Test H-bonds and Zeolite input

test/cif/Clathrate_hydrate.cif

@@ -0,0 +1,100 @@
+
+#=======================================================================
+data_global
+#=======================================================================
+
+_audit_creation_method                   'Jana2006 Version : 23/05/2019'
+
+_journal_name_full                       'Acta Crystallographica Section C'
+_publ_section_references
+;
+Petricek, V., Dusek, M. & Palatinus L. (2014). Z. Kristallogr. 229(5), 345-352.
+
+Palatinus L. & Chapuis G. (2007). J. Appl. Cryst. 40, 786-790.
+;
+# 6. CRYSTAL DATA
+
+_symmetry_cell_setting                   trigonal
+_symmetry_space_group_name_H-M           'R 3 c'
+_symmetry_space_group_name_Hall          'R 3;-2"c'
+_symmetry_Int_Tables_number              161
+
+loop_
+ _space_group_symop_id
+ _space_group_symop_operation_xyz
+ 1   x,y,z
+ 2   -y,x-y,z
+ 3   -x+y,-x,z
+ 4   -y,-x,z+1/2
+ 5   -x+y,y,z+1/2
+ 6   x,x-y,z+1/2
+ 7   x+2/3,y+1/3,z+1/3
+ 8   -y+2/3,x-y+1/3,z+1/3
+ 9   -x+y+2/3,-x+1/3,z+1/3
+ 10  -y+2/3,-x+1/3,z+5/6
+ 11  -x+y+2/3,y+1/3,z+5/6
+ 12  x+2/3,x-y+1/3,z+5/6
+ 13  x+1/3,y+2/3,z+2/3
+ 14  -y+1/3,x-y+2/3,z+2/3
+ 15  -x+y+1/3,-x+2/3,z+2/3
+ 16  -y+1/3,-x+2/3,z+1/6
+ 17  -x+y+1/3,y+2/3,z+1/6
+ 18  x+1/3,x-y+2/3,z+1/6
+
+_cell_length_a                           12.984(4)
+_cell_length_b                           12.984(4)
+_cell_length_c                           6.243(8)
+_cell_angle_alpha                        90
+_cell_angle_beta                         90
+_cell_angle_gamma                        120
+_cell_volume                             911.5(12)
+
+loop_
+ _atom_site_label
+ _atom_site_type_symbol
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_adp_type
+ _atom_site_U_iso_or_equiv
+ _atom_site_site_symmetry_multiplicity
+ _atom_site_occupancy
+ _atom_site_calc_flag
+ _atom_site_refinement_flags
+ _atom_site_disorder_assembly
+ _atom_site_disorder_group
+  O1 O 0.2275(4) 0.1938(3) 0.154(4) Uani 0.0396(19) 18 1 d . . .
+  O2 O 0.1931(3) 0.2280(4) 0.585(4) Uani 0.0392(18) 18 1 d . . .
+  H1 H 0 0 0.329(5) Uiso 0.056(4) 6 2 d . . .
+  H2 H 0.221(3) 0.173(4) 0.621(6) Uiso 0.056(4) 18 1 d . . .
+  H3 H 0.300(4) 0.237(4) 0.093(6) Uiso 0.056(4) 18 1 d . . .
+  H4 H 0.122(5) 0.211(4) 0.598(6) Uiso 0.056(4) 18 1 d . . .
+  H5 H 0.227(4) 0.212(5) 0.275(8) Uiso 0.056(4) 18 1 d . . .
+
+loop_
+ _atom_site_aniso_label
+ _atom_site_aniso_type_symbol
+ _atom_site_aniso_U_11
+ _atom_site_aniso_U_22
+ _atom_site_aniso_U_33
+ _atom_site_aniso_U_12
+ _atom_site_aniso_U_13
+ _atom_site_aniso_U_23
+ O1 O 0.035(2) 0.044(3) 0.0356(15) 0.0176(19) 0.0031(11) -0.0005(11)
+ O2 O 0.031(2) 0.040(3) 0.050(2) 0.0200(18) 0.0002(11) -0.0035(13)
+
+loop_
+ _jana_atom_site_ADP_C_label
+ _jana_atom_site_ADP_C_type_symbol
+ _jana_atom_site_ADP_C_111
+ _jana_atom_site_ADP_C_112
+ _jana_atom_site_ADP_C_113
+ _jana_atom_site_ADP_C_122
+ _jana_atom_site_ADP_C_123
+ _jana_atom_site_ADP_C_133
+ _jana_atom_site_ADP_C_222
+ _jana_atom_site_ADP_C_223
+ _jana_atom_site_ADP_C_233
+ _jana_atom_site_ADP_C_333
+ ? ? ? ? ? ? ? ? ? ? ? ?
+

