{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Complex design example\n",
"\n",
"Design a complex ensemble intend to predominantly adopt a 4-stranded stick figure target structure. \n",
"\n",
"Material: RNA \n",
"Temperature: 23 C\n",
"\n",
"While we illustrate complex design, we recommend performing test tube design so that it is possible to actively design against formation of off-target complexes that can compete with the desired on-target complex in solution (see tube design example notebook). Indeed, we show at the bottom of this example that a test tube analysis reveals that while the designed sequences perform well within the context of the complex ensemble (as intended by the complex design algorithm), the on-target complex is out-competed by off-target complexes in the context of a test tube ensemble. "
]
},
{
"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",
" Domain | \n",
" Sequence | \n",
"
\n",
" \n",
" \n",
" \n",
" da | \n",
" GCGCUACCUCGAAUCUGGGGCCCCGAA | \n",
"
\n",
" \n",
" da* | \n",
" UUCGGGGCCCCAGAUUCGAGGUAGCGC | \n",
"
\n",
" \n",
" db | \n",
" GGGGCCAUGAAAAUUGAGCAUCGACCCGC | \n",
"
\n",
" \n",
" db* | \n",
" GCGGGUCGAUGCUCAAUUUUCAUGGCCCC | \n",
"
\n",
" \n",
" dc | \n",
" AGGGUCGCCAGAUGACCGUUUGCAG | \n",
"
\n",
" \n",
" dc* | \n",
" CUGCAAACGGUCAUCUGGCGACCCU | \n",
"
\n",
" \n",
" dd | \n",
" GGCAAACGGGAGGUAGCA | \n",
"
\n",
" \n",
" dd* | \n",
" UGCUACCUCCCGUUUGCC | \n",
"
\n",
" \n",
"
Strand results:\n",
"\n",
" \n",
" \n",
" Strand | \n",
" Sequence | \n",
"
\n",
" \n",
" \n",
" \n",
" sa | \n",
" GCGCUACCUCGAAUCUGGGGCCCCGAA | \n",
"
\n",
" \n",
" sd | \n",
" GGCAAACGGGAGGUAGCA | \n",
"
\n",
" \n",
" sb | \n",
" GGGGCCAUGAAAAUUGAGCAUCGACCCGC | \n",
"
\n",
" \n",
" sc | \n",
" AGGGUCGCCAGAUGACCGUUUGCAG | \n",
"
\n",
" \n",
"
Objective function:\n",
" \n",
" \n",
" Objective type | \n",
" Value | \n",
"
\n",
" \n",
" \n",
" \n",
" Weighted ensemble defect | \n",
" 0.00757 | \n",
"
\n",
" \n",
"
Ensemble defect: 0.00757
On-target complex defects:\n",
" \n",
" \n",
" Complex | \n",
" Complex defect (nt) | \n",
" Normalized complex defect | \n",
"
\n",
" \n",
" \n",
" \n",
" cstickfigure | \n",
" 0.749 | \n",
" 0.00757 | \n",
"
\n",
" \n",
"
"
],
"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",
"# 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 complex design job\n",
"my_design = complex_design(complexes=[cstickfigure], 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",
" Complex | \n",
" Pfunc | \n",
" ΔG (kcal/mol) | \n",
"
\n",
" \n",
" \n",
" \n",
" (sa) | \n",
" 1.0597e+6 | \n",
" -8.165 | \n",
"
\n",
" \n",
" (sb) | \n",
" 1.8567e+6 | \n",
" -8.495 | \n",
"
\n",
" \n",
" (sc) | \n",
" 1.1835e+6 | \n",
" -8.230 | \n",
"
\n",
" \n",
" (sd) | \n",
" 1.6008e+2 | \n",
" -2.987 | \n",
"
\n",
" \n",
" (sa+sa) | \n",
" 2.5625e+23 | \n",
" -31.720 | \n",
"
\n",
" \n",
" (sa+sb) | \n",
" 4.0097e+20 | \n",
" -27.919 | \n",
"
\n",
" \n",
" (sa+sd) | \n",
" 1.2607e+20 | \n",
" -27.238 | \n",
"
\n",
" \n",
" (sb+sb) | \n",
" 2.4243e+16 | \n",
" -22.202 | \n",
"
\n",
" \n",
" (sc+sa) | \n",
" 5.7933e+21 | \n",
" -29.490 | \n",
"
\n",
" \n",
" (sc+sb) | \n",
" 1.1295e+18 | \n",
" -24.463 | \n",
"
\n",
" \n",
" (sc+sc) | \n",
" 1.3968e+19 | \n",
" -25.943 | \n",
"
\n",
" \n",
" (sc+sd) | \n",
" 2.1601e+18 | \n",
" -24.845 | \n",
"
\n",
" \n",
" (sd+sb) | \n",
" 2.6258e+13 | \n",
" -18.184 | \n",
"
\n",
" \n",
" (sd+sd) | \n",
" 1.0269e+7 | \n",
" -9.501 | \n",
"
\n",
" \n",
" (sa+sa+sa) | \n",
" 1.0229e+37 | \n",
" -50.151 | \n",
"
\n",
" \n",
" (sa+sa+sb) | \n",
" 6.0085e+33 | \n",
" -45.773 | \n",
"
\n",
" \n",
" (sa+sa+sd) | \n",
" 1.4544e+40 | \n",
" -54.423 | \n",
"
\n",
" \n",
" (sa+sb+sb) | \n",
" 2.4946e+31 | \n",
" -42.545 | \n",
"
\n",
" \n",
" (sa+sb+sd) | \n",
" 2.7148e+34 | \n",
" -46.660 | \n",
"
\n",
" \n",
" (sa+sd+sb) | \n",
" 1.7840e+28 | \n",
