From 9a568a4f2da6a9c9112a4ca7055e976fea825de6 Mon Sep 17 00:00:00 2001 From: Daniel Schwalbe-Koda Date: Wed, 15 Jul 2020 08:35:20 -0400 Subject: [PATCH] add examples --- examples/.gitignore | 1 + examples/CHA_TMAda/.gitignore | 1 + examples/CHA_TMAda/CHA.cif | 74 ++++++++ examples/CHA_TMAda/TMAda.xyz | 40 +++++ examples/CHA_TMAda/job.sh | 9 + examples/MOF-5/MOF-5.cif | 236 +++++++++++++++++++++++++ examples/MOF-5/benzene.xyz | 14 ++ examples/MOF-5/job.sh | 5 + examples/MOR_loading/MOR.cif | 63 +++++++ examples/MOR_loading/job.sh | 4 + examples/MOR_loading/triethylamine.xyz | 24 +++ examples/Ni111/Ni111.cif | 32 ++++ examples/Ni111/job.sh | 5 + examples/Ni111/water.xyz | 6 + 14 files changed, 514 insertions(+) create mode 100644 examples/.gitignore create mode 100644 examples/CHA_TMAda/.gitignore create mode 100644 examples/CHA_TMAda/CHA.cif create mode 100644 examples/CHA_TMAda/TMAda.xyz create mode 100755 examples/CHA_TMAda/job.sh create mode 100644 examples/MOF-5/MOF-5.cif create mode 100644 examples/MOF-5/benzene.xyz create mode 100755 examples/MOF-5/job.sh create mode 100644 examples/MOR_loading/MOR.cif create mode 100755 examples/MOR_loading/job.sh create mode 100644 examples/MOR_loading/triethylamine.xyz create mode 100644 examples/Ni111/Ni111.cif create mode 100755 examples/Ni111/job.sh create mode 100644 examples/Ni111/water.xyz diff --git a/examples/.gitignore b/examples/.gitignore new file mode 100644 index 0000000..918c607 --- /dev/null +++ b/examples/.gitignore @@ -0,0 +1 @@ +*docked* diff --git a/examples/CHA_TMAda/.gitignore b/examples/CHA_TMAda/.gitignore new file mode 100644 index 0000000..3f91e5b --- /dev/null +++ b/examples/CHA_TMAda/.gitignore @@ -0,0 +1 @@ +mcdocked vdocked diff --git a/examples/CHA_TMAda/CHA.cif b/examples/CHA_TMAda/CHA.cif new file mode 100644 index 0000000..e1ea1cf --- /dev/null +++ b/examples/CHA_TMAda/CHA.cif @@ -0,0 +1,74 @@ +data_CHA +#************************************************************************** +# +# CIF taken from the IZA-SC Database of Zeolite Structures +# Ch. Baerlocher and L.B. McCusker +# Database of Zeolite Structures: http://www.iza-structure.org/databases/ +# +# The atom coordinates and the cell parameters were optimized with DLS76 +# assuming a pure SiO2 composition. +# +#************************************************************************** + +_cell_length_a 13.6750(0) +_cell_length_b 13.6750(0) +_cell_length_c 14.7670(0) +_cell_angle_alpha 90.0000(0) +_cell_angle_beta 90.0000(0) +_cell_angle_gamma 120.0000(0) + +_symmetry_space_group_name_H-M 'R -3 