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dotsdl/Refactor_subsampling.ipynb

Created January 29, 2020 06:06
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Usage demo of refactored subsampling functions in alchemlyb
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Refactor_subsampling.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Refactoring the `alchemlyb.preprocessing.subsampling` module"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from alchemlyb.preprocessing import subsampling\n",
"from alchemlyb.parsing import gmx\n",
"from alchemtest.gmx import load_expanded_ensemble_case_1\n",
"\n",
"import pandas as pd"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"ds = load_expanded_ensemble_case_1()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Gromacs: Host CB7 and Guest C3 in water\n",
"=======================================\n",
"\n",
"Host CB7 and Guest C3 in water, Guest C3 alchemically turned into Guest C3 in vacuum separated from water and Host CB7. This unpublished data uses Host CB7 and Guest C3 from [Muddana2014a]_. Similar published data can be found in [Monroe2014a]_.\n",
"\n",
"Notes\n",
"-----\n",
"Data Set Characteristics:\n",
" :Number of Legs: 2 (Coulomb, VDW)\n",
" :Number of Windows: 32 total, 20 for Coulomb, 12 for VDW\n",
" :Number of Simulations: 1\n",
" :Length of Simulation: 100ns\n",
" :System Size: 8286 atoms\n",
" :Temperature: 300 K\n",
" :Alchemical Pathway: vdw + coul --> vdw --> vacuum\n",
" :Missing Values: None\n",
" :Energy unit: kJ/mol\n",
" :Time unit: ps\t\t \t\t \n",
" :Creator: \\T. Jensen\n",
" :Donor: Travis Jensen (travis.jensen@colorado.edu)\n",
" :Date: November 2017\n",
" :License: `CC0 <https://creativecommons.org/publicdomain/zero/1.0/>`_ Public Domain Dedication \n",
"\n",
"\n",
"This dataset was generated using the expanded ensemble algorithm in the `Gromacs <http://www.gromacs.org/>`_ molecular dynamics engine.\n",
"\n",
".. [Muddana2014a] H. Muddana, A. Fenley, D. Mobley, and M. Gilson. The SAMPL4 host–guest blind prediction challenge: an overview. Journal of Computer-Aided Molecular Design, 28(4):305–317, 2014. PMID: 24599514. DOI: `10.1007/s10822-014-9735-1 <https://doi.org/10.1007/s10822-014-9735-1>`_.\n",
"\n",
".. [Monroe2014a] J. Monroe and M. Shirts. Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. Journal of Computer-Aided Molecular Design, 28(4):401–415, 2014. PMID: 24610238 DOI: `10.1007/s10822-014-9716-4 <https://doi.org/10.1007/s10822-014-9716-4>`_.\n",
"\n"
]
}
],
"source": [
"print(ds.DESCR)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
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],
"text/plain": [
" (0.0, 0.0, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36416.048617 \n",
"2.0 0.0 1.00 0.4 0.0020 -36472.655852 \n",
"4.0 0.0 1.00 0.3 0.0010 -36420.169969 \n",
"6.0 0.0 0.22 0.0 0.0000 -36480.483060 \n",
"8.0 0.0 0.16 0.0 0.0000 -36556.217962 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36546.252507 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36548.243186 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36800.201423 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36404.518763 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36566.406054 \n",
"\n",
" (0.0, 0.05, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36417.317190 \n",
"2.0 0.0 1.00 0.4 0.0020 -36474.116119 \n",
"4.0 0.0 1.00 0.3 0.0010 -36421.307675 \n",
"6.0 0.0 0.22 0.0 0.0000 -36475.577879 \n",
"8.0 0.0 0.16 0.0 0.0000 -36550.639739 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36540.845355 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36547.664008 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36793.801417 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36405.480799 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36566.014993 \n",
"\n",
" (0.0, 0.1, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36418.585730 \n",
"2.0 0.0 1.00 0.4 0.0020 -36475.576386 \n",
"4.0 0.0 1.00 0.3 0.0010 -36422.445070 \n",
"6.0 0.0 0.22 0.0 0.0000 -36470.672758 \n",
"8.0 0.0 0.16 0.0 0.0000 -36545.061520 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36535.438229 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36547.084795 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36787.401306 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36406.442786 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36565.623970 \n",
"\n",
" (0.0, 0.16, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36420.107981 \n",
"2.0 0.0 1.00 0.4 0.0020 -36477.328670 \n",
"4.0 0.0 1.00 0.3 0.0010 -36423.810059 \n",
"6.0 0.0 0.22 0.0 0.0000 -36464.786695 \n",
"8.0 0.0 0.16 0.0 0.0000 -36538.367687 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36528.949560 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36546.389831 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36779.721219 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36407.597235 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36565.154682 \n",
"\n",
" (0.0, 0.22, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36421.630235 \n",
"2.0 0.0 1.00 0.4 0.0020 -36479.080913 \n",
"4.0 0.0 1.00 0.3 0.0010 -36425.175113 \n",
"6.0 0.0 0.22 0.0 0.0000 -36458.900530 \n",
"8.0 0.0 0.16 0.0 0.0000 -36531.673818 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36522.460915 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36545.694809 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36772.041130 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36408.751553 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36564.685451 \n",
"\n",
" (0.0, 0.28, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36423.152521 \n",
"2.0 0.0 1.00 0.4 0.0020 -36480.833176 \n",
"4.0 0.0 1.00 0.3 0.0010 -36426.540117 \n",
"6.0 0.0 0.22 0.0 0.0000 -36453.014437 \n",
"8.0 0.0 0.16 0.0 0.0000 -36524.979976 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36515.972369 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36544.999807 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36764.361004 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36409.905883 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36564.216229 \n",
"\n",
" (0.0, 0.34, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36424.674698 \n",
"2.0 0.0 1.00 0.4 0.0020 -36482.585473 \n",
"4.0 0.0 1.00 0.3 0.0010 -36427.905183 \n",
"6.0 0.0 0.22 0.0 0.0000 -36447.128270 \n",
"8.0 0.0 0.16 0.0 0.0000 -36518.286112 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36509.483672 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36544.304813 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36756.680928 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36411.060332 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36563.746979 \n",
"\n",
" (0.0, 0.4, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36426.196979 \n",
"2.0 0.0 1.00 0.4 0.0020 -36484.337738 \n",
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"6.0 0.0 0.22 0.0 0.0000 -36441.242239 \n",
"8.0 0.0 0.16 0.0 0.0000 -36511.592274 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36502.995070 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36543.609792 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36749.000852 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36412.214688 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36563.277746 \n",
"\n",
" (0.0, 0.46, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36427.719234 \n",
"2.0 0.0 1.00 0.4 0.0020 -36486.090016 \n",
"4.0 0.0 1.00 0.3 0.0010 -36430.635267 \n",
"6.0 0.0 0.22 0.0 0.0000 -36435.356066 \n",
"8.0 0.0 0.16 0.0 0.0000 -36504.898418 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36496.506480 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36542.914817 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36741.320756 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36413.369122 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36562.808486 \n",
"\n",
" (0.0, 0.52, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36429.241427 \n",