" -38.283 | \n",
"
\n",
" \n",
" (sa+sd+sd) | \n",
" 6.0217e+27 | \n",
" -37.644 | \n",
"
\n",
" \n",
" (sb+sb+sb) | \n",
" 2.8782e+25 | \n",
" -34.499 | \n",
"
\n",
" \n",
" (sc+sa+sa) | \n",
" 6.0344e+35 | \n",
" -48.485 | \n",
"
\n",
" \n",
" (sc+sa+sb) | \n",
" 1.0238e+35 | \n",
" -47.441 | \n",
"
\n",
" \n",
" (sc+sa+sd) | \n",
" 7.2107e+29 | \n",
" -40.460 | \n",
"
\n",
" \n",
" (sc+sb+sa) | \n",
" 5.9588e+29 | \n",
" -40.347 | \n",
"
\n",
" \n",
" (sc+sb+sb) | \n",
" 9.2787e+28 | \n",
" -39.253 | \n",
"
\n",
" \n",
" (sc+sb+sd) | \n",
" 8.6771e+25 | \n",
" -35.148 | \n",
"
\n",
" \n",
" (sc+sc+sa) | \n",
" 1.3566e+33 | \n",
" -44.897 | \n",
"
\n",
" \n",
" (sc+sc+sb) | \n",
" 1.1896e+30 | \n",
" -40.754 | \n",
"
\n",
" \n",
" (sc+sc+sc) | \n",
" 3.6354e+30 | \n",
" -41.412 | \n",
"
\n",
" \n",
" (sc+sc+sd) | \n",
" 4.6909e+29 | \n",
" -40.207 | \n",
"
\n",
" \n",
" (sc+sd+sa) | \n",
" 4.5543e+41 | \n",
" -56.450 | \n",
"
\n",
" \n",
" (sc+sd+sb) | \n",
" 1.2257e+32 | \n",
" -43.482 | \n",
"
\n",
" \n",
" (sc+sd+sd) | \n",
" 7.3386e+24 | \n",
" -33.695 | \n",
"
\n",
" \n",
" (sd+sb+sb) | \n",
" 1.4664e+25 | \n",
" -34.102 | \n",
"
\n",
" \n",
" (sd+sd+sb) | \n",
" 2.5238e+21 | \n",
" -29.001 | \n",
"
\n",
" \n",
" (sd+sd+sd) | \n",
" 1.1394e+13 | \n",
" -17.693 | \n",
"
\n",
" \n",
" cstickfigure | \n",
" 1.8738e+53 | \n",
" -72.188 | \n",
"
\n",
" \n",
" (sa+sa+sa+sa) | \n",
" 1.0299e+55 | \n",
" -74.546 | \n",
"
\n",
" \n",
" (sa+sa+sa+sb) | \n",
" 9.2061e+51 | \n",
" -70.415 | \n",
"
\n",
" \n",
" (sa+sa+sa+sd) | \n",
" 2.9627e+53 | \n",
" -72.458 | \n",
"
\n",
" \n",
" (sa+sa+sb+sb) | \n",
" 1.5702e+45 | \n",
" -61.244 | \n",
"
\n",
" \n",
" (sa+sa+sb+sd) | \n",
" 7.6242e+49 | \n",
" -67.594 | \n",
"
\n",
" \n",
" (sa+sa+sd+sb) | \n",
" 2.0577e+48 | \n",
" -65.468 | \n",
"
\n",
" \n",
" (sa+sa+sd+sd) | \n",
" 1.4858e+46 | \n",
" -62.566 | \n",
"
\n",
" \n",
" (sa+sb+sa+sb) | \n",
" 2.0246e+48 | \n",
" -65.459 | \n",
"
\n",
" \n",
" (sa+sb+sa+sd) | \n",
" 4.2256e+49 | \n",
" -67.247 | \n",
"
\n",
" \n",
" (sa+sb+sb+sb) | \n",
" 3.8497e+42 | \n",
" -57.706 | \n",
"
\n",
" \n",
" (sa+sb+sb+sd) | \n",
" 5.1050e+45 | \n",
" -61.938 | \n",
"
\n",
" \n",
" (sa+sb+sd+sb) | \n",
" 3.8696e+42 | \n",
" -57.709 | \n",
"
\n",
" \n",
" (sa+sb+sd+sd) | \n",
" 1.5428e+46 | \n",
" -62.588 | \n",
"
\n",
" \n",
" (sa+sd+sa+sd) | \n",
" 2.0637e+56 | \n",
" -76.310 | \n",
"
\n",
" \n",
" (sa+sd+sb+sb) | \n",
" 4.4292e+38 | \n",
" -52.369 | \n",
"
\n",
" \n",
" (sa+sd+sb+sd) | \n",
" 5.4192e+38 | \n",
" -52.487 | \n",
"
\n",
" \n",
" (sa+sd+sd+sb) | \n",
" 1.7867e+37 | \n",
" -50.479 | \n",
"
\n",
" \n",
" (sa+sd+sd+sd) | \n",
" 3.8418e+34 | \n",
" -46.865 | \n",
"
\n",
" \n",
" (sb+sb+sb+sb) | \n",
" 6.4718e+35 | \n",
" -48.527 | \n",
"
\n",
" \n",
" (sc+sa+sa+sa) | \n",
" 6.3217e+51 | \n",
" -70.194 | \n",
"
\n",
" \n",
" (sc+sa+sa+sb) | \n",
" 6.1181e+48 | \n",
" -66.109 | \n",
"
\n",
" \n",
" (sc+sa+sa+sd) | \n",
" 8.3118e+49 | \n",
" -67.645 | \n",
"
\n",
" \n",
" (sc+sa+sb+sa) | \n",
" 2.7527e+48 | \n",
" -65.639 | \n",
"
\n",
" \n",
" (sc+sa+sb+sb) | \n",
" 4.3944e+46 | \n",
" -63.204 | \n",
"
\n",
" \n",
" (sc+sa+sb+sd) | \n",
" 1.5949e+44 | \n",
" -59.898 | \n",
"
\n",
" \n",
" (sc+sa+sc+sa) | \n",
" 1.4180e+48 | \n",
" -65.249 | \n",
"
\n",
" \n",
" (sc+sa+sd+sa) | \n",
" 1.7063e+52 | \n",
" -70.778 | \n",
"
\n",
" \n",
" (sc+sa+sd+sb) | \n",
" 2.1218e+41 | \n",
" -56.001 | \n",
"
\n",
" \n",
" (sc+sa+sd+sd) | \n",
" 7.3319e+38 | \n",
" -52.665 | \n",
"
\n",
" \n",
" (sc+sb+sa+sa) | \n",
" 3.8072e+44 | \n",
" -60.410 | \n",
"
\n",
" \n",
" (sc+sb+sa+sb) | \n",
" 2.5332e+44 | \n",
" -60.170 | \n",
"
\n",
" \n",
" (sc+sb+sa+sd) | \n",
" 1.1393e+40 | \n",
" -54.280 | \n",
"
\n",
" \n",
" (sc+sb+sb+sa) | \n",
" 2.6186e+40 | \n",
" -54.769 | \n",
"
\n",
" \n",
" (sc+sb+sb+sb) | \n",
" 5.4074e+39 | \n",
