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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| import pytest | ||
| import json | ||
| import numpy as np | ||
| from molSimplify.Informatics.MOF.MOF_descriptors import get_MOF_descriptors | ||
| from molSimplify.utils.timer import DebugTimer | ||
|
|
||
|
|
||
| @pytest.fixture | ||
| def ref_names(depth=3): | ||
|
|
||
| def RACs_names(starts, properties, depth, scope="all"): | ||
| names = [] | ||
| for start in starts: | ||
| for prop in properties: | ||
| for d in range(depth + 1): | ||
| if scope is None: | ||
| names.append(f"{start}-{prop}-{d}") | ||
| else: | ||
| names.append(f"{start}-{prop}-{d}-{scope}") | ||
| return names | ||
|
|
||
| properties = ["chi", "Z", "I", "T", "S", "Gval"] | ||
|
|
||
| names = RACs_names(["f", "mc", "D_mc"], properties, depth) | ||
| # f-lig does not include the "scope" | ||
| names.extend(RACs_names(["f-lig"], properties, depth, scope=None)) | ||
|
|
||
| # Same for the starts that include the additional property alpha | ||
| properties.append("alpha") | ||
| names.extend( | ||
| RACs_names(["lc", "D_lc", "func", "D_func"], properties, depth)) | ||
| return names | ||
|
|
||
|
|
||
| @pytest.mark.parametrize( | ||
| "name", | ||
| ["odac-21383.cif", | ||
| "odac-21433.cif", | ||
| "odac-21478.cif", | ||
| "odac-21735.cif", | ||
| "odac-21816.cif"]) | ||
| def test_get_MOF_descriptors(resource_path_root, tmpdir, name, ref_names): | ||
| with DebugTimer("get_MOF_descriptors()"): | ||
| full_names, full_descriptors = get_MOF_descriptors( | ||
| str(resource_path_root / "inputs" / "cif_files" / name), | ||
| depth=3, | ||
| path=str(tmpdir), | ||
| xyzpath=str(tmpdir / "test.xyz"), | ||
| Gval=True, | ||
| ) | ||
|
|
||
| with open(resource_path_root / "refs" / "MOF_descriptors" | ||
| / name.replace("cif", "json"), "r") as fin: | ||
| ref = json.load(fin) | ||
|
|
||
| assert full_names == ref_names | ||
| np.testing.assert_allclose(full_descriptors, ref["descriptors"], atol=1e-6) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,261 @@ | ||
| data_image0 | ||
| _chemical_formula_structural Ga36P36O148F16 | ||
| _chemical_formula_sum "Ga36 P36 O148 F16" | ||
| _cell_length_a 17.7002 | ||
| _cell_length_b 32.7061 | ||
| _cell_length_c 10.1684 | ||
| _cell_angle_alpha 90 | ||
| _cell_angle_beta 90 | ||
| _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 | ||
| Ga Ga1 1.0 0.43059 0.92287 0.05643 1.0000 | ||
| Ga Ga2 1.0 0.48410 0.02595 0.02197 1.0000 | ||
| Ga Ga3 1.0 0.15815 0.98867 0.88183 1.0000 | ||
| Ga Ga4 1.0 0.34659 0.50676 0.58670 1.0000 | ||
| Ga Ga5 1.0 0.08393 0.57961 0.42319 1.0000 | ||
