·going·to·be·done·many·times,·which·leads·to·a·slight | 67 | the·trajectories·is·going·to·be·done·many·times,·which·leads·to·a·slight |
| 68 | slowdown.·If·we·manually·center·the·trajectory·and·then·inform·the·rmsd() | 68 | slowdown.·If·we·manually·center·the·trajectory·and·then·inform·the·rmsd() |
| 69 | function·that·the·centering·has·been·precentered,·we·can·achieve·~2x·speedup, | 69 | function·that·the·centering·has·been·precentered,·we·can·achieve·~2x·speedup, |
| 70 | depending·on·your·machine·and·the·number·of·atoms. | 70 | depending·on·your·machine·and·the·number·of·atoms. |
| 71 | In [4]: | 71 | In [4]: |
| Offset 75, 28 lines modified | Offset 75, 28 lines modified | ||
| 75 | start·=·time.time() | 75 | start·=·time.time() |
| 76 | for·i·in·range(100): | 76 | for·i·in·range(100): |
| 77 | ····md.rmsd(t,·t,·0,·precentered=True) | 77 | ····md.rmsd(t,·t,·0,·precentered=True) |
| 78 | print('md.rmsd(precentered=True):·%.2f·rmsds·/·s'·%·((t.n_frames·*·100)·/ | 78 | print('md.rmsd(precentered=True):·%.2f·rmsds·/·s'·%·((t.n_frames·*·100)·/ |
| 79 | (time.time()·-·start))) | 79 | (time.time()·-·start))) |
| 80 | md.rmsd(precentered=True):· | 80 | md.rmsd(precentered=True):·61870.09·rmsds·/·s |
| 81 | Just·for·fun,·let's·compare·this·code·to·the·straightforward·numpy | 81 | Just·for·fun,·let's·compare·this·code·to·the·straightforward·numpy |
| 82 | implementation·of·the·same·algorithm,·which·mdtraj·has·(mostly·for·testing)·in | 82 | implementation·of·the·same·algorithm,·which·mdtraj·has·(mostly·for·testing)·in |
| 83 | the·mdtraj.geometry.alignment·subpackage | 83 | the·mdtraj.geometry.alignment·subpackage |
| 84 | In [5]: | 84 | In [5]: |
| 85 | from·mdtraj.geometry.alignment·import·rmsd_qcp | 85 | from·mdtraj.geometry.alignment·import·rmsd_qcp |
| 86 | start·=·time.time() | 86 | start·=·time.time() |
| 87 | for·k·in·range(t.n_frames): | 87 | for·k·in·range(t.n_frames): |
| 88 | ····rmsd_qcp(t.xyz[0],·t.xyz[k]) | 88 | ····rmsd_qcp(t.xyz[0],·t.xyz[k]) |
| 89 | print('pure·numpy·rmsd_qcp():·%.2f·rmsds·/·s'·%·(t.n_frames·/·(time.time()·- | 89 | print('pure·numpy·rmsd_qcp():·%.2f·rmsds·/·s'·%·(t.n_frames·/·(time.time()·- |
| 90 | start))) | 90 | start))) |
| 91 | pure·numpy·rmsd_qcp():· | 91 | pure·numpy·rmsd_qcp():·815.07·rmsds·/·s |
| 92 | md.rmsd()·code·is·a·lot·faster.·If·you·go·look·at·the·rmsd_qcp·source·code, | 92 | md.rmsd()·code·is·a·lot·faster.·If·you·go·look·at·the·rmsd_qcp·source·code, |
| 93 | you'll·see·that·it's·not·because·that·code·is·particularly·slow·or·unoptimized. | 93 | you'll·see·that·it's·not·because·that·code·is·particularly·slow·or·unoptimized. |
| 94 | It's·about·as·good·as·you·can·do·with·numpy.·The·reason·for·the·speed | 94 | It's·about·as·good·as·you·can·do·with·numpy.·The·reason·for·the·speed |
| 95 | difference·is·that·an·inordinate·amount·of·time·was·put·into·hand-optimizing·an | 95 | difference·is·that·an·inordinate·amount·of·time·was·put·into·hand-optimizing·an |