" -53.841 | \n",
"
\n",
" \n",
" (sc+sb+sb+sd) | \n",
" 1.7050e+36 | \n",
" -49.097 | \n",
"
\n",
" \n",
" (sc+sb+sc+sa) | \n",
" 1.7666e+44 | \n",
" -59.958 | \n",
"
\n",
" \n",
" (sc+sb+sc+sb) | \n",
" 1.0917e+44 | \n",
" -59.675 | \n",
"
\n",
" \n",
" (sc+sb+sd+sa) | \n",
" 9.4107e+47 | \n",
" -65.008 | \n",
"
\n",
" \n",
" (sc+sb+sd+sb) | \n",
" 1.3407e+40 | \n",
" -54.375 | \n",
"
\n",
" \n",
" (sc+sb+sd+sd) | \n",
" 3.0956e+33 | \n",
" -45.382 | \n",
"
\n",
" \n",
" (sc+sc+sa+sa) | \n",
" 2.5123e+47 | \n",
" -64.231 | \n",
"
\n",
" \n",
" (sc+sc+sa+sb) | \n",
" 2.4528e+47 | \n",
" -64.216 | \n",
"
\n",
" \n",
" (sc+sc+sa+sd) | \n",
" 1.2799e+42 | \n",
" -57.058 | \n",
"
\n",
" \n",
" (sc+sc+sb+sa) | \n",
" 2.9037e+42 | \n",
" -57.540 | \n",
"
\n",
" \n",
" (sc+sc+sb+sb) | \n",
" 5.7716e+40 | \n",
" -55.235 | \n",
"
\n",
" \n",
" (sc+sc+sb+sd) | \n",
" 3.9260e+37 | \n",
" -50.943 | \n",
"
\n",
" \n",
" (sc+sc+sc+sa) | \n",
" 2.2602e+45 | \n",
" -61.458 | \n",
"
\n",
" \n",
" (sc+sc+sc+sb) | \n",
" 7.0351e+41 | \n",
" -56.706 | \n",
"
\n",
" \n",
" (sc+sc+sc+sc) | \n",
" 4.2920e+43 | \n",
" -59.125 | \n",
"
\n",
" \n",
" (sc+sc+sc+sd) | \n",
" 4.3767e+41 | \n",
" -56.427 | \n",
"
\n",
" \n",
" (sc+sc+sd+sa) | \n",
" 1.6042e+53 | \n",
" -72.097 | \n",
"
\n",
" \n",
" (sc+sc+sd+sb) | \n",
" 1.7566e+43 | \n",
" -58.600 | \n",
"
\n",
" \n",
" (sc+sc+sd+sd) | \n",
" 9.1479e+37 | \n",
" -51.440 | \n",
"
\n",
" \n",
" (sc+sd+sa+sa) | \n",
" 1.2981e+57 | \n",
" -77.393 | \n",
"
\n",
" \n",
" (sc+sd+sa+sd) | \n",
" 1.3168e+46 | \n",
" -62.495 | \n",
"
\n",
" \n",
" (sc+sd+sb+sa) | \n",
" 6.4436e+49 | \n",
" -67.495 | \n",
"
\n",
" \n",
" (sc+sd+sb+sb) | \n",
" 5.8549e+42 | \n",
" -57.953 | \n",
"
\n",
" \n",
" (sc+sd+sb+sd) | \n",
" 5.1934e+39 | \n",
" -53.817 | \n",
"
\n",
" \n",
" (sc+sd+sc+sa) | \n",
" 2.6029e+51 | \n",
" -69.672 | \n",
"
\n",
" \n",
" (sc+sd+sc+sb) | \n",
" 2.8132e+43 | \n",
" -58.877 | \n",
"
\n",
" \n",
" (sc+sd+sc+sd) | \n",
" 2.5098e+42 | \n",
" -57.455 | \n",
"
\n",
" \n",
" (sc+sd+sd+sa) | \n",
" 3.3264e+51 | \n",
" -69.816 | \n",
"
\n",
" \n",
" (sc+sd+sd+sb) | \n",
" 7.0230e+38 | \n",
" -52.640 | \n",
"
\n",
" \n",
" (sc+sd+sd+sd) | \n",
" 1.7724e+31 | \n",
" -42.344 | \n",
"
\n",
" \n",
" (sd+sb+sb+sb) | \n",
" 1.7512e+36 | \n",
" -49.112 | \n",
"
\n",
" \n",
" (sd+sb+sd+sb) | \n",
" 2.0865e+36 | \n",
" -49.215 | \n",
"
\n",
" \n",
" (sd+sd+sb+sb) | \n",
" 1.0407e+34 | \n",
" -46.096 | \n",
"
\n",
" \n",
" (sd+sd+sd+sb) | \n",
" 6.7116e+27 | \n",
" -37.707 | \n",
"
\n",
" \n",
" (sd+sd+sd+sd) | \n",
" 1.3787e+19 | \n",
" -25.935 | \n",
"
\n",
" \n",
"
Concentration results: \n",
" \n",
" \n",
" Complex | \n",
" Tube (M) | \n",
" | \n",
"
\n",
" \n",
" \n",
" \n",
" (sb) | \n",
" 9.999e-09 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sa) | \n",
" 9.746e-09 | \n",
" | \n",
"
\n",
" \n",
" (sc) | \n",
" 2.511e-10 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sa+sd) | \n",
" 1.162e-10 | \n",
" | \n",
"
\n",
" \n",
" (sd) | \n",
" 1.208e-11 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sd) | \n",
" 6.007e-12 | \n",
" | \n",
"
\n",
" \n",
" (sa) | \n",
" 4.340e-12 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sa+sa) | \n",
" 2.055e-12 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd) | \n",
" 7.040e-13 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd) | \n",
" 6.248e-13 | \n",
" | \n",
"
\n",
" \n",
" cstickfigure | \n",
" 3.900e-13 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb) | \n",
" 1.597e-13 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sd+sa) | \n",
" 9.703e-14 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa) | \n",
" 9.094e-14 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa) | \n",
" 7.765e-14 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb) | \n",
" 2.331e-14 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sd) | \n",