m' +_symmetry_Int_Tables_number 166 +_symmetry_cell_setting trigonal + +loop_ +_symmetry_equiv_pos_as_xyz +'+x,+y,+z' +'2/3+x,1/3+y,1/3+z' +'1/3+x,2/3+y,2/3+z' +'-y,+x-y,+z' +'2/3-y,1/3+x-y,1/3+z' +'1/3-y,2/3+x-y,2/3+z' +'-x+y,-x,+z' +'2/3-x+y,1/3-x,1/3+z' +'1/3-x+y,2/3-x,2/3+z' +'-y,-x,+z' +'2/3-y,1/3-x,1/3+z' +'1/3-y,2/3-x,2/3+z' +'-x+y,+y,+z' +'2/3-x+y,1/3+y,1/3+z' +'1/3-x+y,2/3+y,2/3+z' +'+x,+x-y,+z' +'2/3+x,1/3+x-y,1/3+z' +'1/3+x,2/3+x-y,2/3+z' +'-x,-y,-z' +'2/3-x,1/3-y,1/3-z' +'1/3-x,2/3-y,2/3-z' +'+y,-x+y,-z' +'2/3+y,1/3-x+y,1/3-z' +'1/3+y,2/3-x+y,2/3-z' +'+x-y,+x,-z' +'2/3+x-y,1/3+x,1/3-z' +'1/3+x-y,2/3+x,2/3-z' +'+y,+x,-z' +'2/3+y,1/3+x,1/3-z' +'1/3+y,2/3+x,2/3-z' +'+x-y,-y,-z' +'2/3+x-y,1/3-y,1/3-z' +'1/3+x-y,2/3-y,2/3-z' +'-x,-x+y,-z' +'2/3-x,1/3-x+y,1/3-z' +'1/3-x,2/3-x+y,2/3-z' + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z + O1 O 0.9020 0.0980 0.1227 + O2 O 0.9767 0.3101 0.1667 + O3 O 0.1203 0.2405 0.1315 + O4 O 0.0000 0.2577 0.0000 + T1 Si 0.9997 0.2264 0.1051 + diff --git a/examples/CHA_TMAda/TMAda.xyz b/examples/CHA_TMAda/TMAda.xyz new file mode 100644 index 0000000..f3e3ac6 --- /dev/null +++ b/examples/CHA_TMAda/TMAda.xyz @@ -0,0 +1,40 @@ +38 + +C 2.5089 -1.2089 -0.8054 +N 1.9366 0.0764 -0.1848 +C 2.3857 1.2407 -1.0835 +C 2.6392 0.2656 1.1699 +C 0.3464 0.0137 -0.0331 +C -0.0892 -1.3008 0.6773 +C -1.6221 -1.3564 0.8273 +C -2.2669 -1.3072 -0.5662 +C -1.8764 -0.0039 -1.2785 +C -2.3541 1.1951 -0.4452 +C -1.7097 1.1548 0.9482 +C -2.1007 -0.1531 1.6529 +C -0.176 1.2145 0.808 +C -0.3438 0.0623 -1.4271 +H 2.372 -2.0348 -0.1034 +H 2.0075 -1.4041 -1.7546 +H 3.5799 -1.0602 -0.9792 +H 3.4794 1.292 -1.0598 +H 1.9669 2.1726 -0.7007 +H 2.0592 1.0463 -2.1077 +H 3.7202 0.1936 1.0102 +H 2.4007 1.2581 1.5592 +H 2.3171 -0.5203 1.8549 +H 0.2235 -2.1814 0.1051 +H 0.3628 -1.3835 1.6713 +H -1.9079 -2.2862 1.332 +H -1.9445 -2.171 -1.1605 +H -3.3582 -1.3727 -0.4764 +H -2.343 0.0281 -2.2696 +H -3.447 1.1756 -0.3533 +H -2.0945 2.1326 -0.952 +H -2.0576 2.0092 1.5396 +H -3.189 -0.1973 1.7834 +H -1.6586 -0.1865 2.6562 +H 0.2531 1.2071 1.8161 +H 0.0962 2.17 0.3475 +H -0.0176 -0.7691 -2.0609 +H -0.0984 0.9892 -1.9573 diff --git a/examples/CHA_TMAda/job.sh b/examples/CHA_TMAda/job.sh new file mode 100755 index 0000000..db88adb --- /dev/null +++ b/examples/CHA_TMAda/job.