From 6c8d1529d5a7c8af40d8a03eec67b067b332f74a Mon Sep 17 00:00:00 2001 From: Pau Ferri-Vicedo Date: Mon, 18 Nov 2024 17:06:21 -0500 Subject: [PATCH] Cation-Anion docking example folder added and explained at examples/README.md --- examples/Cation_Anion/.gitignore | 1 + examples/Cation_Anion/DEB+.xyz | 25 +++ examples/Cation_Anion/job.sh | 17 ++ examples/Cation_Anion/structure.cif | 249 ++++++++++++++++++++++++++++ examples/README.md | 1 + 5 files changed, 293 insertions(+) create mode 100644 examples/Cation_Anion/.gitignore create mode 100644 examples/Cation_Anion/DEB+.xyz create mode 100755 examples/Cation_Anion/job.sh create mode 100644 examples/Cation_Anion/structure.cif diff --git a/examples/Cation_Anion/.gitignore b/examples/Cation_Anion/.gitignore new file mode 100644 index 0000000..3f91e5b --- /dev/null +++ b/examples/Cation_Anion/.gitignore @@ -0,0 +1 @@ +mcdocked vdocked diff --git a/examples/Cation_Anion/DEB+.xyz b/examples/Cation_Anion/DEB+.xyz new file mode 100644 index 0000000..20ce3f4 --- /dev/null +++ b/examples/Cation_Anion/DEB+.xyz @@ -0,0 +1,25 @@ +23 + +C 2.8824 -0.9488 0.572 +C 1.4172 -0.9826 0.3101 +C 0.617 0.2149 0.0164 +C 1.1534 1.491 0.2607 +C 0.415 2.6507 0.0142 +C -0.8793 2.5564 -0.4785 +C -1.4323 1.3024 -0.7264 +C -0.6986 0.1219 -0.4908 +C -1.3828 -1.195 -0.7917 +C -2.1371 -1.7357 0.4145 +H 3.087 -0.5902 1.5851 +H 3.2955 -1.9588 0.4837 +H 3.4081 -0.3169 -0.1502 +H 0.9012 -1.9173 0.4953 +H 2.1576 1.6066 0.6605 +H 0.853 3.625 0.2135 +H -1.4591 3.4554 -0.6683 +H -2.4492 1.2451 -1.1101 +H -0.6596 -1.934 -1.154 +H -2.0863 -1.0578 -1.6232 +H -1.4677 -1.912 1.2627 +H -2.9137 -1.0361 0.742 +H -2.6216 -2.6843 0.1624 diff --git a/examples/Cation_Anion/job.sh b/examples/Cation_Anion/job.sh new file mode 100755 index 0000000..d5a9a27 --- /dev/null +++ b/examples/Cation_Anion/job.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# Runs until the first success is found Also with Monte Carlo docking +echo "" +echo "In this example we must supply the --cation_indexes (start counting after the framework, remember 0 indexing)" +echo "and the --acid_sites (oxygens bonded to the heteroatom)" +echo "" +echo "--acid_sites doesn't need all the acid sites present in the system, you can choose to sample for a preferred one if needed" +echo "" +echo "This example runs the docking of a DEB+ molecule into an Al-UTL zeolite framework" +echo "" +echo "If job fails to reach a final pose you can tune --threshold_catan, --threshold and --attempts parameters" +echo "" +echo "Running Monte Carlo docking" +echo "" +python3 ../../scripts/dock.py structure.cif DEB+.xyz -d mcsuccess -s random -f min_catan_distance -o mcdocked --threshold_catan 3.1 --threshold 1.5 --attempts 20000 --cation_indexes 225 --acid_sites 84,92,90,96 +echo "Final pose save to mcdocked folder" diff --git a/examples/Cation_Anion/structure.cif b/examples/Cation_Anion/structure.cif new file mode 100644 index 0000000..e2d4169 --- /dev/null +++ b/examples/Cation_Anion/structure.cif @@ -0,0 +1,249 @@ +data_image0 +_chemical_formula_structural O148AlSi75 +_chemical_formula_sum "O148 Al1 Si75" +_cell_length_a 28.996 +_cell_length_b 13.968 +_cell_length_c 12.449 +_cell_angle_alpha 90 +_cell_angle_beta 104.91 +_cell_angle_gamma 90 + +_space_group_name_H-M_alt "P 1" +_space_group_IT_number 1 + +loop_ + _space_group_symop_operation_xyz + 'x, y, z' + +loop_ + _atom_site_type_symbol + _atom_site_label + _atom_site_symmetry_multiplicity + _atom_site_fract_x + _atom_site_fract_y + _atom_site_fract_z + _atom_site_occupancy + O O1 1.0 0.41940 0.67970 0.74110 1.0000 + O O2 1.0 0.91940 0.17970 0.74110 1.0000 + O O3 1.0 0.58060 0.67970 0.25890 1.0000 + O O4 1.0 0.08060 0.17970 0.25890 1.0000 + O O5 1.0 0.58060 0.32030 0.25890 1.0000 + O O6 1.0 0.08060 0.82030 0.25890 1.0000 + O O7 1.0 0.41940 0.32030 0.74110 1.0000 + O O8 1.0 0.91940 0.82030 0.74110 1.0000 + O O9 1.0 0.50760 0.62900 0.84150 1.0000 + O O10 1.0 0.00760 0.12900 0.84150 1.0000 + O O11 1.0 0.49240 0.62900 0.15850 1.0000 + O O12 1.0 0.99240 0.12900 0.15850 1.0000 + O O13 1.0 0.49240 0.37100 0.15850 1.0000 + O O14 1.0 0.99240 0.87100 0.15850 1.0000 + O O15 1.0 0.50760 0.37100 0.84150 1.0000 + O O16 1.0 0.00760 0.87100 0.84150 1.0000 + O O17 1.0 0.43940 0.50000 0.79880 1.0000 + O O18 1.0 0.93940 0.00000 0.79880 1.0000 + O O19 1.0 0.56060 0.50000 0.20120 1.0000 + O O20 1.0 0.06060 0.00000 0.20120 1.0000 + O O21 1.0 0.44140 0.63100 0.95140 1.0000 + O O22 1.0 0.94140 0.13100 0.95140 1.0000 + O O23 1.0 0.55860 0.63100 0.04860 1.0000 + O O24 1.0 0.05860 0.13100 0.04860 1.0000 + O O25 1.0 0.55860 0.36900 0.04860 1.0000 + O O26 1.0 0.05860 0.86900 0.04860 1.0000 + O O27 1.0 0.44140 0.36900 0.95140 1.0000 + O O28 1.0 0.94140 0.86900 0.95140 1.0000 + O O29 1.0 0.40230 0.68090 0.11120 1.0000 + O O30 1.0 0.90230 0.18090 0.11120 1.0000 + O O31 1.0 0.59770 0.68090 0.88880 1.0000 + O O32 1.0 0.09770 0.18090 0.88880 1.0000 + O O33 1.0 0.59770 0.31910 0.88880 1.0000 + O O34 1.0 0.09770 0.81910 0.88880 1.0000 + O O35 1.0 0.40230 0.31910 0.11120 1.0000 + O O36 1.0 0.90230 0.81910 0.11120 1.0000 + O O37 1.0 0.42520 0.50000 0.08900 1.0000 + O O38 1.0 0.92520 0.00000 0.08900 1.0000 + O O39 1.0 0.57480 0.50000 0.91100 1.0000 + O O40 1.0 0.07480 1.00000 0.91100 1.0000 + O O41 1.0 0.71730 0.50000 0.82440 1.0000 + O O42 1.0 0.28270 0.50000 0.17560 1.0000 + O O43 1.0 0.29570 0.90600 0.83550 1.0000 + O O44 1.0 0.79570 0.40600 0.83550 1.0000 + O O45 1.0 0.70430 0.90600 0.16450 1.0000 + O O46 1.0 0.20430 0.40600 0.16450 1.0000 + O O47 1.0 0.70430 0.09400 0.16450 1.0000 + O O48 1.0 0.20430 0.59400 0.16450 1.0000 + O O49 1.0 0.29570 0.09400 0.83550 1.0000 + O O50 1.0 0.79570 0.59400 0.83550 1.0000 + O O51 1.0 0.75460 0.50000 0.65120 1.0000 + O O52 1.0 0.24540 0.50000 0.34880 1.0000 + O O53 1.0 0.19410 0.40480 0.78530 1.0000 + O O54 1.0 0.69410 0.90480 0.78530 1.0000 + O O55 1.0 0.80590 