"2.0 0.0 1.00 0.4 0.0020 -36487.842279 \n",
"4.0 0.0 1.00 0.3 0.0010 -36432.000316 \n",
"6.0 0.0 0.22 0.0 0.0000 -36429.469962 \n",
"8.0 0.0 0.16 0.0 0.0000 -36498.204568 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36490.017839 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36542.219793 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36733.640693 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36414.523467 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36562.339245 \n",
"\n",
" ... \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda ... \n",
"0.0 0.0 1.00 0.1 0.0002 ... \n",
"2.0 0.0 1.00 0.4 0.0020 ... \n",
"4.0 0.0 1.00 0.3 0.0010 ... \n",
"6.0 0.0 0.22 0.0 0.0000 ... \n",
"8.0 0.0 0.16 0.0 0.0000 ... \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 ... \n",
"99994.0 0.0 0.60 0.0 0.0000 ... \n",
"99996.0 0.0 0.00 0.0 0.0000 ... \n",
"99998.0 0.0 1.00 0.0 0.0001 ... \n",
"100000.0 0.0 0.68 0.0 0.0000 ... \n",
"\n",
" (0.0, 1.0, 0.3, 0.001) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36433.674464 \n",
"2.0 0.0 1.00 0.4 0.0020 -36521.062826 \n",
"4.0 0.0 1.00 0.3 0.0010 -36441.414131 \n",
"6.0 0.0 0.22 0.0 0.0000 -36377.732738 \n",
"8.0 0.0 0.16 0.0 0.0000 -36433.927662 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36423.390664 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36520.191829 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36662.057176 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36410.186669 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36544.017270 \n",
"\n",
" (0.0, 1.0, 0.4, 0.002) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36428.199010 \n",
"2.0 0.0 1.00 0.4 0.0020 -36519.140146 \n",
"4.0 0.0 1.00 0.3 0.0010 -36436.793983 \n",
"6.0 0.0 0.22 0.0 0.0000 -36372.767346 \n",
"8.0 0.0 0.16 0.0 0.0000 -36428.332808 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36417.209752 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36513.682061 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36656.450596 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36404.319812 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36537.780082 \n",
"\n",
" (0.0, 1.0, 0.48, 0.004) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36423.369178 \n",
"2.0 0.0 1.00 0.4 0.0020 -36516.315498 \n",
"4.0 0.0 1.00 0.3 0.0010 -36432.357601 \n",
"6.0 0.0 0.22 0.0 0.0000 -36368.208474 \n",
"8.0 0.0 0.16 0.0 0.0000 -36423.464440 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36412.020063 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36508.302519 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36651.555755 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36399.373632 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36532.534533 \n",
"\n",
" (0.0, 1.0, 0.52, 0.01) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36420.842397 \n",
"2.0 0.0 1.00 0.4 0.0020 -36514.585065 \n",
"4.0 0.0 1.00 0.3 0.0010 -36429.948794 \n",
"6.0 0.0 0.22 0.0 0.0000 -36365.779974 \n",
"8.0 0.0 0.16 0.0 0.0000 -36420.927202 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36409.360316 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36505.566767 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36649.002457 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36396.834263 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36529.844659 \n",
"\n",
" (0.0, 1.0, 0.6, 0.02) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36415.626166 \n",
"2.0 0.0 1.00 0.4 0.0020 -36510.646409 \n",
"4.0 0.0 1.00 0.3 0.0010 -36424.838460 \n",
"6.0 0.0 0.22 0.0 0.0000 -36360.699541 \n",
"8.0 0.0 0.16 0.0 0.0000 -36415.695615 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36403.946548 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36500.035230 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36643.735197 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36391.658260 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36524.367682 \n",
"\n",
" (0.0, 1.0, 0.68, 0.04) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36410.237611 \n",
"2.0 0.0 1.00 0.4 0.0020 -36506.202578 \n",
"4.0 0.0 1.00 0.3 0.0010 -36419.411703 \n",
"6.0 0.0 0.22 0.0 0.0000 -36355.379530 \n",
"8.0 0.0 0.16 0.0 0.0000 -36410.292820 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36398.428717 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36494.434418 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36638.294797 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36386.375961 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36518.784104 \n",
"\n",
" (0.0, 1.0, 0.76, 0.1) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36404.705317 \n",
"2.0 0.0 1.00 0.4 0.0020 -36501.354671 \n",
"4.0 0.0 1.00 0.3 0.0010 -36413.725517 \n",
"6.0 0.0 0.22 0.0 0.0000 -36349.861210 \n",
"8.0 0.0 0.16 0.0 0.0000 -36404.746083 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36392.816424 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36488.758621 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36632.711686 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36381.000093 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36513.104863 \n",
"\n",
" (0.0, 1.0, 0.84, 0.2) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36399.065603 \n",
"2.0 0.0 1.00 0.4 0.0020 -36496.198430 \n",
"4.0 0.0 1.00 0.3 0.0010 -36407.839587 \n",
"6.0 0.0 0.22 0.0 0.0000 -36344.191979 \n",
"8.0 0.0 0.16 0.0 0.0000 -36399.089537 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36387.132412 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36483.024528 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36627.020775 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36375.553599 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36507.353322 \n",
"\n",
" (0.0, 1.0, 0.92, 0.4) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36393.305828 \n",
"2.0 0.0 1.00 0.4 0.0020 -36490.746462 \n",
"4.0 0.0 1.00 0.3 0.0010 -36401.758340 \n",
"6.0 0.0 0.22 0.0 0.0000 -36338.365268 \n",
"8.0 0.0 0.16 0.0 0.0000 -36393.317579 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36381.356231 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36477.191283 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36621.220139 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36370.021459 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36501.510110 \n",
"\n",
" (0.0, 1.0, 1.0, 1.0) \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 -36387.246310 \n",
"2.0 0.0 1.00 0.4 0.0020 -36484.758644 \n",
"4.0 0.0 1.00 0.3 0.0010 -36395.308852 \n",
"6.0 0.0 0.22 0.0 0.0000 -36332.194787 \n",
"8.0 0.0 0.16 0.0 0.0000 -36387.288730 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 -36375.309819 \n",
"99994.0 0.0 0.60 0.0 0.0000 -36470.999236 \n",
"99996.0 0.0 0.00 0.0 0.0000 -36615.185064 \n",
"99998.0 0.0 1.00 0.0 0.0001 -36364.252395 \n",
"100000.0 0.0 0.68 0.0 0.0000 -36495.400679 \n",
"\n",
"[50001 rows x 28 columns]"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"u_nk = gmx.extract_u_nk(ds.data['AllStates'][0], T=300)\n",
"u_nk"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
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" fep coul \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 0.0 -25.370747 \n",
"2.0 0.0 1.00 0.4 0.0020 0.0 -29.204609 \n",
"4.0 0.0 1.00 0.3 0.0010 0.0 -22.750548 \n",
"6.0 0.0 0.22 0.0 0.0000 0.0 98.102009 \n",
"8.0 0.0 0.16 0.0 0.0000 0.0 111.564190 \n",
"... ... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 0.0 108.143665 \n",
"99994.0 0.0 0.60 0.0 0.0000 0.0 11.583392 \n",
"99996.0 0.0 0.00 0.0 0.0000 0.0 128.001486 \n",
"99998.0 0.0 1.00 0.0 0.0001 0.0 -19.239824 \n",
"100000.0 0.0 0.68 0.0 0.0000 0.0 7.820713 \n",
"\n",
" vdw \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 18.818422 \n",
"2.0 0.0 1.00 0.4 0.0020 29.146286 \n",
"4.0 0.0 1.00 0.3 0.0010 39.792327 \n",
"6.0 0.0 0.22 0.0 0.0000 -31.308051 \n",
"8.0 0.0 0.16 0.0 0.0000 11.168792 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 33.530695 \n",
