{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Test tube design example\n", "\n", "Design a test tube ensemble intended to contain a 4-stranded stick figure at 1 M. \n", "\n", "Material: RNA \n", "Temperature: 23 C" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "# Import Python NUPACK module\n", "from nupack import *" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "Domain results:\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
DomainSequence
da
GGGCCACAGCGAUACAGAGCUCCCGAA
da*
UUCGGGAGCUCUGUAUCGCUGUGGCCC
db
GGGAGCCGCAAAAACGAAGCGCAGACCAC
db*
GUGGUCUGCGCUUCGUUUUUGCGGCUCCC
dc
AGGUCUGUCUGUAAACCAGGAUCGG
dc*
CCGAUCCUGGUUUACAGACAGACCU
dd
GGAUCCUGGGCUGUGGCA
dd*
UGCCACAGCCCAGGAUCC
Strand results:\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
StrandSequence
sa
GGGCCACAGCGAUACAGAGCUCCCGAA
sd
GGAUCCUGGGCUGUGGCA
sb
GGGAGCCGCAAAAACGAAGCGCAGACCAC
sc
AGGUCUGUCUGUAAACCAGGAUCGG
Objective function:\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Objective typeValue
Weighted ensemble defect0.00973
Ensemble defect: 0.00973

On-target complex defects:\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
ComplexComplex defect (nt)Normalized complex defect
cstickfigure0.1440.00145
Tube defects:\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
TubeTube defect (M)Normalized tube defect
tfigure9.63e-070.00973
Complex contributions to tube defects:\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
TubeOn-target complexStructural defect (M)Concentration defect (M)Total defect (M)
tfigurecstickfigure1.43e-078.20e-079.63e-07
On-target complex concentrations:\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
TubeComplexConcentration (M)Target concentration (M)
tfigurecstickfigure9.92e-071.00e-06
\n", "\n", "Significant off-target complex concentrations (≥ 1% max complex concentration in tube):\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
TubeComplexConcentration (M)
tfigure——
" ], "text/plain": [ "" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Define physical model\n", "my_model = Model(material='rna', celsius=23)\n", "\n", "# Define sequence domains\n", "da = Domain('N27', name='da')\n", "db = Domain('N29', name='db')\n", "dc = Domain('N25', name='dc')\n", "dd = Domain('N18', name='dd')\n", "\n", "# Define strands containing these domains\n", "sa = TargetStrand([da], name='sa')\n", "sb = TargetStrand([db], name='sb')\n", "sc = TargetStrand([dc], name='sc')\n", "sd = TargetStrand([dd], name='sd')\n", "\n", "# Define a target complex\n", "cstickfigure = TargetComplex([sa, sb, sc, sd], '..((((((((..((((((((((((...+))))))(((.........)))((((((..+.))))))))))))..((((((((..+.)))))))))))))))).', name='cstickfigure')\n", "\n", "#Define a target test tube containing all off-target complexes of up to 4 strands\n", "tstickfigure = TargetTube(on_targets={cstickfigure: 1e-06}, off_targets=SetSpec(max_size=4), name='tfigure')\n", "\n", "# Set a stop condition of 1% and a seed for random number generation to get a reproducible result for this demo\n", "my_options = DesignOptions(f_stop=0.01, seed=93)\n", "\n", "# Define and run the test tube design job\n", "my_design = tube_design(tubes=[tstickfigure], model=my_model, options=my_options)\n", "my_results = my_design.run(trials=1)[0]\n", "\n", "# Display the design results\n", "my_results" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "Complex results: \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " 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\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " 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ComplexPfuncΔG (kcal/mol)
(sa)7.2963e+6-9.300
(sb)1.0985e+5-6.831
(sc)5.3855e+4-6.411
(sd)1.0682e+2-2.749
(sa+sa)1.3227e+17-23.201
(sa+sb)3.5730e+18-25.141
(sb+sb)6.1891e+12-17.334
(sc+sa)1.8364e+15-20.684
(sc+sb)6.6467e+17-24.151
(sc+sc)6.3860e+12-17.352
(sd+sa)1.1953e+22-29.917
(sd+sb)2.0554e+19-26.170
(sd+sc)4.0646e+20-27.927
(sd+sd)1.3046e+14-19.127
(sa+sa+sa)8.0996e+27-37.818
(sa+sa+sb)3.5667e+31-42.756
(sa+sb+sb)9.2621e+27-37.897
(sb+sb+sb)2.1204e+21-28.899
(sc+sa+sa)3.7186e+27-37.360
(sc+sa+sb)1.1711e+33-44.810
(sc+sb+sa)3.4134e+25-34.599
(sc+sb+sb)6.8483e+26-36.364
(sc+sc+sa)1.8138e+25-34.227