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Runs until the first success is found +echo "Running Voronoi docking" +python3 ../../scripts/dock.py CHA.cif TMAda.xyz -d success -s voronoi_cluster -f min_distance -o vdocked + +# Also with Monte Carlo docking +echo "Running Monte Carlo docking" +python3 ../../scripts/dock.py CHA.cif TMAda.xyz -d mcsuccess -s random -f min_distance -o mcdocked diff --git a/examples/MOF-5/MOF-5.cif b/examples/MOF-5/MOF-5.cif new file mode 100644 index 0000000..4354736 --- /dev/null +++ b/examples/MOF-5/MOF-5.cif @@ -0,0 +1,236 @@ +data_cmpd_1 +_audit_creation_method 'generated by CrystalMaker X for macOS' +_cell_length_a 25.669000(3) +_cell_length_b 25.669000(3) +_cell_length_c 25.669000(3) +_cell_angle_alpha 90.000000(0) +_cell_angle_beta 90.000000(0) +_cell_angle_gamma 90.000000(0) + +_symmetry_space_group_name_H-M 'F m -3 m' + +loop_ +_symmetry_equiv_pos_as_xyz +'+x,+y,+z' +'+z,+x,+y' +'+y,+z,+x' +'+x,+y,-z' +'+z,+x,-y' +'+y,+z,-x' +'-x,+y,+z' +'-z,+x,+y' +'-y,+z,+x' +'-x,+y,-z' +'-z,+x,-y' +'-y,+z,-x' +'+y,+x,+z' +'+x,+z,+y' +'+z,+y,+x' +'+y,+x,-z' +'+x,+z,-y' +'+z,+y,-x' +'+y,-x,+z' +'+x,-z,+y' +'+z,-y,+x' +'+y,-x,-z' +'+x,-z,-y' +'+z,-y,-x' +'-x,-y,-z' +'-z,-x,-y' +'-y,-z,-x' +'-x,-y,+z' +'-z,-x,+y' +'-y,-z,+x' +'+x,-y,-z' +'+z,-x,-y' +'+y,-z,-x' +'+x,-y,+z' +'+z,-x,+y' +'+y,-z,+x' +'-y,-x,-z' +'-x,-z,-y' +'-z,-y,-x' +'-y,-x,+z' +'-x,-z,+y' +'-z,-y,+x' +'-y,+x,-z' +'-x,+z,-y' +'-z,+y,-x' +'-y,+x,+z' +'-x,+z,+y' +'-z,+y,+x' +'+x,1/2+y,1/2+z' +'1/2+x,1/2+y,+z' +'1/2+x,+y,1/2+z' +'+z,1/2+x,1/2+y' +'1/2+z,1/2+x,+y' +'1/2+z,+x,1/2+y' +'+y,1/2+z,1/2+x' +'1/2+y,1/2+z,+x' +'1/2+y,+z,1/2+x' +'+x,1/2+y,1/2-z' +'1/2+x,1/2+y,-z' +'1/2+x,+y,1/2-z' +'+z,1/2+x,1/2-y' +'1/2+z,1/2+x,-y' +'1/2+z,+x,1/2-y' +'+y,1/2+z,1/2-x' +'1/2+y,1/2+z,-x' +'1/2+y,+z,1/2-x' +'-x,1/2+y,1/2+z' +'1/2-x,1/2+y,+z' +'1/2-x,+y,1/2+z' +'-z,1/2+x,1/2+y' +'1/2-z,1/2+x,+y' +'1/2-z,+x,1/2+y' +'-y,1/2+z,1/2+x' +'1/2-y,1/2+z,+x' +'1/2-y,+z,1/2+x' +'-x,1/2+y,1/2-z' +'1/2-x,1/2+y,-z' +'1/2-x,+y,1/2-z' +'-z,1/2+x,1/2-y' +'1/2-z,1/2+x,-y' +'1/2-z,+x,1/2-y' +'-y,1/2+z,1/2-x' +'1/2-y,1/2+z,-x' +'1/2-y,+z,1/2-x' +'+y,1/2+x,1/2+z' +'1/2+y,1/2+x,+z' +'1/2+y,+x,1/2+z' +'+x,1/2+z,1/2+y' +'1/2+x,1/2+z,+y' +'1/2+x,+z,1/2+y' +'+z,1/2+y,1/2+x' +'1/2+z,1/2+y,+x' +'1/2+z,+y,1/2+x' +'+y,1/2+x,1/2-z' +'1/2+y,1/2+x,-z' +'1/2+y,+x,1/2-z' +'+x,1/2+z,1/2-y' +'1/2+x,1/2+z,-y' +'1/2+x,+z,1/2-y' +'+z,1/2+y,1/2-x' +'1/2+z,1/2+y,-x' +'1/2+z,+y,1/2-x' +'+y,1/2-x,1/2+z' +'1/2+y,1/2-x,+z' +'1/2+y,-x,1/2+z' +'+x,1/2-z,1/2+y' +'1/2+x,1/2-z,+y' +'1/2+x,-z,1/2+y' +'+z,1/2-y,1/2+x' +'1/2+z,1/2-y,+x' +'1/2+z,-y,1/2+x' +'+y,1/2-x,1/2-z' +'1/2+y,1/2-x,-z' +'1/2+y,-x,1/2-z' +'+x,1/2-z,1/2-y' +'1/2+x,1/2-z,-y' +'1/2+x,-z,1/2-y' +'+z,1/2-y,1/2-x' +'1/2+z,1/2-y,-x' +'1/2+z,-y,1/2-x' +'-x,1/2-y,1/2-z' +'1/2-x,1/2-y,-z' +'1/2-x,-y,1/2-z' +'-z,1/2-x,1/2-y' +'1/2-z,1/2-