"99994.0 0.0 0.60 0.0 0.0000 40.429575 \n",
"99996.0 0.0 0.00 0.0 0.0000 5.099843 \n",
"99998.0 0.0 1.00 0.0 0.0001 28.486784 \n",
"100000.0 0.0 0.68 0.0 0.0000 31.069375 \n",
"\n",
" restraint \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"0.0 0.0 1.00 0.1 0.0002 0.669507 \n",
"2.0 0.0 1.00 0.4 0.0020 0.980692 \n",
"4.0 0.0 1.00 0.3 0.0010 0.697221 \n",
"6.0 0.0 0.22 0.0 0.0000 0.714655 \n",
"8.0 0.0 0.16 0.0 0.0000 0.543152 \n",
"... ... \n",
"99992.0 0.0 0.16 0.0 0.0000 0.641591 \n",
"99994.0 0.0 0.60 0.0 0.0000 0.900641 \n",
"99996.0 0.0 0.00 0.0 0.0000 0.487645 \n",
"99998.0 0.0 1.00 0.0 0.0001 0.552438 \n",
"100000.0 0.0 0.68 0.0 0.0000 0.630800 \n",
"\n",
"[50001 rows x 4 columns]"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dHdl = gmx.extract_dHdl(ds.data['AllStates'][0], T=300)\n",
"dHdl"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Subsampling - slicing"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\u001b[0;31mSignature:\u001b[0m \u001b[0msubsampling\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mslicing\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlower\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mupper\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstep\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mforce\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mDocstring:\u001b[0m\n",
"Subsample an alchemlyb DataFrame using slicing on the outermost index (time).\n",
"\n",
"Slicing will be performed separately on groups of rows corresponding to\n",
"each set of lambda values present in the DataFrame's index. Each group will\n",
"be sorted on the outermost (time) index prior to slicing.\n",
"\n",
"Parameters\n",
"----------\n",
"df : DataFrame\n",
" DataFrame to subsample.\n",
"lower : float\n",
" Lower time to slice from.\n",
"upper : float\n",
" Upper time to slice to (inclusive).\n",
"step : int\n",
" Step between rows to slice by.\n",
"force : bool\n",
" Ignore checks that DataFrame is in proper form for expected behavior.\n",
"\n",
"Returns\n",
"-------\n",
"DataFrame\n",
" `df` subsampled.\n",
"\u001b[0;31mFile:\u001b[0m ~/Library/alchemistry/alchemlyb/src/alchemlyb/preprocessing/subsampling.py\n",
"\u001b[0;31mType:\u001b[0m function\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"subsampling.slicing?"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
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"<div>\n",
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" vertical-align: middle;\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th>(0.0, 0.0, 0.0, 0.0)</th>\n",
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" <th>(0.0, 0.1, 0.0, 0.0)</th>\n",
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" <th>(0.0, 0.22, 0.0, 0.0)</th>\n",
" <th>(0.0, 0.28, 0.0, 0.0)</th>\n",
" <th>(0.0, 0.34, 0.0, 0.0)</th>\n",
" <th>(0.0, 0.4, 0.0, 0.0)</th>\n",
" <th>(0.0, 0.46, 0.0, 0.0)</th>\n",
" <th>(0.0, 0.52, 0.0, 0.0)</th>\n",
" <th>...</th>\n",
" <th>(0.0, 1.0, 0.3, 0.001)</th>\n",
" <th>(0.0, 1.0, 0.4, 0.002)</th>\n",
" <th>(0.0, 1.0, 0.48, 0.004)</th>\n",
" <th>(0.0, 1.0, 0.52, 0.01)</th>\n",
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" <th>(0.0, 1.0, 0.76, 0.1)</th>\n",
" <th>(0.0, 1.0, 0.84, 0.2)</th>\n",
" <th>(0.0, 1.0, 0.92, 0.4)</th>\n",
" <th>(0.0, 1.0, 1.0, 1.0)</th>\n",
" </tr>\n",
" <tr>\n",
" <th>time</th>\n",
" <th>fep-lambda</th>\n",
" <th>coul-lambda</th>\n",
" <th>vdw-lambda</th>\n",
" <th>restraint-lambda</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>290.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.00</th>\n",
" <th>0.0</th>\n",
" <td>-3.656193e+04</td>\n",
" <td>-3.655609e+04</td>\n",
" <td>-3.655025e+04</td>\n",
" <td>-3.654323e+04</td>\n",
" <td>-3.653622e+04</td>\n",
" <td>-3.652921e+04</td>\n",
" <td>-3.652220e+04</td>\n",
" <td>-3.651518e+04</td>\n",
" <td>-3.650817e+04</td>\n",
" <td>-3.650116e+04</td>\n",
" <td>...</td>\n",
" <td>-36432.512958</td>\n",
" <td>-36426.652327</td>\n",
" <td>-36421.647978</td>\n",
" <td>-36419.063674</td>\n",
" <td>-36413.772700</td>\n",
" <td>-36408.349435</td>\n",
" <td>-36402.814008</td>\n",
" <td>-36397.194394</td>\n",
" <td>-36391.480915</td>\n",
" <td>-36385.532717</td>\n",
" </tr>\n",
" <tr>\n",
" <th>590.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.00</th>\n",
" <th>0.0</th>\n",
" <td>-3.660968e+04</td>\n",
" <td>-3.660278e+04</td>\n",
" <td>-3.659588e+04</td>\n",
" <td>-3.658760e+04</td>\n",
" <td>-3.657932e+04</td>\n",
" <td>-3.657105e+04</td>\n",
" <td>-3.656277e+04</td>\n",
" <td>-3.655449e+04</td>\n",
" <td>-3.654621e+04</td>\n",
" <td>-3.653793e+04</td>\n",
" <td>...</td>\n",
" <td>-36458.878063</td>\n",
" <td>-36452.913593</td>\n",
" <td>-36447.816674</td>\n",
" <td>-36445.182281</td>\n",
" <td>-36439.785804</td>\n",
" <td>-36434.248721</td>\n",
" <td>-36428.587469</td>\n",
" <td>-36422.830989</td>\n",
" <td>-36416.961193</td>\n",
" <td>-36410.791425</td>\n",
" </tr>\n",
" <tr>\n",
" <th>890.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.00</th>\n",
" <th>0.0</th>\n",
" <td>-3.653525e+04</td>\n",
" <td>-3.652845e+04</td>\n",
" <td>-3.652164e+04</td>\n",
" <td>-3.651348e+04</td>\n",
" <td>-3.650531e+04</td>\n",
" <td>-3.649715e+04</td>\n",
" <td>-3.648898e+04</td>\n",
" <td>-3.648082e+04</td>\n",
" <td>-3.647265e+04</td>\n",
" <td>-3.646448e+04</td>\n",
" <td>...</td>\n",
" <td>-36395.199989</td>\n",
" <td>-36390.785043</td>\n",
" <td>-36386.701729</td>\n",
" <td>-36384.519671</td>\n",
" <td>-36379.940269</td>\n",
" <td>-36375.131311</td>\n",
" <td>-36370.139531</td>\n",
" <td>-36365.009550</td>\n",
" <td>-36359.752076</td>\n",
" <td>-36354.275654</td>\n",
" </tr>\n",
" <tr>\n",
" <th>912.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.00</th>\n",
" <th>0.0</th>\n",
" <td>-3.661480e+04</td>\n",
" <td>-3.660579e+04</td>\n",
" <td>-3.659679e+04</td>\n",
" <td>-3.658598e+04</td>\n",
" <td>-3.657517e+04</td>\n",
" <td>-3.656437e+04</td>\n",
" <td>-3.655356e+04</td>\n",
" <td>-3.654275e+04</td>\n",
" <td>-3.653195e+04</td>\n",
" <td>-3.652114e+04</td>\n",
" <td>...</td>\n",
" <td>-36433.949548</td>\n",
" <td>-36430.449486</td>\n",
" <td>-36427.074876</td>\n",
" <td>-36425.242310</td>\n",
" <td>-36421.353812</td>\n",
" <td>-36417.228710</td>\n",
" <td>-36412.918602</td>\n",
" <td>-36408.469082</td>\n",
" <td>-36403.897341</td>\n",
" <td>-36399.142000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>938.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.00</th>\n",
" <th>0.0</th>\n",
" <td>-3.648772e+04</td>\n",
" <td>-3.648022e+04</td>\n",
" <td>-3.647273e+04</td>\n",
" <td>-3.646374e+04</td>\n",
" <td>-3.645475e+04</td>\n",
" <td>-3.644576e+04</td>\n",
" <td>-3.643677e+04</td>\n",
" <td>-3.642777e+04</td>\n",
" <td>-3.641878e+04</td>\n",
" <td>-3.640979e+04</td>\n",
" <td>...</td>\n",
" <td>-36327.908324</td>\n",
" <td>-36323.014005</td>\n",
" <td>-36318.803971</td>\n",
" <td>-36316.622174</td>\n",
" <td>-36312.143765</td>\n",
" <td>-36307.540280</td>\n",
" <td>-36302.829456</td>\n",
" <td>-36298.036642</td>\n",
" <td>-36293.151660</td>\n",
" <td>-36288.040117</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>182.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.76</th>\n",
" <th>0.1</th>\n",
" <td>-2.019222e+04</td>\n",
" <td>-2.019354e+04</td>\n",
" <td>-2.019486e+04</td>\n",
" <td>-2.019644e+04</td>\n",
" <td>-2.019802e+04</td>\n",
" <td>-2.019961e+04</td>\n",
" <td>-2.020119e+04</td>\n",
" <td>-2.020277e+04</td>\n",
" <td>-2.020436e+04</td>\n",
" <td>-2.020594e+04</td>\n",
" <td>...</td>\n",
" <td>-36633.585345</td>\n",
" <td>-36649.233087</td>\n",
" <td>-36654.550460</td>\n",
" <td>-36655.737184</td>\n",
" <td>-36656.095117</td>\n",
" <td>-36654.524401</td>\n",
" <td>-36651.614941</td>\n",
" <td>-36647.760167</td>\n",
" <td>-36643.187665</td>\n",
" <td>-36637.895262</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2250.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.76</th>\n",
" <th>0.1</th>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695987e+08</td>\n",
" <td>2.695987e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>2.695988e+08</td>\n",