(sc+sc+sb)1.8165e+27-36.938
(sc+sc+sc)1.5174e+21-28.702
(sd+sa+sa)8.1024e+31-43.238
(sd+sa+sb)9.4843e+35-48.751
(sd+sa+sc)1.2360e+36-48.907
(sd+sb+sa)8.7833e+29-40.576
(sd+sb+sb)7.3575e+27-37.761
(sd+sb+sc)3.7580e+34-46.852
(sd+sc+sa)2.0259e+28-38.358
(sd+sc+sb)1.0165e+27-36.597
(sd+sc+sc)9.2618e+29-40.607
(sd+sd+sa)5.8774e+31-43.050
(sd+sd+sb)5.3791e+28-38.932
(sd+sd+sc)6.7221e+28-39.063
(sd+sd+sd)2.2617e+24-33.002
cstickfigure5.0030e+54-74.121
(sa+sa+sa+sa)4.9539e+39-53.790
(sa+sa+sa+sb)2.7586e+42-57.510
(sa+sa+sb+sb)2.4526e+41-56.086
(sa+sb+sa+sb)6.0933e+44-60.687
(sa+sb+sb+sb)7.3189e+37-51.309
(sb+sb+sb+sb)1.6566e+31-42.304
(sc+sa+sa+sa)3.4036e+39-53.569
(sc+sa+sa+sb)1.5398e+46-62.587
(sc+sa+sb+sa)2.7859e+41-56.161
(sc+sa+sb+sb)2.5443e+43-58.818
(sc+sa+sc+sa)8.1008e+36-50.014
(sc+sb+sa+sa)1.5895e+37-50.410
(sc+sb+sa+sb)1.1887e+42-57.015
(sc+sb+sb+sa)5.6597e+36-49.803
(sc+sb+sb+sb)3.9540e+36-49.592
(sc+sb+sc+sa)2.2230e+39-53.318
(sc+sb+sc+sb)8.6883e+40-55.475
(sc+sc+sa+sa)2.7228e+37-50.727
(sc+sc+sa+sb)5.1991e+43-59.238
(sc+sc+sb+sa)3.2206e+35-48.116
(sc+sc+sb+sb)2.0476e+37-50.559
(sc+sc+sc+sa)7.4614e+34-47.255
(sc+sc+sc+sb)2.8406e+36-49.397
(sc+sc+sc+sc)1.3147e+30-40.813
(sd+sa+sa+sa)7.0757e+44-60.775
(sd+sa+sa+sb)6.7866e+45-62.105
(sd+sa+sa+sc)1.6608e+48-65.342
(sd+sa+sb+sa)1.9106e+46-62.714
(sd+sa+sb+sb)7.7559e+45-62.184
(sd+sa+sc+sa)5.9960e+43-59.322
(sd+sa+sc+sb)3.3892e+42-57.631
(sd+sa+sc+sc)8.3391e+46-63.582
(sd+sa+sd+sa)4.4940e+48-65.928
(sd+sb+sa+sa)2.7919e+40-54.807
(sd+sb+sa+sb)7.9413e+43-59.488
(sd+sb+sa+sc)9.4562e+43-59.590
(sd+sb+sb+sa)1.1982e+39-52.954
(sd+sb+sb+sb)8.6729e+36-50.054
(sd+sb+sb+sc)8.3313e+44-60.871
(sd+sb+sc+sa)4.8736e+42-57.845
(sd+sb+sc+sb)1.4393e+41-55.772
(sd+sb+sc+sc)7.8085e+44-60.833
(sd+sb+sd+sa)4.5687e+45-61.872
(sd+sb+sd+sb)1.3624e+42-57.095
(sd+sb+sd+sc)1.8854e+43-58.641
(sd+sc+sa+sa)7.2662e+41-56.725
(sd+sc+sa+sb)1.9599e+42-57.309
(sd+sc+sa+sc)4.6842e+41-56.467
(sd+sc+sb+sa)1.9310e+40-54.590
(sd+sc+sb+sb)5.8112e+37-51.173
(sd+sc+sb+sc)7.2097e+42-58.076
(sd+sc+sc+sa)1.2886e+39-52.997
(sd+sc+sc+sb)6.3004e+38-52.576
(sd+sc+sc+sc)6.6791e+38-52.610
(sd+sc+sd+sa)3.7955e+47-64.473
(sd+sc+sd+sc)1.5972e+45-61.254
(sd+sd+sa+sa)7.8733e+46-63.548
(sd+sd+sa+sb)3.3319e+48-65.752
(sd+sd+sa+sc)6.1991e+47-64.762
(sd+sd+sb+sa)1.1258e+44-59.693
(sd+sd+sb+sb)4.3339e+41-56.421
(sd+sd+sb+sc)1.5714e+45-61.244
(sd+sd+sc+sa)4.7031e+41-56.469
(sd+sd+sc+sb)1.1504e+39-52.930
(sd+sd+sc+sc)5.0363e+42-57.864
(sd+sd+sd+sa)2.4808e+44-60.158
(sd+sd+sd+sb)2.9435e+39-53.483
(sd+sd+sd+sc)2.7524e+41-56.154
(sd+sd+sd+sd)1.5291e+37-50.388
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Complextfigure (M)
cstickfigure9.917e-07
(sb)7.188e-09
(sa)5.666e-09
(sd+sc)4.821e-09
(sc)2.691e-09
(sd+sa)2.203e-09
(sd+sb+sc)5.289e-10
(sd+sb)3.192e-10
(sd+sa+sb)2.074e-10
(sd+sa+sc)2.065e-10
(sc+sb)3.941e-11
(sa+sb)3.293e-12
(sd)1.398e-12
(sc+sa+sb)9.780e-13
(sd+sd+sa+sb)1.730e-13
(sd+sd+sa+sc)2.458e-14
(sd+sc+sd+sa)1.505e-14
(sd+sb+sb+sc)1.391e-14
(sd+sa+sc+sc)1.262e-14
(sd+sb+sc+sc)9.960e-15
(sd+sc+sc)9.955e-15
(sd+sc+sd+sc)8.149e-15
(sd+sa+sd+sa)5.538e-15
(sd+sd+sb+sc)5.249e-15
(sd+sa+sa+sc)3.907e-15
(sa+sa)2.893e-15
(sd+sd+sa)2.571e-15
(sd+sa+sb+sb)2.013e-15
(sc+sa)1.292e-15
(sb+sb)9.612e-16
(sd+sd)8.104e-16
(sc+sc)5.784e-16
(sa+sa+sb)4.629e-16
(sd+sb+sd+sa)2.372e-16
(sd+sa+sa)2.103e-16
(sd+sd+sb)1.983e-16
(sd+sb+sa)1.921e-16
(sd+sd+sc)1.892e-16
(sc+sa+sa+sb)1.811e-16
(sd+sb+sb)1.356e-16
(sc+sc+sb)9.762e-17
(sd+sc+sb+sc)9.196e-17
(sd+sb+sd+sc)6.298e-17
(sd+sa+sb+sa)5.886e-17
(sd+sd+sa+sa)4.851e-17
(sc+sb+sb)4.819e-17
(sc+sc+sa+sb)3.935e-17
(sc+sa+sb+sb)2.522e-17
(sd+sa+sa+sb)2.091e-17
(sd+sb+sa+sb)2.061e-17
(sa+sb+sa+sb)1.877e-17
(sd+sb+sa+sc)1.874e-17
(sd+sc+sb)1.431e-17
(sd+sd+sc+sc)1.285e-17
(sd+sb+sd+sb)1.192e-17
(sc+sb+sc+sb)1.108e-17
(sa+sb+sb)1.013e-17
(sd+sd+sb+sa)5.844e-18
(sd+sc+sa)3.384e-18
(sd+sd+sd+sa)2.576e-18
(sd+sb+sc+sb)2.404e-18
(sd+sd+sb+sb)1.896e-18
(sc+sb+sa+sb)1.178e-18
(sd+sb+sc+sa)9.661e-19
(sd+sa+sc+sb)6.718e-19
(sd+sc+sa+sb)3.885e-19
(sd+sd+sd+sc)1.839e-19
(sd+sa+sc+sa)1.411e-19
(sd+sc+sa+sc)7.091e-20
(sc+sa+sa)3.686e-20
(sc+sb+sa)2.851e-20
(sd+sa+sa+sa)2.587e-20
(sd+sd+sc+sa)1.865e-20
(sc+sc+sa)1.157e-20