" 1.474e-14 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sd+sa) | \n",
" 1.316e-14 | \n",
" | \n",
"
\n",
" \n",
" (sb+sb) | \n",
" 1.270e-14 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc) | \n",
" 1.136e-14 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sb) | \n",
" 3.449e-15 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sc+sa) | \n",
" 2.135e-16 | \n",
" | \n",
"
\n",
" \n",
" (sd+sb) | \n",
" 1.928e-16 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sb) | \n",
" 1.563e-16 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sb+sa) | \n",
" 1.341e-16 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sd+sa) | \n",
" 2.701e-17 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sd+sd) | \n",
" 1.142e-17 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sa+sd) | \n",
" 9.052e-18 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sb+sd) | \n",
" 3.063e-18 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sd+sa) | \n",
" 1.959e-18 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sa+sd) | \n",
" 1.698e-18 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sb) | \n",
" 9.666e-19 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sa) | \n",
" 7.007e-19 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sd) | \n",
" 5.200e-19 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sa+sd) | \n",
" 3.841e-19 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sb+sd) | \n",
" 2.696e-19 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sa) | \n",
" 2.293e-19 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sb) | \n",
" 1.863e-19 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sb) | \n",
" 1.771e-19 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sa+sd) | \n",
" 1.316e-19 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sb) | \n",
" 9.409e-20 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sd+sb) | \n",
" 8.266e-20 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sa) | \n",
" 8.161e-20 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sd) | \n",
" 4.583e-20 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sa+sb) | \n",
" 2.007e-20 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sa+sa) | \n",
" 1.708e-20 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sb+sb) | \n",
" 1.602e-20 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sd) | \n",
" 1.543e-20 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sc) | \n",
" 1.133e-20 | \n",
" | \n",
"
\n",
" \n",
" (sd+sb+sb) | \n",
" 1.047e-20 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sb) | \n",
" 9.688e-21 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sd+sd) | \n",
" 8.365e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sb+sb) | \n",
" 6.525e-21 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sa+sb) | \n",
" 5.803e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sc+sd) | \n",
" 3.793e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sc+sb) | \n",
" 3.033e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sd) | \n",
" 2.894e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sd) | \n",
" 2.441e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sd+sb) | \n",
" 1.894e-21 | \n",
" | \n",
"
\n",
" \n",
" (sb+sb+sb) | \n",
" 1.466e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sa+sb) | \n",
" 1.435e-21 | \n",
" | \n",
"
\n",
" \n",
" (sd+sd) | \n",
" 1.057e-21 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sa) | \n",
" 9.098e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sc+sb) | \n",
" 8.398e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sa+sb) | \n",
" 6.910e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sa+sa) | \n",
" 5.430e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sb+sd) | \n",
" 3.319e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sb+sa) | \n",
