.. _plot_probe_data: Plotting Probe Data ------------------- The SilcsBio software provides a utility to monitor probe concentrations and excess chemical potentials (:math:`\mu_\mathrm{ex}`) as a function of GCMC-MD cycle. The following python script will generate these plots: :: python $SILCSBIODIR/utils/python/plot_probe_data.py --prot optional arguments: -h, --help show this help message and exit --prot PROT protein PDB file (Required) --numsys NUMSYS number of runs (Default=10) --halogen HALOGEN halgen probes True/False (Default=False) --begin BEGIN first gcmc-md cycle (Default=1) --end END number of gcmc-md cycles (Default=100) --vertical VERTICAL plot together vertically/horizontally (Default=False) Below is an example of an output from running the python script: :: 1 BENX Acceptance: ins = 1.724% del = 1.771% trn = 15.665% rot = 2.013% 1 PRPX Acceptance: ins = 9.596% del = 10.202% trn = 24.742% rot = 8.106% 1 DMEE Acceptance: ins = 2.396% del = 2.438% trn = 18.753% rot = 2.162% 1 MEOH Acceptance: ins = 1.014% del = 1.037% trn = 13.012% rot = 0.680% 1 FORM Acceptance: ins = 0.772% del = 0.809% trn = 14.391% rot = 0.639% 1 IMIA Acceptance: ins = 1.183% del = 1.211% trn = 8.683% rot = 0.664% 1 ACEY Acceptance: ins = 1.453% del = 1.496% trn = 4.402% rot = 0.644% 1 MAMY Acceptance: ins = 3.865% del = 4.031% trn = 8.300% rot = 2.009% 1 SOL Acceptance: ins = 0.505% del = 0.506% trn = 10.704% rot = 1.026% The output lists the SILCS simulation number, SILCS solute, and the accepted insertions (``ins``), deletions (``del``), translations (``trn``), and rotations (``rot``). A detailed output for each simulation system will be stored in ``status..txt`` text file in the ``2a_run_gcmd`` directory. An example of the contents of ``status..txt`` is shown below: :: cycle fragname curr_N targ_N percent hfe muexdx vardx dxdx muex 1 benx 118 98 120.41 -0.790 1.000 0.000 0.000 -2.790 1 prpx 118 98 120.41 1.960 0.500 0.000 0.000 1.460 1 dmee 118 98 120.41 -1.440 1.000 0.000 0.000 -1.440 1 meoh 118 98 120.41 -5.360 2.000 0.000 0.000 -5.360 1 form 118 98 120.41 -10.920 2.500 0.000 0.000 -10.920 1 imia 118 98 120.41 -14.180 3.000 0.000 0.000 -14.180 1 acey 118 98 120.41 -97.310 10.000 0.000 0.000 -97.310 1 mamy 118 98 120.41 -68.490 7.000 0.000 0.000 -68.490 1 sol 21750 21750 100.00 -5.600 0.500 0.000 0.000 -5.600 2 benx 121 98 123.47 -0.790 1.000 -0.920 -0.300 -3.790 2 prpx 109 98 111.22 1.960 0.500 -0.220 0.450 1.690 2 dmee 118 98 120.41 -1.440 1.000 -1.600 -0.000 -2.440 ... 99 imia 100 98 102.04 -14.180 3.000 -0.240 0.000 -7.160 99 acey 109 98 111.22 -97.310 10.000 0.000 1.000 -95.310 99 mamy 104 98 106.12 -68.490 7.000 0.000 0.700 -83.890 99 sol 21818 21750 100.31 -5.600 0.500 -0.031 0.000 -6.071 100 benx 100 98 102.04 -0.790 1.000 -0.080 0.000 -5.330 100 prpx 94 98 95.92 1.960 0.500 0.080 0.000 1.610 100 dmee 113 98 115.31 -1.440 1.000 -1.200 -0.000 -2.280 100 meoh 107 98 109.18 -5.360 2.000 -0.720 -0.400 -3.600 100 form 98 98 100.00 -10.920 2.500 2.500 0.000 -8.820 100 imia 109 98 111.22 -14.180 3.000 -1.320 -2.700 -11.180 100 acey 106 98 108.16 -97.310 10.000 -3.200 3.000 -95.510 100 mamy 105 98 107.14 -68.490 7.000 -1.960 -0.700 -86.550 100 sol 21793 21750 100.20 -5.600 0.500 -0.020 0.000 -6.090 In the ``status..txt`` file, each row corresponds to a given solute molecule in a given cycle. In each row, the following information is provided: - the cycle (``cycle``), - SILCS solute (``fragname``), - number of the solute molecule in the cycle (``curr_N``), - targeted number of the solute molecule (``targ_N``), - the percent number of the solute molecule over the targeted number of that solute molecule (``percent``), - the approximate hydration free energy in kcal/mol of the solute obtained from free energy perturbation simulations (``hfe``) :cite:`Lakkaraju:2014`, - the estimated magnitude of excess chemical potential variation (``muexdx``), - the standard variation in excess chemical potential (``vardx``), - the instantaneous variation in the excess chemical potential (``dxdx``), and - the excess chemical potential (``muex``). More information on GCMC cycles and each variable is available in reference :cite:`Zhao:2023`. In addition, the python script will produce plots as ``.png`` files for each probe in each simulation system. These plots will be stored in ``2a_run_gcmd/acceptance_analysis/`` as ``count...png``. Below is an example of the output plots: .. figure:: images/count-plot-example.png :width: 100%