" <td>...</td>\n",
" <td>-36390.379798</td>\n",
" <td>-36469.798914</td>\n",
" <td>-36500.131374</td>\n",
" <td>-36509.588921</td>\n",
" <td>-36521.491100</td>\n",
" <td>-36527.250601</td>\n",
" <td>-36529.150014</td>\n",
" <td>-36528.518543</td>\n",
" <td>-36526.155112</td>\n",
" <td>-36522.495104</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2242.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.84</th>\n",
" <th>0.2</th>\n",
" <td>8.544438e+06</td>\n",
" <td>8.544434e+06</td>\n",
" <td>8.544429e+06</td>\n",
" <td>8.544423e+06</td>\n",
" <td>8.544418e+06</td>\n",
" <td>8.544413e+06</td>\n",
" <td>8.544408e+06</td>\n",
" <td>8.544402e+06</td>\n",
" <td>8.544396e+06</td>\n",
" <td>8.544391e+06</td>\n",
" <td>...</td>\n",
" <td>-36385.189833</td>\n",
" <td>-36454.475237</td>\n",
" <td>-36480.226679</td>\n",
" <td>-36488.041590</td>\n",
" <td>-36497.485390</td>\n",
" <td>-36501.527818</td>\n",
" <td>-36502.182706</td>\n",
" <td>-36500.619806</td>\n",
" <td>-36497.532982</td>\n",
" <td>-36493.267744</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2240.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.92</th>\n",
" <th>0.4</th>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347833e+08</td>\n",
" <td>2.347833e+08</td>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347832e+08</td>\n",
" <td>2.347833e+08</td>\n",
" <td>...</td>\n",
" <td>-36223.652251</td>\n",
" <td>-36413.551688</td>\n",
" <td>-36487.619093</td>\n",
" <td>-36511.498725</td>\n",
" <td>-36543.370398</td>\n",
" <td>-36561.563310</td>\n",
" <td>-36571.348912</td>\n",
" <td>-36575.733504</td>\n",
" <td>-36576.507256</td>\n",
" <td>-36574.706628</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2236.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>1.00</th>\n",
" <th>1.0</th>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>4.657014e+16</td>\n",
" <td>...</td>\n",
" <td>-36238.122552</td>\n",
" <td>-36443.032424</td>\n",
" <td>-36522.889328</td>\n",
" <td>-36548.735117</td>\n",
" <td>-36583.509112</td>\n",
" <td>-36603.771607</td>\n",
" <td>-36615.142691</td>\n",
" <td>-36620.812769</td>\n",
" <td>-36622.668762</td>\n",
" <td>-36621.775368</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>160 rows × 28 columns</p>\n",
"</div>"
],
"text/plain": [
" (0.0, 0.0, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.656193e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.660968e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.653525e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.661480e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.648772e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.019222e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544438e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.05, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.655609e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.660278e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.652845e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.660579e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.648022e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.019354e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544434e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.1, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.655025e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.659588e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.652164e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.659679e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.647273e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.019486e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544429e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.16, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.654323e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.658760e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.651348e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.658598e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.646374e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.019644e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544423e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347833e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.22, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.653622e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.657932e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.650531e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.657517e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.645475e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.019802e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695987e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544418e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347833e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.28, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.652921e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.657105e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.649715e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.656437e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.644576e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.019961e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695987e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544413e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.34, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.652220e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.656277e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.648898e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.655356e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.643677e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.020119e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544408e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.4, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.651518e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.655449e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.648082e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.654275e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.642777e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.020277e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544402e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.46, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.650817e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.654621e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.647265e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.653195e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.641878e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.020436e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544396e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347832e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" (0.0, 0.52, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -3.650116e+04 \n",
"590.0 0.0 0.0 0.00 0.0 -3.653793e+04 \n",
"890.0 0.0 0.0 0.00 0.0 -3.646448e+04 \n",
"912.0 0.0 0.0 0.00 0.0 -3.652114e+04 \n",
"938.0 0.0 0.0 0.00 0.0 -3.640979e+04 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -2.020594e+04 \n",
"2250.0 0.0 1.0 0.76 0.1 2.695988e+08 \n",
"2242.0 0.0 1.0 0.84 0.2 8.544391e+06 \n",
"2240.0 0.0 1.0 0.92 0.4 2.347833e+08 \n",
"2236.0 0.0 1.0 1.00 1.0 4.657014e+16 \n",
"\n",
" ... \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda ... \n",
"290.0 0.0 0.0 0.00 0.0 ... \n",
"590.0 0.0 0.0 0.00 0.0 ... \n",
"890.0 0.0 0.0 0.00 0.0 ... \n",
"912.0 0.0 0.0 0.00 0.0 ... \n",
"938.0 0.0 0.0 0.00 0.0 ... \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 ... \n",
"2250.0 0.0 1.0 0.76 0.1 ... \n",
"2242.0 0.0 1.0 0.84 0.2 ... \n",
"2240.0 0.0 1.0 0.92 0.4 ... \n",
"2236.0 0.0 1.0 1.00 1.0 ... \n",
"\n",
" (0.0, 1.0, 0.3, 0.001) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36432.512958 \n",
"590.0 0.0 0.0 0.00 0.0 -36458.878063 \n",
"890.0 0.0 0.0 0.00 0.0 -36395.199989 \n",