" 3.109e-22 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sd+sb) | \n",
" 2.044e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sb+sd) | \n",
" 1.992e-22 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sa+sb) | \n",
" 3.762e-23 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sd+sb) | \n",
" 3.669e-23 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sd+sb) | \n",
" 2.693e-23 | \n",
" | \n",
"
\n",
" \n",
" (sd+sd+sb) | \n",
" 2.526e-23 | \n",
" | \n",
"
\n",
" \n",
" (sa+sb+sb+sb) | \n",
" 1.451e-23 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sc+sa) | \n",
" 6.310e-24 | \n",
" | \n",
"
\n",
" \n",
" (sa+sa+sb+sb) | \n",
" 4.501e-24 | \n",
" | \n",
"
\n",
" \n",
" (sd+sb+sd+sb) | \n",
" 2.031e-24 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sc+sd) | \n",
" 1.859e-24 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sa+sa) | \n",
" 1.118e-24 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sb+sb) | \n",
" 1.056e-24 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sc+sa) | \n",
" 1.034e-24 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sc+sa) | \n",
" 5.211e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sc+sc) | \n",
" 5.126e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sb+sb) | \n",
" 4.440e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sd+sb) | \n",
" 4.416e-25 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sb+sd) | \n",
" 4.012e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sc+sb) | \n",
" 2.133e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sd+sd) | \n",
" 1.382e-25 | \n",
" | \n",
"
\n",
" \n",
" (sd+sb+sb+sb) | \n",
" 1.216e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sa+sd) | \n",
" 1.050e-25 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sa+sa) | \n",
" 4.300e-26 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sa+sd) | \n",
" 2.371e-26 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sb+sb) | \n",
" 2.339e-26 | \n",
" | \n",
"
\n",
" \n",
" (sc+sa+sd+sd) | \n",
" 2.139e-26 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sb+sa) | \n",
" 1.699e-26 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sd+sb) | \n",
" 1.323e-26 | \n",
" | \n",
"
\n",
" \n",
" (sd+sd+sb+sb) | \n",
" 1.013e-26 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sb+sd) | \n",
" 4.666e-27 | \n",
" | \n",
"
\n",
" \n",
" (sc+sc+sb+sd) | \n",
" 4.233e-27 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sb+sa) | \n",
" 3.888e-27 | \n",
" | \n",
"
\n",
" \n",
" (sb+sb+sb+sb) | \n",
" 3.207e-27 | \n",
" | \n",
"
\n",
" \n",
" (sa+sd+sd+sd) | \n",
" 3.986e-28 | \n",
" | \n",
"
\n",
" \n",
" (sc+sb+sd+sd) | \n",
" 1.187e-28 | \n",
" | \n",
"
\n",
" \n",
" (sc+sd+sd+sd) | \n",
" 9.527e-30 | \n",
" | \n",
"
\n",
" \n",
" (sd+sd+sd) | \n",
" 1.598e-30 | \n",
" | \n",
"
\n",
" \n",
" (sd+sd+sd+sb) | \n",
" 9.156e-32 | \n",
" | \n",
"
\n",
" \n",
" (sd+sd+sd+sd) | \n",
" 2.636e-39 | \n",
" | \n",
"
\n",
" \n",
"
"
],
"text/plain": [
"Result(tubes={Tube({: 1e-08, : 1e-08, : 1e-08, : 1e-08}, complexes=[, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ], name='Tube'): }, complexes={: nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.925965483E+37, free_energy: -50.942513184053134}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.751165123E+36, free_energy: -49.11232636117192}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.454400996E+40, free_energy: -54.4233383091073}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 11394069163333.33333333333333, free_energy: -17.69274303063441}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 9.278745612E+28, free_energy: -39.25304050894512}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.034419013E+35, free_energy: -48.485345770439665}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.424343757E+16, free_energy: -22.202308729914478}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 9.206133687E+51, free_energy: -70.41507848639363}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.356559985E+33, free_energy: -44.89684826608889}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.321652604E+51, free_energy: -70.1938674817425}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.512287385E+47, free_energy: -64.23051800681051}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.793274681E+21, free_energy: -29.490334291266734}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.260159076E+45, free_energy: -61.45813464236617}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.841834448E+34, free_energy: -46.86454818016195}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.260746829E+20, free_energy: -27.23780281057037}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.024625255E+48, free_energy: -65.45858654953352}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.706316883E+52, free_energy: -70.77821401123524}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.594941457E+44, free_energy: -59.89791224511029}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 9.147850749E+37, free_energy: -51.4403295862042}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 6.711550486E+27, free_energy: -37.70735512840071}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.139344506E+40, free_energy: -54.279661218463865}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.407408552E+39, free_energy: -53.841070571343046}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.602917099E+51, free_energy: -69.67166290073234}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.063693609E+56, free_energy: -76.310412323734}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.023018617E+38, free_energy: -52.639845966891905}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1059661.507, free_energy: -8.164536745355198}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.873821969E+53, free_energy: -72.18839519210763}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.854887132E+42, free_energy: -57.95307704026436}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 9.410735746E+47, free_energy: -65.00772546275071}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.784000427E+28, free_energy: -38.282680984094675}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.63536047E+30, free_energy: -41.411749466028155}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.225627319E+49, free_energy: -67.24666743480999}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.429184662E+38, free_energy: -52.368560461089494}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.533193265E+44, free_energy: -60.17017820775662}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.376692408E+41, free_energy: -56.42676093365913}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.714847500E+34, free_energy: -46.66021249143298}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.298141846E+57, free_energy: -77.39267725940185}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 5.193442782E+39, free_energy: -53.8173109619057}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.022909619E+37, free_energy: -50.151003003587775}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.040719716E+34, free_energy: -46.09594461564143}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1183498.711, free_energy: -8.22958106715837}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.2919639925E+43, free_energy: -59.1254009060048}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.311777183E+49, free_energy: -67.64479131803293}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.338605634E+24, free_energy: -33.694702599883406}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.849670498E+42, free_energy: -57.7063252037428}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 