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@dprada
dprada committed Jun 13, 2024
1 parent 1ac585f commit a38e2ac
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Binary file added docs/contents/user/tools/molecular_mechanics/1brs.mmtf
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90 changes: 45 additions & 45 deletions docs/contents/user/tools/molecular_mechanics/get_forces.ipynb
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{
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},
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},
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"id": "42b77409-d419-44e3-8502-a7af7cdee043",
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"source": [
"molecular_system = msm.convert(msm.systems.demo['Barnase-Barstar']['barnase_barstar.msmpk'])"
"molecular_system = msm.convert(msm.systems['Barnase-Barstar']['barnase_barstar.h5msm'])"
]
},
{
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"execution_count": 4,
"execution_count": 5,
"id": "31b81f82-4c43-4f3f-ac05-072084782bda",
"metadata": {},
"outputs": [
Expand All @@ -77,51 +77,51 @@
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" <td id=\"T_15bd9_row1_col0\" class=\"data row1 col0\" >1</td>\n",
" <td id=\"T_15bd9_row1_col1\" class=\"data row1 col1\" >protein 1</td>\n",
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}
Expand All @@ -132,7 +132,7 @@
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"metadata": {},
"outputs": [],
Expand All @@ -142,14 +142,14 @@
},
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{
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"<table><tbody><tr><th>Magnitude</th><td style='text-align:left;'><pre>[[67.1392933872994 -49.24023595824838 -126.36911331489682]<br> [7.590139269828796 -4.8426863215863705 2.0255396582651883]<br> [-69.2170457537286 -72.70544024370611 73.83748572319746]<br> ...<br> [-29.609317913651466 383.96366426721215 -554.4305481649935]<br> [2.5788150089792907 2.188007801771164 -2.544081619940698]<br> [0.9272228211630136 0.6260932385921478 -1.185140285640955]]</pre></td></tr><tr><th>Units</th><td style='text-align:left;'>kilojoule/(mole nanometer)</td></tr></tbody></table>"
"<table><tbody><tr><th>Magnitude</th><td style='text-align:left;'><pre>[[64.11752532888204 -25.612546341493726 -95.41171813267283]<br> [29.116464272607118 -6.594275672920048 9.10719308629632]<br> [-9.741821856005117 92.62677688943222 14.043880816083401]<br> ...<br> [-92.37486266554333 288.4447076302022 -452.25065422523767]<br> [-1.4295995784923434 -1.4202567636966705 -0.5309852324426174]<br> [-2.964325251057744 -0.30357155576348305 -2.1877003610134125]]</pre></td></tr><tr><th>Units</th><td style='text-align:left;'>kilojoule/(mole nanometer)</td></tr></tbody></table>"
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"$\\begin{pmatrix} & & \\\\ \n",
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" [-9.23748627e+01, 2.88444708e+02, -4.52250654e+02],\n",
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" [-2.96432525e+00, -3.03571556e-01, -2.18770036e+00]]) <Unit('kilojoule / mole / nanometer')>"
]
},
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"execution_count": 7,
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}
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