"912.0 0.0 0.0 0.00 0.0 -36433.949548 \n",
"938.0 0.0 0.0 0.00 0.0 -36327.908324 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36633.585345 \n",
"2250.0 0.0 1.0 0.76 0.1 -36390.379798 \n",
"2242.0 0.0 1.0 0.84 0.2 -36385.189833 \n",
"2240.0 0.0 1.0 0.92 0.4 -36223.652251 \n",
"2236.0 0.0 1.0 1.00 1.0 -36238.122552 \n",
"\n",
" (0.0, 1.0, 0.4, 0.002) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36426.652327 \n",
"590.0 0.0 0.0 0.00 0.0 -36452.913593 \n",
"890.0 0.0 0.0 0.00 0.0 -36390.785043 \n",
"912.0 0.0 0.0 0.00 0.0 -36430.449486 \n",
"938.0 0.0 0.0 0.00 0.0 -36323.014005 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36649.233087 \n",
"2250.0 0.0 1.0 0.76 0.1 -36469.798914 \n",
"2242.0 0.0 1.0 0.84 0.2 -36454.475237 \n",
"2240.0 0.0 1.0 0.92 0.4 -36413.551688 \n",
"2236.0 0.0 1.0 1.00 1.0 -36443.032424 \n",
"\n",
" (0.0, 1.0, 0.48, 0.004) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36421.647978 \n",
"590.0 0.0 0.0 0.00 0.0 -36447.816674 \n",
"890.0 0.0 0.0 0.00 0.0 -36386.701729 \n",
"912.0 0.0 0.0 0.00 0.0 -36427.074876 \n",
"938.0 0.0 0.0 0.00 0.0 -36318.803971 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36654.550460 \n",
"2250.0 0.0 1.0 0.76 0.1 -36500.131374 \n",
"2242.0 0.0 1.0 0.84 0.2 -36480.226679 \n",
"2240.0 0.0 1.0 0.92 0.4 -36487.619093 \n",
"2236.0 0.0 1.0 1.00 1.0 -36522.889328 \n",
"\n",
" (0.0, 1.0, 0.52, 0.01) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36419.063674 \n",
"590.0 0.0 0.0 0.00 0.0 -36445.182281 \n",
"890.0 0.0 0.0 0.00 0.0 -36384.519671 \n",
"912.0 0.0 0.0 0.00 0.0 -36425.242310 \n",
"938.0 0.0 0.0 0.00 0.0 -36316.622174 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36655.737184 \n",
"2250.0 0.0 1.0 0.76 0.1 -36509.588921 \n",
"2242.0 0.0 1.0 0.84 0.2 -36488.041590 \n",
"2240.0 0.0 1.0 0.92 0.4 -36511.498725 \n",
"2236.0 0.0 1.0 1.00 1.0 -36548.735117 \n",
"\n",
" (0.0, 1.0, 0.6, 0.02) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36413.772700 \n",
"590.0 0.0 0.0 0.00 0.0 -36439.785804 \n",
"890.0 0.0 0.0 0.00 0.0 -36379.940269 \n",
"912.0 0.0 0.0 0.00 0.0 -36421.353812 \n",
"938.0 0.0 0.0 0.00 0.0 -36312.143765 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36656.095117 \n",
"2250.0 0.0 1.0 0.76 0.1 -36521.491100 \n",
"2242.0 0.0 1.0 0.84 0.2 -36497.485390 \n",
"2240.0 0.0 1.0 0.92 0.4 -36543.370398 \n",
"2236.0 0.0 1.0 1.00 1.0 -36583.509112 \n",
"\n",
" (0.0, 1.0, 0.68, 0.04) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36408.349435 \n",
"590.0 0.0 0.0 0.00 0.0 -36434.248721 \n",
"890.0 0.0 0.0 0.00 0.0 -36375.131311 \n",
"912.0 0.0 0.0 0.00 0.0 -36417.228710 \n",
"938.0 0.0 0.0 0.00 0.0 -36307.540280 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36654.524401 \n",
"2250.0 0.0 1.0 0.76 0.1 -36527.250601 \n",
"2242.0 0.0 1.0 0.84 0.2 -36501.527818 \n",
"2240.0 0.0 1.0 0.92 0.4 -36561.563310 \n",
"2236.0 0.0 1.0 1.00 1.0 -36603.771607 \n",
"\n",
" (0.0, 1.0, 0.76, 0.1) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36402.814008 \n",
"590.0 0.0 0.0 0.00 0.0 -36428.587469 \n",
"890.0 0.0 0.0 0.00 0.0 -36370.139531 \n",
"912.0 0.0 0.0 0.00 0.0 -36412.918602 \n",
"938.0 0.0 0.0 0.00 0.0 -36302.829456 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36651.614941 \n",
"2250.0 0.0 1.0 0.76 0.1 -36529.150014 \n",
"2242.0 0.0 1.0 0.84 0.2 -36502.182706 \n",
"2240.0 0.0 1.0 0.92 0.4 -36571.348912 \n",
"2236.0 0.0 1.0 1.00 1.0 -36615.142691 \n",
"\n",
" (0.0, 1.0, 0.84, 0.2) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36397.194394 \n",
"590.0 0.0 0.0 0.00 0.0 -36422.830989 \n",
"890.0 0.0 0.0 0.00 0.0 -36365.009550 \n",
"912.0 0.0 0.0 0.00 0.0 -36408.469082 \n",
"938.0 0.0 0.0 0.00 0.0 -36298.036642 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36647.760167 \n",
"2250.0 0.0 1.0 0.76 0.1 -36528.518543 \n",
"2242.0 0.0 1.0 0.84 0.2 -36500.619806 \n",
"2240.0 0.0 1.0 0.92 0.4 -36575.733504 \n",
"2236.0 0.0 1.0 1.00 1.0 -36620.812769 \n",
"\n",
" (0.0, 1.0, 0.92, 0.4) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36391.480915 \n",
"590.0 0.0 0.0 0.00 0.0 -36416.961193 \n",
"890.0 0.0 0.0 0.00 0.0 -36359.752076 \n",
"912.0 0.0 0.0 0.00 0.0 -36403.897341 \n",
"938.0 0.0 0.0 0.00 0.0 -36293.151660 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36643.187665 \n",
"2250.0 0.0 1.0 0.76 0.1 -36526.155112 \n",
"2242.0 0.0 1.0 0.84 0.2 -36497.532982 \n",
"2240.0 0.0 1.0 0.92 0.4 -36576.507256 \n",
"2236.0 0.0 1.0 1.00 1.0 -36622.668762 \n",
"\n",
" (0.0, 1.0, 1.0, 1.0) \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 -36385.532717 \n",
"590.0 0.0 0.0 0.00 0.0 -36410.791425 \n",
"890.0 0.0 0.0 0.00 0.0 -36354.275654 \n",
"912.0 0.0 0.0 0.00 0.0 -36399.142000 \n",
"938.0 0.0 0.0 0.00 0.0 -36288.040117 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 -36637.895262 \n",
"2250.0 0.0 1.0 0.76 0.1 -36522.495104 \n",
"2242.0 0.0 1.0 0.84 0.2 -36493.267744 \n",
"2240.0 0.0 1.0 0.92 0.4 -36574.706628 \n",
"2236.0 0.0 1.0 1.00 1.0 -36621.775368 \n",
"\n",
"[160 rows x 28 columns]"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"subsampling.slicing(u_nk, lower=100, upper=3000, step=10)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
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" <td>-40.728267</td>\n",
" <td>0.294076</td>\n",
" </tr>\n",
" <tr>\n",
" <th>938.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.00</th>\n",
" <th>0.0</th>\n",
" <td>0.0</td>\n",
" <td>149.854084</td>\n",
" <td>13.357666</td>\n",
" <td>0.499978</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>182.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.76</th>\n",
" <th>0.1</th>\n",
" <td>0.0</td>\n",
" <td>-26.388845</td>\n",
" <td>42.316035</td>\n",
" <td>0.620489</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2250.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.76</th>\n",
" <th>0.1</th>\n",
" <td>NaN</td>\n",
" <td>65.767734</td>\n",
" <td>-6.112316</td>\n",
" <td>0.299711</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2242.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.84</th>\n",
" <th>0.2</th>\n",
" <td>NaN</td>\n",
" <td>-90.706405</td>\n",
" <td>29.514282</td>\n",
" <td>0.381848</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2240.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>0.92</th>\n",
" <th>0.4</th>\n",
" <td>NaN</td>\n",
" <td>34.875238</td>\n",
" <td>6.554448</td>\n",
" <td>0.349549</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2236.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>1.00</th>\n",
" <th>1.0</th>\n",
" <td>NaN</td>\n",
" <td>1509.785782</td>\n",
" <td>20.159137</td>\n",
" <td>0.460674</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>160 rows × 4 columns</p>\n",
"</div>"
],
"text/plain": [
" fep coul \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 0.0 116.874139 \n",
"590.0 0.0 0.0 0.00 0.0 0.0 137.979172 \n",
"890.0 0.0 0.0 0.00 0.0 0.0 136.098361 \n",
"912.0 0.0 0.0 0.00 0.0 0.0 180.106604 \n",
"938.0 0.0 0.0 0.00 0.0 0.0 149.854084 \n",
"... ... ... \n",
"182.0 0.0 1.0 0.76 0.1 0.0 -26.388845 \n",
"2250.0 0.0 1.0 0.76 0.1 NaN 65.767734 \n",
"2242.0 0.0 1.0 0.84 0.2 NaN -90.706405 \n",
"2240.0 0.0 1.0 0.92 0.4 NaN 34.875238 \n",
"2236.0 0.0 1.0 1.00 1.0 NaN 1509.785782 \n",
"\n",
" vdw \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 20.943497 \n",
"590.0 0.0 0.0 0.00 0.0 22.070111 \n",
"890.0 0.0 0.0 0.00 0.0 -27.874864 \n",
"912.0 0.0 0.0 0.00 0.0 -40.728267 \n",
"938.0 0.0 0.0 0.00 0.0 13.357666 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 42.316035 \n",
"2250.0 0.0 1.0 0.76 0.1 -6.112316 \n",
"2242.0 0.0 1.0 0.84 0.2 29.514282 \n",
"2240.0 0.0 1.0 0.92 0.4 6.554448 \n",
"2236.0 0.0 1.0 1.00 1.0 20.159137 \n",
"\n",
" restraint \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"290.0 0.0 0.0 0.00 0.0 0.527360 \n",
"590.0 0.0 0.0 0.00 0.0 0.682844 \n",
"890.0 0.0 0.0 0.00 0.0 0.394012 \n",
"912.0 0.0 0.0 0.00 0.0 0.294076 \n",
"938.0 0.0 0.0 0.00 0.0 0.499978 \n",
"... ... \n",
"182.0 0.0 1.0 0.76 0.1 0.620489 \n",
"2250.0 0.0 1.0 0.76 0.1 0.299711 \n",
"2242.0 0.0 1.0 0.84 0.2 0.381848 \n",