| 96 | SSE3·implementation·in·C·for·the·md.rmsd()·code. | 96 | SSE3·implementation·in·C·for·the·md.rmsd()·code. |
| 97 | (rmsd-benchmark.ipynb.gz;·rmsd-benchmark_eval.ipynb.gz;·rmsd-benchmark.py) | 97 | (rmsd-benchmark.ipynb.gz;·rmsd-benchmark_eval.ipynb.gz;·rmsd-benchmark.py) |
| 98 | Next·Previous | 98 | Next·Previous |
| Offset 458, 17 lines modified | Offset 458, 17 lines modified | ||
| 458 | <div·class="jupyter·output_wrapper"> | 458 | <div·class="jupyter·output_wrapper"> |
| 459 | <div·class="jupyter·output"> | 459 | <div·class="jupyter·output"> |
| 460 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> | 460 | <div·class="jupyter·output_area"><div·class="jupyter·prompt"></div> |
| 461 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> | 461 | <div·class="jupyter·output_subarea·output_stream·output_stdout·output_text"> |
| 462 | <pre>[2·2· | 462 | <pre>[2·2·3·3·3·3·3·2·3·3·3·3·2·2·3·3·3·2·3·1·1·1·1·1·1·1·1·1·2·1·3·3·3·2·2·2·2 |
| 463 | ·1·1·1·1·1·1·1·1·3·3·3·3·3·3·3·2·2·2·3·3·3·3·2·3·3·3·3·2·2·3·3·3·3·3·3·3·2 | ||
| 464 | · | 463 | ·2·1·1·1·1·1·1·1·2·2·2·3·2·3·3·2·2·2·3·3·2·2·2·3·3·3·2·2·2·2·3·2·2·2·3·3·2 |
| 464 | ·3·2·3·2·2·3·2·3·3·3·2·2·3·2·2·1·1·1·1·1·1·1·1·1·1·1] | ||
| 465 | (100,) | 465 | (100,) |
| 466 | </pre> | 466 | </pre> |
| 467 | </div> | 467 | </div> |
| 468 | </div> | 468 | </div> |
| 469 | </div> | 469 | </div> |
| 470 | </div> | 470 | </div> |
| Offset 120, 17 lines modified | Offset 120, 17 lines modified | ||
| 120 | labels·=·[] | 120 | labels·=·[] |
| 121 | for·frame·in·md.iterload('ala2.h5',·chunk=1): | 121 | for·frame·in·md.iterload('ala2.h5',·chunk=1): |
| 122 | ····labels.append(leader_labels[np.argmin(md.rmsd(leaders,·frame,·0))]) | 122 | ····labels.append(leader_labels[np.argmin(md.rmsd(leaders,·frame,·0))]) |
| 123 | labels·=·np.array(labels) | 123 | labels·=·np.array(labels) |
| 124 | print(labels) | 124 | print(labels) |
| 125 | print(labels.shape) | 125 | print(labels.shape) |
| 126 | [2·2· | 126 | [2·2·3·3·3·3·3·2·3·3·3·3·2·2·3·3·3·2·3·1·1·1·1·1·1·1·1·1·2·1·3·3·3·2·2·2·2 |
| 127 | ·1·1·1·1·1·1·1·1·3·3·3·3·3·3·3·2·2·2·3·3·3·3·2·3·3·3·3·2·2·3·3·3·3·3·3·3·2 | ||
| 128 | · | 127 | ·2·1·1·1·1·1·1·1·2·2·2·3·2·3·3·2·2·2·3·3·2·2·2·3·3·3·2·2·2·2·3·2·2·2·3·3·2 |
| 128 | ·3·2·3·2·2·3·2·3·3·3·2·2·3·2·2·1·1·1·1·1·1·1·1·1·1·1] | ||
| 129 | (100,) | 129 | (100,) |
| 130 | (two-pass-clustering.ipynb.gz;·two-pass-clustering_eval.ipynb.gz;·two-pass- | 130 | (two-pass-clustering.ipynb.gz;·two-pass-clustering_eval.ipynb.gz;·two-pass- |
| 131 | clustering.py) | 131 | clustering.py) |
| 132 | Next·Previous | 132 | Next·Previous |
| 133 | =============================================================================== | 133 | =============================================================================== |
| 134 | ©·Copyright·2021,·Stanford·University·and·the·Authors. | 134 | ©·Copyright·2021,·Stanford·University·and·the·Authors. |
| 135 | ··1.9.5 | 135 | ··1.9.5 |
| Offset 252, 28 lines modified | Offset 252, 27 lines modified | ||