| Ga Ga6 1.0 0.02252 0.47611 0.45525 1.0000 | ||
| Ga Ga7 1.0 0.34114 0.66620 0.58927 1.0000 | ||
| Ga Ga8 1.0 0.17185 0.82627 0.88792 1.0000 | ||
| Ga Ga9 1.0 0.30408 0.75647 0.92147 1.0000 | ||
| Ga Ga10 1.0 0.57037 0.07744 0.55502 1.0000 | ||
| Ga Ga11 1.0 0.51611 0.97446 0.52138 1.0000 | ||
| Ga Ga12 1.0 0.84196 0.01129 0.38288 1.0000 | ||
| Ga Ga13 1.0 0.65341 0.49313 0.08664 1.0000 | ||
| Ga Ga14 1.0 0.91594 0.42029 0.92329 1.0000 | ||
| Ga Ga15 1.0 0.97747 0.52383 0.95523 1.0000 | ||
| Ga Ga16 1.0 0.65877 0.33342 0.08974 1.0000 | ||
| Ga Ga17 1.0 0.82830 0.17378 0.38821 1.0000 | ||
| Ga Ga18 1.0 0.69648 0.24360 0.42307 1.0000 | ||
| Ga Ga19 1.0 0.92996 0.07736 0.05544 1.0000 | ||
| Ga Ga20 1.0 0.98407 0.97427 0.02212 1.0000 | ||
| Ga Ga21 1.0 0.65807 0.01135 0.88314 1.0000 | ||
| Ga Ga22 1.0 0.84658 0.49311 0.58664 1.0000 | ||
| Ga Ga23 1.0 0.58408 0.42027 0.42331 1.0000 | ||
| Ga Ga24 1.0 0.52254 0.52381 0.45523 1.0000 | ||
| Ga Ga25 1.0 0.84123 0.33342 0.58976 1.0000 | ||
| Ga Ga26 1.0 0.67187 0.17378 0.88815 1.0000 | ||
| Ga Ga27 1.0 0.80356 0.24360 0.92309 1.0000 | ||
| Ga Ga28 1.0 0.07041 0.92272 0.55490 1.0000 | ||
| Ga Ga29 1.0 0.01582 0.02574 0.52223 1.0000 | ||
| Ga Ga30 1.0 0.34172 0.98885 0.38206 1.0000 | ||
| Ga Ga31 1.0 0.15340 0.50686 0.08665 1.0000 | ||
| Ga Ga32 1.0 0.41599 0.57969 0.92325 1.0000 | ||
| Ga Ga33 1.0 0.47749 0.47615 0.95522 1.0000 | ||
| Ga Ga34 1.0 0.15876 0.66660 0.08951 1.0000 | ||
| Ga Ga35 1.0 0.32817 0.82575 0.38620 1.0000 | ||
| Ga Ga36 1.0 0.19617 0.75627 0.42252 1.0000 | ||
| P P1 1.0 0.31337 0.99434 0.05803 1.0000 | ||
| P P2 1.0 0.52467 0.95466 0.82822 1.0000 | ||
| P P3 1.0 0.06651 0.90510 0.84888 1.0000 | ||
| P P4 1.0 0.98376 0.54782 0.64882 1.0000 | ||
| P P5 1.0 0.19351 0.50343 0.40645 1.0000 | ||
| P P6 1.0 0.43845 0.59028 0.62901 1.0000 | ||
| P P7 1.0 0.34400 0.75646 0.60991 1.0000 | ||
| P P8 1.0 0.32414 0.83918 0.05928 1.0000 | ||
| P P9 1.0 0.30802 0.66116 0.89815 1.0000 | ||
| P P10 1.0 0.68688 0.00560 0.55914 1.0000 | ||
| P P11 1.0 0.47548 0.04576 0.32815 1.0000 | ||
| P P12 1.0 0.93349 0.09497 0.34958 1.0000 | ||
| P P13 1.0 0.01619 0.45214 0.14882 1.0000 | ||
| P P14 1.0 0.80646 0.49652 0.90645 1.0000 | ||
| P P15 1.0 0.56162 0.40957 0.12895 1.0000 | ||
| P P16 1.0 0.65635 0.24318 0.11197 1.0000 | ||
| P P17 1.0 0.67615 0.16085 0.56051 1.0000 | ||
| P P18 1.0 0.69209 0.33884 0.39813 1.0000 | ||
| P P19 1.0 0.81321 0.00562 0.05928 1.0000 | ||
| P P20 1.0 0.02477 0.04560 0.82869 1.0000 | ||
| P P21 1.0 0.56658 0.09505 0.84935 1.0000 | ||
| P P22 1.0 0.48383 0.45210 0.64886 1.0000 | ||
| P P23 1.0 0.69355 0.49651 0.40640 1.0000 | ||
| P P24 1.0 0.93839 0.40956 0.62898 1.0000 | ||