x,-y' +'1/2-z,-x,1/2-y' +'-y,1/2-z,1/2-x' +'1/2-y,1/2-z,-x' +'1/2-y,-z,1/2-x' +'-x,1/2-y,1/2+z' +'1/2-x,1/2-y,+z' +'1/2-x,-y,1/2+z' +'-z,1/2-x,1/2+y' +'1/2-z,1/2-x,+y' +'1/2-z,-x,1/2+y' +'-y,1/2-z,1/2+x' +'1/2-y,1/2-z,+x' +'1/2-y,-z,1/2+x' +'+x,1/2-y,1/2-z' +'1/2+x,1/2-y,-z' +'1/2+x,-y,1/2-z' +'+z,1/2-x,1/2-y' +'1/2+z,1/2-x,-y' +'1/2+z,-x,1/2-y' +'+y,1/2-z,1/2-x' +'1/2+y,1/2-z,-x' +'1/2+y,-z,1/2-x' +'+x,1/2-y,1/2+z' +'1/2+x,1/2-y,+z' +'1/2+x,-y,1/2+z' +'+z,1/2-x,1/2+y' +'1/2+z,1/2-x,+y' +'1/2+z,-x,1/2+y' +'+y,1/2-z,1/2+x' +'1/2+y,1/2-z,+x' +'1/2+y,-z,1/2+x' +'-y,1/2-x,1/2-z' +'1/2-y,1/2-x,-z' +'1/2-y,-x,1/2-z' +'-x,1/2-z,1/2-y' +'1/2-x,1/2-z,-y' +'1/2-x,-z,1/2-y' +'-z,1/2-y,1/2-x' +'1/2-z,1/2-y,-x' +'1/2-z,-y,1/2-x' +'-y,1/2-x,1/2+z' +'1/2-y,1/2-x,+z' +'1/2-y,-x,1/2+z' +'-x,1/2-z,1/2+y' +'1/2-x,1/2-z,+y' +'1/2-x,-z,1/2+y' +'-z,1/2-y,1/2+x' +'1/2-z,1/2-y,+x' +'1/2-z,-y,1/2+x' +'-y,1/2+x,1/2-z' +'1/2-y,1/2+x,-z' +'1/2-y,+x,1/2-z' +'-x,1/2+z,1/2-y' +'1/2-x,1/2+z,-y' +'1/2-x,+z,1/2-y' +'-z,1/2+y,1/2-x' +'1/2-z,1/2+y,-x' +'1/2-z,+y,1/2-x' +'-y,1/2+x,1/2+z' +'1/2-y,1/2+x,+z' +'1/2-y,+x,1/2+z' +'-x,1/2+z,1/2+y' +'1/2-x,1/2+z,+y' +'1/2-x,+z,1/2+y' +'-z,1/2+y,1/2+x' +'1/2-z,1/2+y,+x' +'1/2-z,+y,1/2+x' + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_occupancy +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_U_iso_or_equiv + C(1) C 1.0 0.25000000(0) 0.25000000(0) 0.11050000(70000) 0.08733 + C(2) C 1.0 0.28310000(40000) 0.21690000(40000) 0.02630000(60000) 0.12300 + C(3) C 1.0 0.25000000(0) 0.25000000(0) 0.05380000(60000) 0.09867 + H(2A) H 1.0 0.30590000(0) 0.19410000(0) 0.04520000(0) 0.14800 + O(1) O 1.0 0.25000000(0) 0.25000000(0) 0.25000000(0) 0.04200 + O(2) O 1.0 0.28180000(30000) 0.21820000(30000) 0.13390000(40000) 0.09600 + Zn(1) Zn 1.0 0.29350000(10000) 0.20650000(10000) 0.20650000(10000) 0.05100 + +loop_ +_atom_site_aniso_label +_atom_site_aniso_U_11 +_atom_site_aniso_U_22 +_atom_site_aniso_U_33 +_atom_site_aniso_U_23 +_atom_site_aniso_U_13 +_atom_site_aniso_U_12 +C(1) 0.09900 0.09900 0.06400 0.00000 0.00000 0.00200 +C(2) 0.16000 0.16000 0.04900 0.00400 -0.00400 0.09300 +C(3) 0.13000 0.13000 0.03600 0.00000 0.00000 0.04000 +O(1) 0.04200 0.04200 0.04200 0.00000 0.00000 0.00000 +O(2) 0.11700 0.11700 0.05400 -0.00500 0.00500 0.02900 +Zn(1) 0.05100 0.05100 0.05100 -0.00100 0.00100 0.00100 diff --git a/examples/MOF-5/benzene.xyz b/examples/MOF-5/benzene.xyz new file mode 100644 index 0000000..a797761 --- /dev/null +++ b/examples/MOF-5/benzene.xyz @@ -0,0 +1,14 @@ +12 +SMILES=c1ccccc1, name=benzene +C -1.389893 -0.209288 0.005912 +C -0.876197 1.099026 -0.001376 +C 0.51369 1.308324 -0.007291 +C 1.389893 0.209288 -0.005912 +C 0.876197 -1.099026 0.001376 +C -0.51369 -1.308324 0.007291 +H -2.478693 -0.37322 0.010536 +H -1.562598 1.959978 -0.002456 +H 0.916052 2.33324 -0.012998 +H 2.478693 0.37322 -0.010536 +H 1.562598 -1.959978 0.002456 +H -0.916052 -2.33324 0.012998 diff --git a/examples/MOF-5/job.sh b/examples/MOF-5/job.sh new file mode 100755 index 0000000..448096b --- /dev/null +++ b/examples/MOF-5/job.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +# Runs until the first success is found +echo "Running Voronoi docking on MOF-5" +python3 ../../scripts/dock.py MOF-5.cif benzene.xyz -d batch -s voronoi_cluster -f min_distance -o docked --subdock --num_clusters 4 diff --git a/examples/MOR_loading/MOR.cif b/examples/MOR_loading/MOR.cif new file mode 100644 index 0000000..87f2b00 --- /dev/null +++ b/examples/MOR_loading/MOR.cif @@ -0,0 +1,63 @@ +data_MOR +#************************************************************************** +# +# CIF taken from the IZA-SC Database of Zeolite Structures +# Ch. Baerlocher and L.B. McCusker +# Database of Zeolite Structures: http://www.iza-structure.org/databases/ +# +# The atom coordinates and the cell parameters were optimized with DLS76 +# assuming a pure SiO2 composition. +# +#************************************************************************** + +_cell_length_a 18.2560(0) +_cell_length_b 20.5340(0) +_cell_length_c 7.5420(0) +_cell_angle_alpha 90.0000(0) +_cell_angle_beta 90.0000(0) +_cell_angle_gamma 90.0000(0) + +_symmetry_space_group_name_H-M 'C m c m' +_symmetry_Int_Tables_number 63 +_symmetry_cell_setting orthorhombic + +loop_ +_symmetry_equiv_pos_as_xyz +'+x,+y,+z' +'1/2+x,1/2+y,+z' +'-x,+y,+z' +'1/2-x,1/2+y,+z' +'+x,-y,1/2+z' +'1/2+x,1/2-y,1/2+z' +'-x,-y,1/2+z' +'1/2-x,1/2-y,1/2+z' +'-x,-y,-z' +'1/2-x,1/2-y,-z' +'+x,-y,-z' +'1/2+x,1/2-y,-z' +'-x,+y,1/2-z' +'1/2-x,1/2+y,1/2-z' +'+x,+y,1/2-z' +'1/2+x,1/2+y,1/2-z' + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z + O1 O 0.2811 0.0000 0.0000 + O2 O 0.3268 0.0795 0.2500 + O3 O 0.3757 0.0924 0.9243 + O4 O 0.2391 0.1223 0.9992 + O5 O 0.3253 0.3089 0.2500 + O6 O 0.2500 0.2500 0.0000 + O7 O 0.3757 0.3058 0.9242 + O8 O 0.0000 0.4005 0.2500 + O9 O 0.0906 0.3009 0.2500 + O10 O 0.0000 0.2013 0.2500 + T1 Si 0.3057 0.0736 0.0435 + T2 Si 0.3028 0.3106 0.0437 + T3 Si 0.0848 0.3791 0.2500 + T4 Si 0.0848 0.2227 0.2500 + diff --git a/examples/MOR_loading/job.sh b/examples/MOR_loading/job.sh new file mode 100755 index 0000000..c923f27 --- /dev/null +++ b/examples/MOR_loading/job.