test/cif/Lithosite.cif

@@ -0,0 +1,83 @@
+#*********************************************************************************
+#
+# Crystallographic Information File for Lithosite
+#
+# Reference :
+# Pudovkina, Z.V., Solov'eva, L.P. and Pyatenko, Yu.A.
+# Sov. Phys. Dokl., 31, 941-942, (1986)
+#
+#
+# CIF downloaded from the IZA-SC Database of Zeolite Structures
+# Ch. Baerlocher, L.B. McCusker and D.H. Brouwer
+# Database of Zeolite Structures: https://www.iza-structure.org/databases/
+#
+#**********************************************************************************
+data_Lithosite
+_chemical_name_systematic 'Lithosite'
+
+_cell_length_a 15.197
+_cell_length_b 10.233
+_cell_length_c 8.435
+_cell_angle_alpha 90
+_cell_angle_beta 90.31
+_cell_angle_gamma 90
+_cell_formula_units_Z 1
+
+_space_group.name_H-M_ref 'P 1 21 1'
+_symmetry_space_group_name_H-M 'P 1 21 1'
+_symmetry_space_group_name_Hall 'P 2yb'
+_space_group.IT_number 4
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+_atom_site_occupancy
+Si1 Si 0.262 0.219 0.435 0.62 1
+Si2 Si 0.259 0.221 0.063 0.37 1
+Si3 Si 0.561 0.192 0.053 0.87 1
+Si4 Si 0.914 0.111 0.559 0.81 1
+Si5 Si 0.243 0.778 0.939 0.98 1
+Si6 Si 0.237 0.777 0.565 0.68 1
+Si7 Si 0.586 0.886 0.439 0.78 1
+Si8 Si 0.94 0.807 0.942 0.86 1
+Al1 Al 0.91 0.11 0.93 0.64 1
+Al2 Al 0.563 0.188 0.443 0.83 1
+Al3 Al 0.936 0.809 0.558 0.7 1
+Al4 Al 0.59 0.891 0.064 0.65 1
+K1 K 0.697 0.054 0.752 1.42 1
+K2 K 0.422 0.046 0.752 1.84 1
+K3 K 0.136 0.064 0.738 2.13 1
+K4 K 0.801 0.947 0.247 1.43 1
+K5 K 0.078 0.938 0.248 1.9 1
+K6 K 0.37 0.944 0.244 1.9 1
+O1 O 0.248 0.188 0.249 1.4 1
+O2 O 0.995 0.219 0.948 1.09 1
+O3 O 0.005 0.721 0.436 1.56 1
+O4 O 0.293 0.101 0.958 1.21 1
+O5 O 0.548 0.027 0.501 1.38 1
+O6 O 0.552 0.039 0.997 1.18 1
+O7 O 0.706 0.597 0.468 1.03 1
+O8 O 0.547 0.218 0.245 1.39 1
+O9 O 0.824 0.153 0.453 1.31 1
+O10 O 0.824 0.153 0.054 1.46 1
+O11 O 0.123 0.598 0.257 1.49 1
+O12 O 0.167 0.272 0.501 1.37 1
+O13 O 0.156 0.245 0.001 1.43 1
+O14 O 0.247 0.821 0.754 1.06 1
+O15 O 0.507 0.781 0.451 1.87 1
+O16 O 0.511 0.773 0.051 1.73 1
+O17 O 0.196 0.908 0.479 1.24 1
+O18 O 0.947 0.961 0 1.28 1
+O19 O 0.946 0.97 0.486 0.98 1
+O20 O 0.204 0.904 0.024 1.06 1
+O21 O 0.048 0.295 0.24 1.61 1
+O22 O 0.69 0.854 0.97 1.6 1
+O23 O 0.665 0.844 0.56 1.21 1
+O24 O 0.624 0.898 0.263 1.14 1
+O25 O 0.663 0.234 0.001 1.43 1
+O26 O 0.331 0.745 0.494 1.33 1
+# End of data for Lithosite

test/runtests.jl

@@ -160,6 +160,12 @@ import CrystalNets.Clustering: SingleNodes, AllNodes, Standard, PE, PEM
     @test_broken bexvad[1][1] == bexvad[2][1]
 end
 
+@testset "Other kinds of structures" begin
+    cifs, crystalnetsdir = _finddirs()
+    @test string(determine_topology(joinpath(cifs, "Clathrate_hydrate.cif"); Hbonds=true)) == "ict"
+    @test string(determine_topology(joinpath(cifs, "Lithosite.cif"); structure=StructureType.Zeolite, ignore_atoms=(:K,))) == "-LIT"
+end
+
 @testset "Archive" begin
     @info "Checking that all known topologies are recognized (this can take a few minutes)."
     Threads.nthreads() == 1 && @info "Use multiple threads to reduce this time"