| P P25 1.0 0.84372 0.24318 0.61195 1.0000 | ||
| P P26 1.0 0.82395 0.16081 0.06056 1.0000 | ||
| P P27 1.0 0.80794 0.33884 0.89816 1.0000 | ||
| P P28 1.0 0.18650 0.99472 0.55712 1.0000 | ||
| P P29 1.0 0.97498 0.95435 0.32876 1.0000 | ||
| P P30 1.0 0.43347 0.90507 0.34924 1.0000 | ||
| P P31 1.0 0.51619 0.54784 0.14887 1.0000 | ||
| P P32 1.0 0.30646 0.50345 0.90646 1.0000 | ||
| P P33 1.0 0.06160 0.59043 0.12887 1.0000 | ||
| P P34 1.0 0.15658 0.75695 0.11105 1.0000 | ||
| P P35 1.0 0.17591 0.83898 0.55953 1.0000 | ||
| P P36 1.0 0.19176 0.66107 0.39794 1.0000 | ||
| O O1 1.0 0.36930 0.56124 0.63882 1.0000 | ||
| O O2 1.0 0.13538 0.93385 0.83366 1.0000 | ||
| O O3 1.0 0.13323 0.47188 0.45118 1.0000 | ||
| O O4 1.0 0.35030 0.77223 0.75240 1.0000 | ||
| O O5 1.0 0.02578 0.50758 0.62007 1.0000 | ||
| O O6 1.0 0.20934 0.77214 0.83963 1.0000 | ||
| O O7 1.0 0.37244 0.02727 0.02004 1.0000 | ||
| O O8 1.0 0.48241 0.99468 0.85946 1.0000 | ||
| O O9 1.0 0.26051 0.74525 0.58022 1.0000 | ||
| O O10 1.0 0.25240 0.85096 0.98186 1.0000 | ||
| O O11 1.0 0.26725 0.49188 0.47540 1.0000 | ||
| O O12 1.0 0.34503 0.70353 0.92025 1.0000 | ||
| O O13 1.0 0.24142 0.00420 0.98193 1.0000 | ||
| O O14 1.0 0.00114 0.92187 0.93177 1.0000 | ||
| O O15 1.0 0.35517 0.79645 0.02209 1.0000 | ||
| O O16 1.0 0.50873 0.57242 0.56275 1.0000 | ||
| O O17 1.0 0.49419 0.91819 0.90872 1.0000 | ||
| O O18 1.0 0.02066 0.58375 0.57395 1.0000 | ||
| O O19 1.0 0.61031 0.95927 0.85926 1.0000 | ||
| O O20 1.0 0.33849 0.95034 0.02262 1.0000 | ||
| O O21 1.0 0.17320 0.54790 0.44401 1.0000 | ||
| O O22 1.0 0.89885 0.54430 0.60927 1.0000 | ||
| O O23 1.0 0.29692 0.65271 0.74928 1.0000 | ||
| O O24 1.0 0.51714 0.94311 0.68271 1.0000 | ||
| O O25 1.0 0.29712 0.99885 0.20677 1.0000 | ||
| O O26 1.0 0.20409 0.49766 0.25662 1.0000 | ||
| O O27 1.0 0.30596 0.84210 0.20712 1.0000 | ||
| O O28 1.0 0.45944 0.60410 0.77088 1.0000 | ||
| O O29 1.0 0.98309 0.55794 0.79664 1.0000 | ||
| O O30 1.0 0.41696 0.62880 0.54922 1.0000 | ||
| O O31 1.0 0.03144 0.89719 0.71005 1.0000 | ||
| O O32 1.0 0.09016 0.86348 0.90607 1.0000 | ||
| O O33 1.0 0.38689 0.86952 0.02345 1.0000 | ||
| O O34 1.0 0.35971 0.62936 0.96217 1.0000 | ||
| O O35 1.0 0.37646 0.78989 0.51811 1.0000 | ||
| O O36 1.0 0.22762 0.65917 0.95502 1.0000 | ||
| O O37 1.0 0.39109 0.71673 0.59096 1.0000 | ||
| O O38 1.0 0.63080 0.43859 0.13845 1.0000 | ||
| O O39 1.0 0.86463 0.06617 0.33478 1.0000 | ||
| O O40 1.0 0.86677 0.52806 0.95121 1.0000 | ||
| O O41 1.0 0.65035 0.22706 0.25425 1.0000 | ||
| O O42 1.0 0.97419 0.49239 0.12012 1.0000 | ||
| O O43 1.0 0.79109 0.22794 0.34040 1.0000 | ||
| O O44 1.0 0.62792 0.97264 0.52061 1.0000 | ||