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# Runs until the first success is found +python3 ../../scripts/dock.py MOR.cif triethylamine.xyz -d batch -s voronoi_cluster -f min_distance --subdock diff --git a/examples/MOR_loading/triethylamine.xyz b/examples/MOR_loading/triethylamine.xyz new file mode 100644 index 0000000..48f8ebc --- /dev/null +++ b/examples/MOR_loading/triethylamine.xyz @@ -0,0 +1,24 @@ +22 + +C -2.0079 -1.4307 0.3941 +C -1.3197 -0.4007 -0.4976 +N -0.0027 0.0035 0.0334 +C 1.0105 -1.0342 -0.2433 +C 2.2195 -0.9185 0.6811 +C 0.4122 1.3008 -0.5366 +C -0.3081 2.4747 0.1212 +H -3.0215 -1.622 0.0259 +H -2.0906 -1.0655 1.4234 +H -1.4805 -2.3883 0.4098 +H -1.2329 -0.7831 -1.5226 +H -1.9972 0.4586 -0.5453 +H 0.5957 -2.0337 -0.0748 +H 1.3304 -1.0053 -1.2926 +H 2.7946 -0.0054 0.5043 +H 2.8938 -1.7659 0.5178 +H 1.9124 -0.9346 1.7323 +H 1.4814 1.4711 -0.3712 +H 0.2602 1.3225 -1.6232 +H 0.1041 3.4186 -0.2512 +H -1.3803 2.48 -0.093 +H -0.1736 2.4581 1.2081 diff --git a/examples/Ni111/Ni111.cif b/examples/Ni111/Ni111.cif new file mode 100644 index 0000000..14e13b2 --- /dev/null +++ b/examples/Ni111/Ni111.cif @@ -0,0 +1,32 @@ +# generated using pymatgen +data_Ni +_symmetry_space_group_name_H-M 'P 1' +_cell_length_a 2.47978671 +_cell_length_b 2.47978671 +_cell_length_c 24.29465569 +_cell_angle_alpha 90.00000000 +_cell_angle_beta 90.00000000 +_cell_angle_gamma 120.00000000 +_symmetry_Int_Tables_number 1 +_chemical_formula_structural Ni +_chemical_formula_sum Ni6 +_cell_volume 129.38086106 +_cell_formula_units_Z 6 +loop_ + _symmetry_equiv_pos_site_id + _symmetry_equiv_pos_as_xyz + 1 '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 + Ni Ni1 1 0.333334 0.666668 0.082544 1 + Ni Ni2 1 0.000000 0.000000 0.999689 1 + Ni Ni3 1 0.666666 0.333332 0.166332 1 + Ni Ni4 1 0.333334 0.666668 0.334122 1 + Ni Ni5 1 0.000000 0.000000 0.250335 1 + Ni Ni6 1 0.666666 0.333332 0.416978 1 diff --git a/examples/Ni111/job.sh b/examples/Ni111/job.sh new file mode 100755 index 0000000..e613e0d --- /dev/null +++ b/examples/Ni111/job.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +# Runs until the first success is found +echo "Running Monte Carlo docking of water on Ni(111)" +python3 ../../scripts/dock.py Ni111.cif water.xyz -d mcdocker -s random -f min_distance_target -o docked --target 1.6 diff --git a/examples/Ni111/water.xyz b/examples/Ni111/water.xyz new file mode 100644 index 0000000..21642dd --- /dev/null +++ b/examples/Ni111/water.xyz @@ -0,0 +1,6 @@ +3 + +O 0.008129 0.408345 0.0 +H -0.762669 -0.18912 0.0 +H 0.75454 -0.219325 0.0 +