"2240.0 0.0 1.0 0.92 0.4 0.349549 \n",
"2236.0 0.0 1.0 1.00 1.0 0.460674 \n",
"\n",
"[160 rows x 4 columns]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"subsampling.slicing(dHdl, lower=100, upper=3000, step=10)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Subsampling - statistical inefficiency"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\u001b[0;31mSignature:\u001b[0m\n",
"\u001b[0msubsampling\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstatistical_inefficiency\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mcolumn\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mlower\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mupper\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mstep\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mconservative\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mreturn_calculated\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mforce\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mDocstring:\u001b[0m\n",
"Subsample an alchemlyb DataFrame based on the calculated statistical inefficiency\n",
"of one of its columns.\n",
"\n",
"Calculation of statistical inefficiency and subsequent subsampling will be\n",
"performed separately on groups of rows corresponding to each set of lambda\n",
"values present in the DataFrame's index. Each group will be sorted on the\n",
"outermost (time) index prior to any calculation.\n",
"\n",
"Parameters\n",
"----------\n",
"df : DataFrame\n",
" DataFrame to subsample according statistical inefficiency of `series`.\n",
"column : label\n",
" Label of column to use for calculating statistical inefficiency.\n",
"lower : float\n",
" Lower time to pre-slice data from.\n",
"upper : float\n",
" Upper time to pre-slice data to (inclusive).\n",
"step : int\n",
" Step between rows to pre-slice by.\n",
"conservative : bool\n",
" ``True`` use ``ceil(statistical_inefficiency)`` to slice the data in uniform\n",
" intervals (the default). ``False`` will sample at non-uniform intervals to\n",
" closely match the (fractional) statistical_inefficieny, as implemented\n",
" in :func:`pymbar.timeseries.subsampleCorrelatedData`.\n",
"return_calculated : bool\n",
" ``True`` return a tuple, with the second item a dict giving, e.g. `statinef`\n",
" for each group.\n",
"force : bool\n",
" Ignore checks that DataFrame is in proper form for expected behavior.\n",
"\n",
"Returns\n",
"-------\n",
"DataFrame\n",
" `df` subsampled according to subsampled `column`.\n",
"\n",
"Note\n",
"----\n",
"For a non-integer statistical ineffciency :math:`g`, the default value\n",
"``conservative=True`` will provide _fewer_ data points than allowed by\n",
":math:`g` and thus error estimates will be _higher_. For large numbers of\n",
"data points and converged free energies, the choice should not make a\n",
"difference. For small numbers of data points, ``conservative=True``\n",
"decreases a false sense of accuracy and is deemed the more careful and\n",
"conservative approach.\n",
"\n",
"See Also\n",
"--------\n",
"pymbar.timeseries.statisticalInefficiency : detailed background\n",
"pymbar.timeseries.subsampleCorrelatedData : used for subsampling\n",
"\n",
"\n",
".. versionchanged:: 0.4.0\n",
" The ``series`` keyword was replaced with the ``column`` keyword.\n",
" The function no longer takes an arbitrary series as input for\n",
" calculating statistical inefficiency.\n",
"\n",
".. versionchanged:: 0.2.0\n",
" The ``conservative`` keyword was added and the method is now using\n",
" ``pymbar.timeseries.subsampleCorrelatedData()``; previously, the statistical\n",
" inefficiency was _rounded_ (instead of ``ceil()``) and thus one could\n",
" end up with correlated data.\n",
"\u001b[0;31mFile:\u001b[0m ~/Library/alchemistry/alchemlyb/src/alchemlyb/preprocessing/subsampling.py\n",
"\u001b[0;31mType:\u001b[0m function\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"subsampling.statistical_inefficiency?"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
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" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" <th>(0.0, 0.52, 0.0, 0.0)</th>\n",
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" <th>(0.0, 1.0, 0.4, 0.002)</th>\n",
" <th>(0.0, 1.0, 0.48, 0.004)</th>\n",
" <th>(0.0, 1.0, 0.52, 0.01)</th>\n",
" <th>(0.0, 1.0, 0.6, 0.02)</th>\n",
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" <th>(0.0, 1.0, 0.76, 0.1)</th>\n",
" <th>(0.0, 1.0, 0.84, 0.2)</th>\n",
" <th>(0.0, 1.0, 0.92, 0.4)</th>\n",
" <th>(0.0, 1.0, 1.0, 1.0)</th>\n",
" </tr>\n",
" <tr>\n",
" <th>time</th>\n",
" <th>fep-lambda</th>\n",
" <th>coul-lambda</th>\n",
" <th>vdw-lambda</th>\n",
" <th>restraint-lambda</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
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" <tbody>\n",
" <tr>\n",
" <th>12.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <td>-3.650390e+04</td>\n",
" <td>-3.649806e+04</td>\n",
" <td>-3.649223e+04</td>\n",
" <td>-3.648523e+04</td>\n",
" <td>-3.647823e+04</td>\n",
" <td>-3.647123e+04</td>\n",
" <td>-3.646423e+04</td>\n",
" <td>-3.645723e+04</td>\n",
" <td>-3.645023e+04</td>\n",
" <td>-3.644323e+04</td>\n",
" <td>...</td>\n",
" <td>-36376.036789</td>\n",
" <td>-36370.350100</td>\n",
" <td>-36365.447161</td>\n",
" <td>-36362.904515</td>\n",
" <td>-36357.683820</td>\n",
" <td>-36352.317151</td>\n",
" <td>-36346.826982</td>\n",
" <td>-36341.243899</td>\n",
" <td>-36335.557366</td>\n",
" <td>-36329.614291</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <td>-3.668470e+04</td>\n",
" <td>-3.667614e+04</td>\n",
" <td>-3.666758e+04</td>\n",
" <td>-3.665731e+04</td>\n",
" <td>-3.664703e+04</td>\n",
" <td>-3.663676e+04</td>\n",
" <td>-3.662649e+04</td>\n",
" <td>-3.661622e+04</td>\n",
" <td>-3.660595e+04</td>\n",
" <td>-3.659568e+04</td>\n",
" <td>...</td>\n",
" <td>-36512.131230</td>\n",
" <td>-36507.829961</td>\n",
" <td>-36503.703236</td>\n",
" <td>-36501.464073</td>\n",
" <td>-36496.717557</td>\n",
" <td>-36491.682054</td>\n",
" <td>-36486.409417</td>\n",
" <td>-36480.954769</td>\n",
" <td>-36475.319456</td>\n",
" <td>-36469.330918</td>\n",
" </tr>\n",
" <tr>\n",
" <th>40.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <td>-3.618335e+04</td>\n",
" <td>-3.617500e+04</td>\n",
" <td>-3.616664e+04</td>\n",
" <td>-3.615661e+04</td>\n",
" <td>-3.614659e+04</td>\n",
" <td>-3.613656e+04</td>\n",
" <td>-3.612653e+04</td>\n",
" <td>-3.611650e+04</td>\n",
" <td>-3.610648e+04</td>\n",
" <td>-3.609645e+04</td>\n",
" <td>...</td>\n",
" <td>-36012.313889</td>\n",
" <td>-36007.504158</td>\n",
" <td>-36003.063149</td>\n",
" <td>-36000.693358</td>\n",
" <td>-35995.728792</td>\n",
" <td>-35990.525869</td>\n",
" <td>-35985.132191</td>\n",
" <td>-35979.595441</td>\n",
" <td>-35973.920626</td>\n",
" <td>-35967.979199</td>\n",
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" <td>-3.642886e+04</td>\n",
" <td>-3.641994e+04</td>\n",
" <td>-3.641102e+04</td>\n",
" <td>-3.640210e+04</td>\n",
" <td>-3.639318e+04</td>\n",
" <td>-3.638426e+04</td>\n",
" <td>-3.637533e+04</td>\n",
" <td>-3.636641e+04</td>\n",
" <td>...</td>\n",
" <td>-36290.681903</td>\n",
" <td>-36285.830601</td>\n",
" <td>-36281.327291</td>\n",
" <td>-36278.915281</td>\n",
" <td>-36273.847176</td>\n",
" <td>-36268.515610</td>\n",
" <td>-36262.966681</td>\n",
" <td>-36257.251438</td>\n",
" <td>-36251.368071</td>\n",
" <td>-36245.140929</td>\n",
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" <tr>\n",
" <th>290.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <th>0.0</th>\n",
" <td>-3.656193e+04</td>\n",
" <td>-3.655609e+04</td>\n",
" <td>-3.655025e+04</td>\n",
" <td>-3.654323e+04</td>\n",
" <td>-3.653622e+04</td>\n",
" <td>-3.652921e+04</td>\n",
" <td>-3.652220e+04</td>\n",
" <td>-3.651518e+04</td>\n",
" <td>-3.650817e+04</td>\n",
" <td>-3.650116e+04</td>\n",
" <td>...</td>\n",
" <td>-36432.512958</td>\n",
" <td>-36426.652327</td>\n",
" <td>-36421.647978</td>\n",
" <td>-36419.063674</td>\n",
" <td>-36413.772700</td>\n",
" <td>-36408.349435</td>\n",
" <td>-36402.814008</td>\n",
" <td>-36397.194394</td>\n",
" <td>-36391.480915</td>\n",