(sd+sc+sc+sb)8.036e-21
(sd+sc+sc+sc)6.506e-21
(sd+sd+sd)5.002e-21
(sd+sd+sc+sb)3.843e-21
(sd+sc+sb+sa)3.828e-21
(sa+sa+sb+sb)3.778e-21
(sa+sa+sa)3.743e-21
(sc+sa+sb+sa)3.277e-21
(sd+sd+sd+sb)2.575e-21
(sd+sc+sa+sa)1.709e-21
(sc+sb+sc+sa)1.683e-21
(sc+sc+sb+sb)1.306e-21
(sd+sc+sb+sb)9.706e-22
(sb+sb+sb)5.862e-22
(sa+sa+sa+sb)5.043e-22
(sc+sb+sb+sb)3.302e-22
(sd+sb+sb+sa)3.110e-22
(sd+sc+sc+sa)1.951e-22
(sd+sb+sb+sb)1.897e-22
(sc+sc+sc)1.868e-22
(sc+sc+sc+sb)1.383e-22
(sa+sb+sb+sb)9.498e-23
(sd+sb+sa+sa)8.601e-23
(sd+sd+sd+sd)1.070e-23
(sc+sb+sb+sa)5.609e-24
(sc+sa+sa+sa)4.751e-25
(sc+sc+sa+sa)2.446e-25
(sc+sc+sb+sa)2.438e-25
(sc+sb+sa+sa)1.870e-25
(sc+sa+sc+sa)1.455e-25
(sc+sc+sc+sa)4.313e-26
(sa+sa+sa+sa)4.299e-26
(sb+sb+sb+sb)7.246e-27
(sc+sc+sc+sc)1.956e-28
" ], "text/plain": [ "Result(tubes={Tube({: 1e-06, : 1e-06, : 1e-06, : 1e-06}, complexes=[, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ], name='tfigure'): }, complexes={: nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.544284811026830803705260324E+43, free_energy: -58.81767708462843}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.589476070288794383384557813E+37, free_energy: -50.410386502253786}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.568730417625749213876507522E+45, free_energy: -61.87232131472013}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.877424756436274409022616782E+31, free_energy: -43.04954342994555}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.931018775394350185833714819E+40, free_energy: -54.59015086330549}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.808512635439643494099865662E+44, free_energy: -60.83267301490221}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6189123051624.958161122794995, free_energy: -17.33358149447413}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.910602740340594220477749539E+46, free_energy: -62.71432914153174}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.362414345992277977799368707E+42, free_energy: -57.09503267086502}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.758036308089081432401269137E+34, free_energy: -46.85156973920628}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.333886056722796966694630209E+41, free_energy: -56.42097675814823}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.266158713012223382828904224E+41, free_energy: -56.72509208489151}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.09334151984997818802463804E+44, free_energy: -60.686714393706104}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.722834919555519783634010627E+37, free_energy: -50.72715810461238}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.873636740667201754124795658E+42, free_energy: -57.84512470676748}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7357486819876679998065923468, free_energy: -37.76143149672111}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.786560114986642096417462238E+45, free_energy: -62.105196126146886}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.003034250374144871681101682E+54, free_energy: -74.12141271775798, pairs: [[9.99994424e-01 0.00000000e+00 0.00000000e+00 ... 0.00000000e+00\n", " 0.00000000e+00 0.00000000e+00]\n", " [0.00000000e+00 9.99068539e-01 0.00000000e+00 ... 0.00000000e+00\n", " 9.31074879e-04 0.00000000e+00]\n", " [0.00000000e+00 0.00000000e+00 1.33339752e-03 ... 0.00000000e+00\n", " 9.98660813e-01 0.00000000e+00]\n", " ...\n", " [0.00000000e+00 0.00000000e+00 0.00000000e+00 ... 0.00000000e+00\n", " 0.00000000e+00 0.00000000e+00]\n", " [0.00000000e+00 9.31074879e-04 9.98660813e-01 ... 0.00000000e+00\n", " 4.01037439e-04 0.00000000e+00]\n", " [0.00000000e+00 0.00000000e+00 0.00000000e+00 ... 