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Cation-Anion docking example folder added and explained at examples/R…
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Pau Ferri-Vicedo committed Nov 18, 2024
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1 change: 1 addition & 0 deletions examples/Cation_Anion/.gitignore
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mcdocked vdocked
25 changes: 25 additions & 0 deletions examples/Cation_Anion/DEB+.xyz
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23

C 2.8824 -0.9488 0.572
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C -0.6986 0.1219 -0.4908
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H 3.087 -0.5902 1.5851
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H 0.9012 -1.9173 0.4953
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H 0.853 3.625 0.2135
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H -2.9137 -1.0361 0.742
H -2.6216 -2.6843 0.1624
17 changes: 17 additions & 0 deletions examples/Cation_Anion/job.sh
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#!/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"
249 changes: 249 additions & 0 deletions examples/Cation_Anion/structure.cif
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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
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O O29 1.0 0.40230 0.68090 0.11120 1.0000
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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
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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
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O O132 1.0 0.84790 0.73300 0.79510 1.0000
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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
1 change: 1 addition & 0 deletions examples/README.md
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Expand Up @@ -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.

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