0.40480 0.21470 1.0000 + O O56 1.0 0.30590 0.90480 0.21470 1.0000 + O O57 1.0 0.80590 0.59520 0.21470 1.0000 + O O58 1.0 0.30590 0.09520 0.21470 1.0000 + O O59 1.0 0.19410 0.59520 0.78530 1.0000 + O O60 1.0 0.69410 0.09520 0.78530 1.0000 + O O61 1.0 0.27080 0.50000 0.77760 1.0000 + O O62 1.0 0.77080 0.00000 0.77760 1.0000 + O O63 1.0 0.72920 0.50000 0.22240 1.0000 + O O64 1.0 0.22920 0.00000 0.22240 1.0000 + O O65 1.0 0.24180 0.50000 0.96080 1.0000 + O O66 1.0 0.74180 0.00000 0.96080 1.0000 + O O67 1.0 0.75820 0.50000 0.03920 1.0000 + O O68 1.0 0.25820 1.00000 0.03920 1.0000 + O O69 1.0 0.27360 0.50000 0.56640 1.0000 + O O70 1.0 0.77360 0.00000 0.56640 1.0000 + O O71 1.0 0.72640 0.50000 0.43360 1.0000 + O O72 1.0 0.22640 1.00000 0.43360 1.0000 + O O73 1.0 0.33790 0.40620 0.71610 1.0000 + O O74 1.0 0.83790 0.90620 0.71610 1.0000 + O O75 1.0 0.66210 0.40620 0.28390 1.0000 + O O76 1.0 0.16210 0.90620 0.28390 1.0000 + O O77 1.0 0.66210 0.59380 0.28390 1.0000 + O O78 1.0 0.16210 0.09380 0.28390 1.0000 + O O79 1.0 0.33790 0.59380 0.71610 1.0000 + O O80 1.0 0.83790 0.09380 0.71610 1.0000 + O O81 1.0 0.19670 0.40550 0.46700 1.0000 + O O82 1.0 0.69670 0.90550 0.46700 1.0000 + O O83 1.0 0.80330 0.40550 0.53300 1.0000 + O O84 1.0 0.30330 0.90550 0.53300 1.0000 + O O85 1.0 0.80330 0.59450 0.53300 1.0000 + O O86 1.0 0.30330 0.09450 0.53300 1.0000 + O O87 1.0 0.19670 0.59450 0.46700 1.0000 + O O88 1.0 0.69670 0.09450 0.46700 1.0000 + O O89 1.0 0.32880 0.72540 0.19190 1.0000 + O O90 1.0 0.82880 0.22540 0.19190 1.0000 + O O91 1.0 0.67120 0.72540 0.80810 1.0000 + O O92 1.0 0.17120 0.22540 0.80810 1.0000 + O O93 1.0 0.67120 0.27460 0.80810 1.0000 + O O94 1.0 0.17120 0.77460 0.80810 1.0000 + O O95 1.0 0.32880 0.27460 0.19190 1.0000 + O O96 1.0 0.82880 0.77460 0.19190 1.0000 + O O97 1.0 0.24010 0.76930 0.19020 1.0000 + O O98 1.0 0.74010 0.26930 0.19020 1.0000 + O O99 1.0 0.75990 0.76930 0.80980 1.0000 + O O100 1.0 0.25990 0.26930 0.80980 1.0000 + O O101 1.0 0.75990 0.23070 0.80980 1.0000 + O O102 1.0 0.25990 0.73070 0.80980 1.0000 + O O103 1.0 0.24010 0.23070 0.19020 1.0000 + O O104 1.0 0.74010 0.73070 0.19020 1.0000 + O O105 1.0 0.30850 0.78300 0.37510 1.0000 + O O106 1.0 0.80850 0.28300 0.37510 1.0000 + O O107 1.0 0.69150 0.78300 0.62490 1.0000 + O O108 1.0 0.19150 0.28300 0.62490 1.0000 + O O109 1.0 0.69150 0.21700 0.62490 1.0000 + O O110 1.0 0.19150 0.71700 0.62490 1.0000 + O O111 1.0 0.30850 0.21700 0.37510 1.0000 + O O112 1.0 0.80850 0.71700 0.37510 1.0000 + O O113 1.0 0.34340 0.73760 0.58370 1.0000 + O O114 1.0 0.84340 0.23760 0.58370 1.0000 + O O115 1.0 0.65660 0.73760 0.41630 1.0000 + O O116 1.0 0.15660 0.23760 0.41630 1.0000 + O O117 1.0 0.65660 0.26240 0.41630 1.0000 + O O118 1.0 0.15660 0.76240 0.41630 1.0000 + O O119 1.0 0.34340 0.26240 0.58370 1.0000 + O O120 1.0 0.84340 0.76240 0.58370 1.0000 + O O121 1.0 0.25000 0.75000 0.50000 1.0000 + O O122 1.0 0.75000 0.25000 0.50000 1.0000 + O O123 1.0 