" <td>-36385.532717</td>\n",
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" <tr>\n",
" <th>...</th>\n",
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" <th>...</th>\n",
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" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
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" <tr>\n",
" <th>96880.0</th>\n",
" <th>0.0</th>\n",
" <th>1.0</th>\n",
" <th>1.0</th>\n",
" <th>1.0</th>\n",
" <td>1.349412e+09</td>\n",
" <td>1.349412e+09</td>\n",
" <td>1.349412e+09</td>\n",
" <td>1.349412e+09</td>\n",
" <td>1.349413e+09</td>\n",
" <td>1.349413e+09</td>\n",
" <td>1.349413e+09</td>\n",
" <td>1.349413e+09</td>\n",
" <td>1.349413e+09</td>\n",
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"<p>36419 rows × 28 columns</p>\n",
"</div>"
],
"text/plain": [
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" ... \\\n",
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"96896.0 0.0 1.0 1.0 1.0 -36539.761463 \n",
"\n",
" (0.0, 1.0, 0.84, 0.2) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"12.0 0.0 0.0 0.0 0.0 -36341.243899 \n",
"18.0 0.0 0.0 0.0 0.0 -36480.954769 \n",
"40.0 0.0 0.0 0.0 0.0 -35979.595441 \n",
"46.0 0.0 0.0 0.0 0.0 -36257.251438 \n",
"290.0 0.0 0.0 0.0 0.0 -36397.194394 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36618.049801 \n",
"96882.0 0.0 1.0 1.0 1.0 -36736.937278 \n",
"96886.0 0.0 1.0 1.0 1.0 -36494.933908 \n",
"96888.0 0.0 1.0 1.0 1.0 -36702.391771 \n",
"96896.0 0.0 1.0 1.0 1.0 -36549.818624 \n",
"\n",
" (0.0, 1.0, 0.92, 0.4) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"12.0 0.0 0.0 0.0 0.0 -36335.557366 \n",
"18.0 0.0 0.0 0.0 0.0 -36475.319456 \n",
"40.0 0.0 0.0 0.0 0.0 -35973.920626 \n",
"46.0 0.0 0.0 0.0 0.0 -36251.368071 \n",
"290.0 0.0 0.0 0.0 0.0 -36391.480915 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36621.634447 \n",
"96882.0 0.0 1.0 1.0 1.0 -36739.031984 \n",
"96886.0 0.0 1.0 1.0 1.0 -36500.449121 \n",
"96888.0 0.0 1.0 1.0 1.0 -36705.716350 \n",
"96896.0 0.0 1.0 1.0 1.0 -36554.442952 \n",
"\n",
" (0.0, 1.0, 1.0, 1.0) \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"12.0 0.0 0.0 0.0 0.0 -36329.614291 \n",
"18.0 0.0 0.0 0.0 0.0 -36469.330918 \n",
"40.0 0.0 0.0 0.0 0.0 -35967.979199 \n",
"46.0 0.0 0.0 0.0 0.0 -36245.140929 \n",
"290.0 0.0 0.0 0.0 0.0 -36385.532717 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36621.825482 \n",
"96882.0 0.0 1.0 1.0 1.0 -36738.326905 \n",
"96886.0 0.0 1.0 1.0 1.0 -36500.770146 \n",
"96888.0 0.0 1.0 1.0 1.0 -36705.643692 \n",
"96896.0 0.0 1.0 1.0 1.0 -36555.318874 \n",
"\n",
"[36419 rows x 28 columns]"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"subsampling.statistical_inefficiency(u_nk, u_nk.columns[0])"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
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"text/plain": [
" fep coul \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"12.0 0.0 0.0 0.0 0.0 0.0 116.673721 \n",
"1062.0 0.0 0.0 0.0 0.0 0.0 147.371790 \n",
"2374.0 0.0 0.0 0.0 0.0 0.0 166.229338 \n",
"2690.0 0.0 0.0 0.0 0.0 0.0 149.320223 \n",
"4264.0 0.0 0.0 0.0 0.0 NaN 135.257112 \n",
"... ... ... \n",
"96880.0 0.0 1.0 1.0 1.0 0.0 -57.343249 \n",
"96882.0 0.0 1.0 1.0 1.0 0.0 466.215728 \n",
"96886.0 0.0 1.0 1.0 1.0 0.0 -80.455455 \n",
"96888.0 0.0 1.0 1.0 1.0 0.0 -44.661570 \n",
"96896.0 0.0 1.0 1.0 1.0 0.0 44.294170 \n",
"\n",
" vdw \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"12.0 0.0 0.0 0.0 0.0 11.782893 \n",
"1062.0 0.0 0.0 0.0 0.0 -15.249458 \n",
"2374.0 0.0 0.0 0.0 0.0 7.532304 \n",
"2690.0 0.0 0.0 0.0 0.0 -10.006220 \n",
"4264.0 0.0 0.0 0.0 0.0 -15.601191 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 12.085948 \n",
"96882.0 0.0 1.0 1.0 1.0 16.068576 \n",
"96886.0 0.0 1.0 1.0 1.0 -5.530314 \n",
"96888.0 0.0 1.0 1.0 1.0 14.952239 \n",
"96896.0 0.0 1.0 1.0 1.0 5.813643 \n",
"\n",
" restraint \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"12.0 0.0 0.0 0.0 0.0 0.572718 \n",
"1062.0 0.0 0.0 0.0 0.0 0.766306 \n",
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"... ... \n",
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"96896.0 0.0 1.0 1.0 1.0 0.150873 \n",
"\n",
"[25939 rows x 4 columns]"
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},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"subsampling.statistical_inefficiency(dHdl, 'coul')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Subsampling - equilibrium detection"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\u001b[0;31mSignature:\u001b[0m\n",
"\u001b[0msubsampling\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mequilibrium_detection\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mcolumn\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mlower\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mupper\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mstep\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mconservative\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mreturn_calculated\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m \u001b[0mforce\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\n",
"\u001b[0;34m\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mDocstring:\u001b[0m\n",
"Subsample a DataFrame using automated equilibrium detection on one of\n",
"its columns.\n",
"\n",
"Equilibrium detection and subsequent subsampling will be performed\n",
"separately on groups of rows corresponding to each set of lambda values\n",
"present in the DataFrame's index. Each group will be sorted on the\n",
"outermost (time) index prior to any calculation.\n",
"\n",
"Parameters\n",
"----------\n",
"df : DataFrame\n",
" DataFrame to subsample according to equilibrium detection on `series`.\n",
"column : label\n",
" Label of column to use for equilibrium detection.\n",
"lower : float\n",
" Lower time to pre-slice data from.\n",
"upper : float\n",
" Upper time to pre-slice data to (inclusive).\n",
"step : int\n",
" Step between rows to pre-slice by.\n",
"conservative : bool\n",
" ``True`` use ``ceil(statistical_inefficiency)`` to slice the data in uniform\n",
" intervals (the default). ``False`` will sample at non-uniform intervals to\n",
" closely match the (fractional) statistical_inefficieny, as implemented\n",
" in :func:`pymbar.timeseries.subsampleCorrelatedData`.\n",
"return_calculated : bool\n",
" ``True`` return a tuple, with the second item a dict giving, e.g. `statinef`\n",
" for each group.\n",
"force : bool\n",
" Ignore checks that DataFrame is in proper form for expected behavior.\n",
"\n",
"Returns\n",
"-------\n",
"DataFrame\n",
" `df` subsampled according to subsampled `column`.\n",
"\n",
"Note\n",
"----\n",
"For a non-integer statistical ineffciency :math:`g`, the default value\n",
"``conservative=True`` will provide _fewer_ data points than allowed by\n",
":math:`g` and thus error estimates will be _higher_. For large numbers of\n",
"data points and converged free energies, the choice should not make a\n",
"difference. For small numbers of data points, ``conservative=True``\n",
"decreases a false sense of accuracy and is deemed the more careful and\n",
"conservative approach.\n",
"\n",
"See Also\n",
"--------\n",
"pymbar.timeseries.detectEquilibration : detailed background\n",
"pymbar.timeseries.subsampleCorrelatedData : used for subsampling\n",
"\n",
"\n",
".. versionchanged:: 0.4.0\n",
" The ``series`` keyword was replaced with the ``column`` keyword.\n",
" The function no longer takes an arbitrary series as input for\n",
" calculating statistical inefficiency.\n",
"\n",
".. versionchanged:: 0.4.0\n",
" The ``conservative`` keyword was added and the method is now using\n",
" ``pymbar.timeseries.subsampleCorrelatedData()``; previously, the statistical\n",
" inefficiency was _rounded_ (instead of ``ceil()``) and thus one could\n",
" end up with correlated data.\n",
"\u001b[0;31mFile:\u001b[0m ~/Library/alchemistry/alchemlyb/src/alchemlyb/preprocessing/subsampling.py\n",
"\u001b[0;31mType:\u001b[0m function\n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"subsampling.equilibrium_detection?"