| 252 | ········"0x105a98e90":·1, | 252 | ········"0x105a98e90":·1, |
| 253 | ········"0x109b91310":·109, | 253 | ········"0x109b91310":·109, |
| 254 | ········"0x109b97810":·109, | 254 | ········"0x109b97810":·109, |
| 255 | ········"0x109f0a3d0":·109, | 255 | ········"0x109f0a3d0":·109, |
| 256 | ········"0x110740a90":·[55,·58,·60,·61,·62,·64,·69,·71,·73], | 256 | ········"0x110740a90":·[55,·58,·60,·61,·62,·64,·69,·71,·73], |
| 257 | ········"0x11136e410":·[58,·60,·61,·64], | 257 | ········"0x11136e410":·[58,·60,·61,·64], |
| 258 | ········"0x18236e4a0":·58, | 258 | ········"0x18236e4a0":·58, |
| 259 | ········"0xffff9 | 259 | ········"0xffff951213d0":·114, |
| 260 | ········"100":·[2,·29,·40,·50,·51,·55,·80,·81,·82,·104,·105,·109,·110,·114,·116,·117,·118], | 260 | ········"100":·[2,·29,·40,·50,·51,·55,·80,·81,·82,·104,·105,·109,·110,·114,·116,·117,·118], |
| 261 | ········"1000":·[2,·69,·99,·116,·124,·126], | 261 | ········"1000":·[2,·69,·99,·116,·124,·126], |
| 262 | ········"10000":·[80,·81,·82,·99], | 262 | ········"10000":·[80,·81,·82,·99], |
| 263 | ········"1000000":·93, | 263 | ········"1000000":·93, |
| 264 | ········"1000x":·[22,·23], | 264 | ········"1000x":·[22,·23], |
| 265 | ········"1002":·[25,·57,·126], | 265 | ········"1002":·[25,·57,·126], |
| 266 | ········"100k":·126, | 266 | ········"100k":·126, |
| 267 | ········"101":·110, | 267 | ········"101":·110, |
| 268 | ········"1013":·126, | 268 | ········"1013":·126, |
| 269 | ········"1016":·121, | 269 | ········"1016":·121, |
| 270 | ········"102":·110, | 270 | ········"102":·110, |
| 271 | ········"1021":·[24,·86], | 271 | ········"1021":·[24,·86], |
| 272 | ········"1022681":·116, | ||
| 273 | ········"1030":·126, | 272 | ········"1030":·126, |
| 274 | ········"1038":·126, | 273 | ········"1038":·126, |
| 275 | ········"1039":·126, | 274 | ········"1039":·126, |
| 276 | ········"1057":·126, | 275 | ········"1057":·126, |
| 277 | ········"1058":·126, | 276 | ········"1058":·126, |
| 278 | ········"1061":·126, | 277 | ········"1061":·126, |
| 279 | ········"1063":·86, | 278 | ········"1063":·86, |
| Offset 427, 35 lines modified | Offset 426, 34 lines modified | ||
| 427 | ········"2007":·12, | 426 | ········"2007":·12, |
| 428 | ········"2008":·[85,·117], | 427 | ········"2008":·[85,·117], |
| 429 | ········"2010":·[9,·62], | 428 | ········"2010":·[9,·62], |
| 430 | ········"2011":·8, | 429 | ········"2011":·8, |
| 431 | ········"2012":·[7,·24,·54,·85,·87,·117], | 430 | ········"2012":·[7,·24,·54,·85,·87,·117], |
| 432 | ········"2013":·111, | 431 | ········"2013":·111, |
| 433 | ········"2015":·121, | 432 | ········"2015":·121, |
| 434 | ········"2056":·116, | ||
| 435 | ········"20nm":·19, | 433 | ········"20nm":·19, |
| 436 | ········"20x":·13, | 434 | ········"20x":·13, |
| 437 | ········"231":·[6,·98,·114], | 435 | ········"231":·[6,·98,·114], |
| 438 | ········"24364147":·[83,·84], | 436 | ········"24364147":·[83,·84], |