0.75000 0.75000 0.50000 1.0000 + O O124 1.0 0.25000 0.25000 0.50000 1.0000 + O O125 1.0 0.34790 0.76700 0.79510 1.0000 + O O126 1.0 0.84790 0.26700 0.79510 1.0000 + O O127 1.0 0.65210 0.76700 0.20490 1.0000 + O O128 1.0 0.15210 0.26700 0.20490 1.0000 + O O129 1.0 0.65210 0.23300 0.20490 1.0000 + O O130 1.0 0.15210 0.73300 0.20490 1.0000 + O O131 1.0 0.34790 0.23300 0.79510 1.0000 + O O132 1.0 0.84790 0.73300 0.79510 1.0000 + O O133 1.0 0.32810 0.77530 0.98810 1.0000 + O O134 1.0 0.82810 0.27530 0.98810 1.0000 + O O135 1.0 0.67190 0.77530 0.01190 1.0000 + O O136 1.0 0.17190 0.27530 0.01190 1.0000 + O O137 1.0 0.67190 0.22470 0.01190 1.0000 + O O138 1.0 0.17190 0.72470 0.01190 1.0000 + O O139 1.0 0.32810 0.22470 0.98810 1.0000 + O O140 1.0 0.82810 0.72470 0.98810 1.0000 + O O141 1.0 0.32120 0.59430 0.03640 1.0000 + O O142 1.0 0.82120 0.09430 0.03640 1.0000 + O O143 1.0 0.67880 0.59430 0.96360 1.0000 + O O144 1.0 0.17880 0.09430 0.96360 1.0000 + O O145 1.0 0.67880 0.40570 0.96360 1.0000 + O O146 1.0 0.17880 0.90570 0.96360 1.0000 + O O147 1.0 0.32120 0.40570 0.03640 1.0000 + O O148 1.0 0.82120 0.90570 0.03640 1.0000 + Al Al1 1.0 0.45210 0.60990 0.83300 1.0000 + Si Si1 1.0 0.95210 0.10990 0.83300 1.0000 + Si Si2 1.0 0.54790 0.60990 0.16700 1.0000 + Si Si3 1.0 0.04790 0.10990 0.16700 1.0000 + Si Si4 1.0 0.54790 0.39010 0.16700 1.0000 + Si Si5 1.0 0.04790 0.89010 0.16700 1.0000 + Si Si6 1.0 0.45210 0.39010 0.83300 1.0000 + Si Si7 1.0 0.95210 0.89010 0.83300 1.0000 + Si Si8 1.0 0.44010 0.60990 0.07770 1.0000 + Si Si9 1.0 0.94010 0.10990 0.07770 1.0000 + Si Si10 1.0 0.55990 0.60990 0.92230 1.0000 + Si Si11 1.0 0.05990 0.10990 0.92230 1.0000 + Si Si12 1.0 0.55990 0.39010 0.92230 1.0000 + Si Si13 1.0 0.05990 0.89010 0.92230 1.0000 + Si Si14 1.0 0.44010 0.39010 0.07770 1.0000 + Si Si15 1.0 0.94010 0.89010 0.07770 1.0000 + Si Si16 1.0 0.29540 0.79540 0.24220 1.0000 + Si Si17 1.0 0.79540 0.29540 0.24220 1.0000 + Si Si18 1.0 0.70460 0.79540 0.75780 1.0000 + Si Si19 1.0 0.20460 0.29540 0.75780 1.0000 + Si Si20 1.0 0.70460 0.20460 0.75780 1.0000 + Si Si21 1.0 0.20460 0.70460 0.75780 1.0000 + Si Si22 1.0 0.29540 0.20460 0.24220 1.0000 + Si Si23 1.0 0.79540 0.70460 0.24220 1.0000 + Si Si24 1.0 0.30100 0.79410 0.49820 1.0000 + Si Si25 1.0 0.80100 0.29410 0.49820 1.0000 + Si Si26 1.0 0.69900 0.79410 0.50180 1.0000 + Si Si27 1.0 0.19900 0.29410 0.50180 1.0000 + Si Si28 1.0 0.69900 0.20590 0.50180 1.0000 + Si Si29 1.0 0.19900 0.70590 0.50180 1.0000 + Si Si30 1.0 0.30100 0.20590 0.49820 1.0000 + Si Si31 1.0 0.80100 0.70590 0.49820 1.0000 + Si Si32 1.0 0.30720 0.79380 0.85690 1.0000 + Si Si33 1.0 0.80720 0.29380 0.85690 1.0000 + Si Si34 1.0 0.69280 0.79380 0.14310 1.0000 + Si Si35 1.0 0.19280 0.29380 0.14310 1.0000 + Si Si36 1.0 0.69280 0.20620 0.14310 1.0000 + Si Si37 1.0 0.19280 0.70620 0.14310 1.0000 + Si Si38 1.0 0.30720 0.20620 0.85690 1.0000 + Si Si39 1.0 0.80720 0.70620 0.85690 1.0000 + Si Si40 1.0 