]
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{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
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"</table>\n",
"<p>36907 rows × 28 columns</p>\n",
"</div>"
],
"text/plain": [
" (0.0, 0.0, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.642371e+04 \n",
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"... ... \n",
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"\n",
" (0.0, 0.05, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.641796e+04 \n",
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"\n",
" (0.0, 0.1, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.641222e+04 \n",
"884.0 0.0 0.0 0.0 0.0 -3.665637e+04 \n",
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"\n",
" (0.0, 0.16, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.640532e+04 \n",
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"\n",
" (0.0, 0.22, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.639843e+04 \n",
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"\n",
" (0.0, 0.28, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.639154e+04 \n",
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"... ... \n",
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"\n",
" (0.0, 0.34, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.638464e+04 \n",
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"... ... \n",
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"\n",
" (0.0, 0.4, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.637775e+04 \n",
"884.0 0.0 0.0 0.0 0.0 -3.661289e+04 \n",
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"898.0 0.0 0.0 0.0 0.0 -3.667503e+04 \n",
"... ... \n",
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"96896.0 0.0 1.0 1.0 1.0 2.689752e+09 \n",
"\n",
" (0.0, 0.46, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.637086e+04 \n",
"884.0 0.0 0.0 0.0 0.0 -3.660419e+04 \n",
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"... ... \n",
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"96896.0 0.0 1.0 1.0 1.0 2.689752e+09 \n",
"\n",
" (0.0, 0.52, 0.0, 0.0) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -3.636396e+04 \n",
"884.0 0.0 0.0 0.0 0.0 -3.659550e+04 \n",
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"... ... \n",
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"96896.0 0.0 1.0 1.0 1.0 2.689752e+09 \n",
"\n",
" ... \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda ... \n",
"756.0 0.0 0.0 0.0 0.0 ... \n",
"884.0 0.0 0.0 0.0 0.0 ... \n",
"888.0 0.0 0.0 0.0 0.0 ... \n",
"894.0 0.0 0.0 0.0 0.0 ... \n",
"898.0 0.0 0.0 0.0 0.0 ... \n",
"... ... \n",
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"96888.0 0.0 1.0 1.0 1.0 ... \n",
"96896.0 0.0 1.0 1.0 1.0 ... \n",
"\n",
" (0.0, 1.0, 0.3, 0.001) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36296.125603 \n",
"884.0 0.0 0.0 0.0 0.0 -36517.290261 \n",
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"894.0 0.0 0.0 0.0 0.0 -36424.647402 \n",
"898.0 0.0 0.0 0.0 0.0 -36577.351897 \n",
"... ... \n",
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"96888.0 0.0 1.0 1.0 1.0 -36221.237451 \n",
"96896.0 0.0 1.0 1.0 1.0 -35990.979100 \n",
"\n",
" (0.0, 1.0, 0.4, 0.002) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36290.209409 \n",
"884.0 0.0 0.0 0.0 0.0 -36512.297582 \n",
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"898.0 0.0 0.0 0.0 0.0 -36573.675893 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36379.330849 \n",
"96882.0 0.0 1.0 1.0 1.0 -36555.142138 \n",
"96886.0 0.0 1.0 1.0 1.0 -36220.626347 \n",
"96888.0 0.0 1.0 1.0 1.0 -36474.310944 \n",
"96896.0 0.0 1.0 1.0 1.0 -36284.693077 \n",
"\n",
" (0.0, 1.0, 0.48, 0.004) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36285.171549 \n",
"884.0 0.0 0.0 0.0 0.0 -36507.909193 \n",
"888.0 0.0 0.0 0.0 0.0 -36472.091177 \n",
"894.0 0.0 0.0 0.0 0.0 -36416.154418 \n",
"898.0 0.0 0.0 0.0 0.0 -36570.136405 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36485.250313 \n",
"96882.0 0.0 1.0 1.0 1.0 -36637.051738 \n",
"96886.0 0.0 1.0 1.0 1.0 -36335.940125 \n",
"96888.0 0.0 1.0 1.0 1.0 -36574.677272 \n",
"96896.0 0.0 1.0 1.0 1.0 -36400.784123 \n",
"\n",
" (0.0, 1.0, 0.52, 0.01) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36282.574211 \n",
"884.0 0.0 0.0 0.0 0.0 -36505.613735 \n",
"888.0 0.0 0.0 0.0 0.0 -36469.714988 \n",
"894.0 0.0 0.0 0.0 0.0 -36414.018685 \n",
"898.0 0.0 0.0 0.0 0.0 -36568.220555 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36519.645494 \n",
"96882.0 0.0 1.0 1.0 1.0 -36663.422849 \n",
"96886.0 0.0 1.0 1.0 1.0 -36374.871434 \n",
"96888.0 0.0 1.0 1.0 1.0 -36607.539623 \n",
"96896.0 0.0 1.0 1.0 1.0 -36438.770842 \n",
"\n",
" (0.0, 1.0, 0.6, 0.02) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36277.262374 \n",
"884.0 0.0 0.0 0.0 0.0 -36500.867819 \n",
"888.0 0.0 0.0 0.0 0.0 -36464.820480 \n",
"894.0 0.0 0.0 0.0 0.0 -36409.565104 \n",
"898.0 0.0 0.0 0.0 0.0 -36564.169525 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36566.176057 \n",
"96882.0 0.0 1.0 1.0 1.0 -36698.804505 \n",
"96886.0 0.0 1.0 1.0 1.0 -36429.283830 \n",
"96888.0 0.0 1.0 1.0 1.0 -36652.264324 \n",
"96896.0 0.0 1.0 1.0 1.0 -36490.549196 \n",
"\n",
" (0.0, 1.0, 0.68, 0.04) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36271.825213 \n",
"884.0 0.0 0.0 0.0 0.0 -36495.956646 \n",
"888.0 0.0 0.0 0.0 0.0 -36459.773463 \n",
"894.0 0.0 0.0 0.0 0.0 -36404.917884 \n",
"898.0 0.0 0.0 0.0 0.0 -36559.891357 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36593.670575 \n",
"96882.0 0.0 1.0 1.0 1.0 -36719.408008 \n",
"96886.0 0.0 1.0 1.0 1.0 -36462.903953 \n",
"96888.0 0.0 1.0 1.0 1.0 -36678.845335 \n",
"96896.0 0.0 1.0 1.0 1.0 -36521.529936 \n",
"\n",
" (0.0, 1.0, 0.76, 0.1) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36266.284534 \n",
"884.0 0.0 0.0 0.0 0.0 -36490.913621 \n",
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"894.0 0.0 0.0 0.0 0.0 -36400.117349 \n",
"898.0 0.0 0.0 0.0 0.0 -36555.440261 \n",
"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36609.561640 \n",
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"96896.0 0.0 1.0 1.0 1.0 -36539.761463 \n",
"\n",
" (0.0, 1.0, 0.84, 0.2) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36260.667217 \n",
"884.0 0.0 0.0 0.0 0.0 -36485.772194 \n",
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"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36618.049801 \n",
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"96896.0 0.0 1.0 1.0 1.0 -36549.818624 \n",
"\n",
" (0.0, 1.0, 0.92, 0.4) \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36254.968789 \n",
"884.0 0.0 0.0 0.0 0.0 -36480.538579 \n",
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"894.0 0.0 0.0 0.0 0.0 -36390.180835 \n",
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"... ... \n",
"96880.0 0.0 1.0 1.0 1.0 -36621.634447 \n",
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"96896.0 0.0 1.0 1.0 1.0 -36554.442952 \n",
"\n",
" (0.0, 1.0, 1.0, 1.0) \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"756.0 0.0 0.0 0.0 0.0 -36249.078206 \n",
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"... ... \n",
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"\n",
"[36907 rows x 28 columns]"
]
},
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"metadata": {},
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],
"source": [
"subsampling.equilibrium_detection(u_nk, u_nk.columns[0])"
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" fep coul \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
"330.0 0.0 0.0 0.0 0.0 0.0 161.047660 \n",
"1764.0 0.0 0.0 0.0 0.0 0.0 160.991429 \n",
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"4860.0 0.0 0.0 0.0 0.0 0.0 131.460735 \n",
"... ... ... \n",
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"96896.0 0.0 1.0 1.0 1.0 0.0 44.294170 \n",
"\n",
" vdw \\\n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
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"96896.0 0.0 1.0 1.0 1.0 5.813643 \n",
"\n",
" restraint \n",
"time fep-lambda coul-lambda vdw-lambda restraint-lambda \n",
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"96896.0 0.0 1.0 1.0 1.0 0.150873 \n",
"\n",
"[26660 rows x 4 columns]"
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},
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"metadata": {},
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],
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]
},
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