| 439 | ········"250":·[58,·60,·61,·64], | 437 | ········"250":·[58,·60,·61,·64], |
| 440 | ········"257":·7, | 438 | ········"257":·7, |
| 441 | ········"2577":·[25,·57], | 439 | ········"2577":·[25,·57], |
| 442 | ········"265":·[6,·98], | 440 | ········"265":·[6,·98], |
| 443 | ········"275":·112, | 441 | ········"275":·112, |
| 444 | ········"276":·112, | 442 | ········"276":·112, |
| 445 | ········"276734":·116, | ||
| 446 | ········"277":·112, | 443 | ········"277":·112, |
| 447 | ········"278":·112, | 444 | ········"278":·112, |
| 448 | ········"279":·112, | 445 | ········"279":·112, |
| 449 | ········"298":·8, | 446 | ········"298":·8, |
| 450 | ········"2eqq":·[69,·107], | 447 | ········"2eqq":·[69,·107], |
| 451 | ········"2mi7":·111, | 448 | ········"2mi7":·111, |
| 452 | ········"300":·99, | 449 | ········"300":·99, |
| 453 | ········"304":·98, | 450 | ········"304":·98, |
| 454 | ········"308":·110, | 451 | ········"308":·110, |
| 452 | ········"30880":·116, | ||
| 455 | ········"309":·110, | 453 | ········"309":·110, |
| 456 | ········"310":·110, | 454 | ········"310":·110, |
| 457 | ········"311":·110, | 455 | ········"311":·110, |
| 458 | ········"312":·110, | 456 | ········"312":·110, |
| 459 | ········"31m":·[110,·112,·113], | 457 | ········"31m":·[110,·112,·113], |
| 460 | ········"31mmodulenotfounderror":·113, | 458 | ········"31mmodulenotfounderror":·113, |
| 461 | ········"31moserror":·[110,·112], | 459 | ········"31moserror":·[110,·112], |
| Offset 482, 18 lines modified | Offset 480, 20 lines modified | ||
| 482 | ········"36m_assert_files_exist":·110, | 480 | ········"36m_assert_files_exist":·110, |
| 483 | ········"36mchemical_shifts_spartaplu":·112, | 481 | ········"36mchemical_shifts_spartaplu":·112, |
| 484 | ········"36mload_fram":·110, | 482 | ········"36mload_fram":·110, |
| 485 | ········"3x3":·95, | 483 | ········"3x3":·95, |
| 486 | ········"423":·[55,·58,·60,·61,·62,·64,·69,·71,·73,·107], | 484 | ········"423":·[55,·58,·60,·61,·62,·64,·69,·71,·73,·107], |
| 487 | ········"500":·[58,·60,·61,·62,·64,·71,·73], | 485 | ········"500":·[58,·60,·61,·62,·64,·71,·73], |
| 488 | ········"526":·111, | 486 | ········"526":·111, |
| 487 | ········"61870":·116, | ||
| 489 | ········"6360":·[10,·11,·12], | 488 | ········"6360":·[10,·11,·12], |
| 490 | ········"6368":·[10,·11,·12], | 489 | ········"6368":·[10,·11,·12], |
| 491 | ········"637":·[25,·57], | 490 | ········"637":·[25,·57], |
| 492 | ········"69715095":·104, | 491 | ········"69715095":·104, |
| 492 | ········"815":·116, | ||
| 493 | ········"861":·126, | 493 | ········"861":·126, |
| 494 | ········"871":·126, | 494 | ········"871":·126, |
| 495 | ········"87260383":·104, | 495 | ········"87260383":·104, |
| 496 | ········"878":·126, | 496 | ········"878":·126, |
| 497 | ········"885":·126, | 497 | ········"885":·126, |
| 498 | ········"891":·126, | 498 | ········"891":·126, |
| 499 | ········"893":·126, | 499 | ········"893":·126, |