0.34530 0.69500 0.08270 1.0000 + Si Si41 1.0 0.84530 0.19500 0.08270 1.0000 + Si Si42 1.0 0.65470 0.69500 0.91730 1.0000 + Si Si43 1.0 0.15470 0.19500 0.91730 1.0000 + Si Si44 1.0 0.65470 0.30500 0.91730 1.0000 + Si Si45 1.0 0.15470 0.80500 0.91730 1.0000 + Si Si46 1.0 0.34530 0.30500 0.08270 1.0000 + Si Si47 1.0 0.84530 0.80500 0.08270 1.0000 + Si Si48 1.0 0.36240 0.69570 0.70760 1.0000 + Si Si49 1.0 0.86240 0.19570 0.70760 1.0000 + Si Si50 1.0 0.63760 0.69570 0.29240 1.0000 + Si Si51 1.0 0.13760 0.19570 0.29240 1.0000 + Si Si52 1.0 0.63760 0.30430 0.29240 1.0000 + Si Si53 1.0 0.13760 0.80430 0.29240 1.0000 + Si Si54 1.0 0.36240 0.30430 0.70760 1.0000 + Si Si55 1.0 0.86240 0.80430 0.70760 1.0000 + Si Si56 1.0 0.26600 0.00000 0.78470 1.0000 + Si Si57 1.0 0.76600 0.50000 0.78470 1.0000 + Si Si58 1.0 0.73400 0.00000 0.21530 1.0000 + Si Si59 1.0 0.23400 0.50000 0.21530 1.0000 + Si Si60 1.0 0.22470 0.50000 0.82700 1.0000 + Si Si61 1.0 0.77530 0.50000 0.17300 1.0000 + Si Si62 1.0 0.27530 0.00000 0.17300 1.0000 + Si Si63 1.0 0.72470 0.00000 0.82700 1.0000 + Si Si64 1.0 0.30460 0.50000 0.69360 1.0000 + Si Si65 1.0 0.69540 0.50000 0.30640 1.0000 + Si Si66 1.0 0.19540 0.00000 0.30640 1.0000 + Si Si67 1.0 0.80460 0.00000 0.69360 1.0000 + Si Si68 1.0 0.22780 0.50000 0.46120 1.0000 + Si Si69 1.0 0.77220 0.50000 0.53880 1.0000 + Si Si70 1.0 0.27220 0.00000 0.53880 1.0000 + Si Si71 1.0 0.72780 0.00000 0.46120 1.0000 + Si Si72 1.0 0.29210 0.50000 0.05360 1.0000 + Si Si73 1.0 0.70790 0.50000 0.94640 1.0000 + Si Si74 1.0 0.20790 0.00000 0.94640 1.0000 + Si Si75 1.0 0.79210 0.00000 0.05360 1.0000 diff --git a/examples/README.md b/examples/README.md index f18ddf6..0f619dc 100644 --- a/examples/README.md +++ b/examples/README.md @@ -7,5 +7,6 @@ The following examples are currently available in this repository: 3. [Docking triethylamine to MOR zeolite](MOR_loading): several triethylamine molecules are docked to MOR zeolite with Voronoi batch docker. 4. [Docking benzene to MOF-5](MOF-5): several benzene molecules are docked to MOF-5 using the Voronoi batched docker. The MOF-5 structure was retrieved from the Cambridge Structural Database (ID [SAHYIK](https://www.ccdc.cam.ac.uk/structures/search?identifier=SAHYIK)) 5. [Docking water to a Ni(111) surface](Ni111): one water molecule is docked to a Ni(111) surface using the Gaussian target fitness function. The Ni(111) surface structure was retrieved from the [Materials Project](https://materialsproject.org) (ID [mp-23](https://materialsproject.org/materials/mp-23/surfaces/[1,%201,%201]/cif)) +6. [Docking Diethylbenzenium cation (DEB+) into an acid UTL zeolite](Cation_Anion): One DEB+ molecule is docked to a UTL framework containing one Al atom, hence 4 acid sites. The minimmum cation-anion fitness ensures a close positioning of the docked molecule with respect to the acid sites of the host. Each example has a `job.sh` script file showing how to run the docker.