8.677079671E+25, free_energy: -35.14836994136604}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.279882576E+42, free_energy: -57.058257255318935}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.129467216E+18, free_energy: -24.462947869627612}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.210678533E+29, free_energy: -40.45971453936263}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.618616652E+40, free_energy: -54.76940717523887}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.570248082E+45, free_energy: -61.24380186994228}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.417959674E+48, free_energy: -65.24898293240331}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.786694886E+37, free_energy: 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free_energy: -62.566322811130334}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.121819240E+41, free_energy: -56.00067521382114}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.766646407E+44, free_energy: -59.95808407573519}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.772387143E+31, free_energy: -42.34405422108897}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.340702767E+40, free_energy: -54.375434259395554}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.316823893E+46, free_energy: -62.495291608669845}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.807231662E+44, free_energy: -60.409946015913185}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 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'rna06.json', T=296.15 K), pfunc: 5.105040513E+45, free_energy: -61.937640756256975}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.452769954E+47, free_energy: -64.21640831703188}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.5098088405E+42, free_energy: -57.45457593457835}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.5625210395E+23, free_energy: -31.720435373955596}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.023777671E+35, free_energy: -47.44135772391766}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 4.690892642E+29, free_energy: -40.206694583023356}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.624179204E+49, free_energy: -67.5939750295437}), : nupack.analysis.ComplexResult({model: 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nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.331888564E+38, free_energy: -52.665175025867235}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.494630233E+31, free_energy: -42.54521142945244}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 7.035146294E+41, free_energy: -56.706078054192595}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 1.0299467155E+55, free_energy: -74.54633800581672}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 3.095615459E+33, free_energy: -45.382381495367916}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.625847910E+13, free_energy: -18.184079644381853}), : nupack.analysis.ComplexResult({model: Model('stacking', 'rna06.json', T=296.15 K), pfunc: 2.0864652525E+36, free_energy: -49.215425755000005})})"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Analyze a test tube ensemble containing the designed sequences formaing all complexes of up to 4 strands\n",
"# Fromn the list of concentrations below, we see that the on-target complex \"cstickfigure\" is dominated by \n",
"# many off-target complexes. This can be avoided by activately designing against formation of the off-target \n",
"# complexes using test tube design. \n",
"\n",
"\n",
"on_target = my_results.to_analysis(cstickfigure)\n",
"my_tube = Tube(strands={s: 1e-8 for s in on_target.strands}, \n",
" complexes=SetSpec(max_size=4, include=[on_target]), name='Tube')\n",
"tube_analysis(tubes=[my_tube], model=my_model)"
]
}
],
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