0.00000000e+00\n", " 0.00000000e+00 9.99999620e-01]]}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.403568965828856660353375460E+39, free_energy: -53.56862702600549}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.300378508077805072508768829E+38, free_energy: -52.57594458379157}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3718621340710530939146953808, free_energy: -37.35985917865833}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.660768832727184605050817483E+48, free_energy: -65.3420022807908}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 132268925918904365.5665910929, free_energy: -23.200812173598372}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.722135997409701190711290203E+28, free_energy: -39.06335482269422}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.571352530179481964560602740E+45, free_energy: -61.24421565139995}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.339088911084841578060445250E+46, free_energy: -63.5815051918645}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.025864404554114277178991718E+28, free_energy: -38.357501866485734}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.331298939573458336117592107E+44, free_energy: -60.87081071066809}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2261672905755167709142750.534, free_energy: -33.00201168552128}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.672875945201362197140375964E+36, free_energy: -50.05387938240768}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.379098682208472125755117207E+28, free_energy: -38.93218683445771}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.188704482757775431233315468E+42, free_energy: -57.01476455011915}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.389196637530676401135364609E+42, free_energy: -57.63135340395438}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.223020467305858276175647198E+39, free_energy: -53.317950730548276}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.452566131695420063093207908E+41, free_energy: -56.085925983869856}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.679139230345414689064515018E+38, free_energy: -52.61030088923777}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.791864170843433089621274009E+40, free_energy: -54.8071084829783}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.288639164342157458193306895E+39, free_energy: -52.99705318086303}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3572990070740708383.154641273, free_energy: -25.140698333659763}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.959920606269993436380977157E+42, free_energy: -57.30903824155615}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 34134368253602243773147216.64, free_energy: -34.59931944731638}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.102426796059121327834251288E+31, free_energy: -43.23847849344226}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.885422242957555598902208887E+43, free_energy: -58.64130481324193}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 9.456170346659172539010548487E+43, free_energy: -59.59027092736584}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.688336070366307130393451495E+40, free_energy: -55.47521645117254}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.684171798022777472941911062E+41, free_energy: -56.46671766330743}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.493968725621461479402231829E+48, free_energy: -65.9278282757944}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.220595511809000174663998719E+35, free_energy: -48.115818547183714}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.953956919143205259482339901E+36, free_energy: -49.59162196204926}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.941316491744040258347628352E+43, free_energy: -59.487525579828755}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1836438601753438.344881865200, free_energy: -20.68379067722919}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8099590740599410444452758033, free_energy: -37.817983515678726}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.480801421737116811651782615E+44, free_energy: -60.15787913494589}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.461365129520877984837010208E+34, free_energy: -47.25518792636268}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 9262142466027659908599799570, free_energy: -37.89691428049043}), : 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T=296.15 K), pfunc: 3.566688228697953914526589612E+31, free_energy: -42.75559854551109}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 106.8202319689570600405195505, free_energy: -2.7489720608520134}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.659734920976677209134369380E+36, free_energy: -49.80269364819048}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.943517636006589811055540147E+39, free_energy: -53.48316544822558}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.703133528782668942484302605E+41, free_energy: -56.46909512964943}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 53855.15781598668633780373038, free_energy: -6.4111547693182045}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.811193585932796332804646267E+37, free_energy: -51.1733075511765}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 664671136603147385.4336657391, free_energy: -24.15091970865827}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.840577982354796966463712364E+36, free_energy: -49.396999418328264}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 11952757497989701636737.77755, free_energy: -29.916564116890296}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.199088841712758054332674780E+47, free_energy: -64.76205666828247}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.529110639431551904833848668E+37, free_energy: -50.38760084895049}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1517364998043931757753.389314, free_energy: -28.701907111078043}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.539757735743711889434146211E+46, free_energy: -62.58733447930865}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.752391823008671654572441954E+41, free_energy: -56.153800918491214}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6386025385224.995953957853155, free_energy: -17.3520125409488}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.785939209880330178304214940E+41, free_energy: -56.16093046412121}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.314700924552781952507404892E+30, free_energy: -40.81318626290341}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1816505678607953227273151928, free_energy: -36.93823495960752}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.755850393504699548415462444E+45, free_energy: -62.18376283881961}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.439260383902813481083121967E+41, free_energy: -55.77225202586549}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 406462509739921430536.8778525, free_energy: -27.92671152229136}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.125787285665219310535580485E+44, free_energy: -59.69290552475951}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.199074458835117348962723911E+43, free_energy: -59.23823772714207}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.075676349384822278900963149E+44, free_energy: -60.77467543814712}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.036341714963579414028088933E+42, free_energy: -57.86445079252854}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7296317.210958786528648361474, free_energy: -9.300001299038938}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.209671398717080156831590727E+42, free_energy: -58.07557142894261}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.783290241314234392400555472E+29, free_energy: -40.57581861913995}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.95391790622138528766145831E+39, free_energy: -53.78952311104192}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.171057435378845335958397486E+33, free_energy: -44.81031226005474}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.150407012108254691372221343E+39, free_energy: -52.930275483752915}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.873252380825980941628426093E+46, free_energy: -63.54767658432633}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 20554237143251957119.42285325, free_energy: -26.170376470110003}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 130459230680290.9419459003166, free_energy: -19.127488044073267})})" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# For more detail, display the analysis results performed on the designed tube ensemble\n", "my_results.analysis_result" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "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": "3.7.8" } }, "nbformat": 4, "nbformat_minor": 4 }