add examples

learningmatter-mit · Jul 15, 2020 · 9a568a4 · 9a568a4
1 parent fd7ab27
commit 9a568a4
Show file tree

Hide file tree

Showing 14 changed files with 514 additions and 0 deletions.
diff --git a/examples/.gitignore b/examples/.gitignore
@@ -0,0 +1 @@
+*docked*
diff --git a/examples/CHA_TMAda/.gitignore b/examples/CHA_TMAda/.gitignore
@@ -0,0 +1 @@
+mcdocked vdocked
diff --git a/examples/CHA_TMAda/CHA.cif 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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