| O O45 1.0 0.51828 0.00588 0.35879 1.0000 | ||
| O O46 1.0 0.73962 0.25472 0.08150 1.0000 | ||
| O O47 1.0 0.74868 0.14943 0.48499 1.0000 | ||
| O O48 1.0 0.73273 0.50809 0.97540 1.0000 | ||
| O O49 1.0 0.65515 0.29645 0.42014 1.0000 | ||
| O O50 1.0 0.75906 0.99570 0.48383 1.0000 | ||
| O O51 1.0 0.99891 0.07817 0.43222 1.0000 | ||
| O O52 1.0 0.64543 0.20379 0.52464 1.0000 | ||
| O O53 1.0 0.49140 0.42745 0.06253 1.0000 | ||
| O O54 1.0 0.50551 0.08228 0.40883 1.0000 | ||
| O O55 1.0 0.97927 0.41620 0.07401 1.0000 | ||
| O O56 1.0 0.38972 0.04098 0.35840 1.0000 | ||
| O O57 1.0 0.66225 0.04962 0.52348 1.0000 | ||
| O O58 1.0 0.82674 0.45206 0.94402 1.0000 | ||
| O O59 1.0 0.10110 0.45567 0.10921 1.0000 | ||
| O O60 1.0 0.70310 0.34730 0.24929 1.0000 | ||
| O O61 1.0 0.48190 0.05759 0.18258 1.0000 | ||
| O O62 1.0 0.70271 0.00112 0.70804 1.0000 | ||
| O O63 1.0 0.79589 0.50230 0.75663 1.0000 | ||
| O O64 1.0 0.69299 0.15733 0.70856 1.0000 | ||
| O O65 1.0 0.54054 0.39589 0.27094 1.0000 | ||
| O O66 1.0 0.01692 0.44200 0.29663 1.0000 | ||
| O O67 1.0 0.58300 0.37090 0.04979 1.0000 | ||
| O O68 1.0 0.96869 0.10281 0.21083 1.0000 | ||
| O O69 1.0 0.90998 0.13662 0.40655 1.0000 | ||
| O O70 1.0 0.61388 0.13072 0.52021 1.0000 | ||
| O O71 1.0 0.64035 0.37061 0.46216 1.0000 | ||
| O O72 1.0 0.62400 0.20954 0.02083 1.0000 | ||
| O O73 1.0 0.77248 0.34088 0.45509 1.0000 | ||
| O O74 1.0 0.60895 0.28284 0.09347 1.0000 | ||
| O O75 1.0 0.86921 0.43858 0.63850 1.0000 | ||
| O O76 1.0 0.63547 0.06626 0.83488 1.0000 | ||
| O O77 1.0 0.63325 0.52804 0.45116 1.0000 | ||
| O O78 1.0 0.84968 0.22707 0.75423 1.0000 | ||
| O O79 1.0 0.52585 0.49234 0.62010 1.0000 | ||
| O O80 1.0 0.70899 0.22793 0.84042 1.0000 | ||
| O O81 1.0 0.87235 0.97278 0.02073 1.0000 | ||
| O O82 1.0 0.98231 0.00562 0.85957 1.0000 | ||
| O O83 1.0 0.76046 0.25473 0.58146 1.0000 | ||
| O O84 1.0 0.75143 0.14937 0.98501 1.0000 | ||
| O O85 1.0 0.76727 0.50808 0.47539 1.0000 | ||
| O O86 1.0 0.84486 0.29644 0.92017 1.0000 | ||
| O O87 1.0 0.74119 0.99564 0.98348 1.0000 | ||
| O O88 1.0 0.50101 0.07834 0.93188 1.0000 | ||
| O O89 1.0 0.85465 0.20374 0.02451 1.0000 | ||
| O O90 1.0 0.00861 0.42743 0.56256 1.0000 | ||
| O O91 1.0 0.99443 0.08214 0.90892 1.0000 | ||
| O O92 1.0 0.52079 0.41616 0.57408 1.0000 | ||
| O O93 1.0 0.11043 0.04089 0.85990 1.0000 | ||
| O O94 1.0 0.83796 0.04964 0.02387 1.0000 | ||
| O O95 1.0 0.67328 0.45204 0.44394 1.0000 | ||
| O O96 1.0 0.39893 0.45560 0.60918 1.0000 | ||
| O O97 1.0 0.79690 0.34730 0.74932 1.0000 | ||
| O O98 1.0 0.01811 0.05723 0.68309 1.0000 | ||
| O O99 1.0 0.79723 0.00104 0.20807 1.0000 | ||
| O O100 1.0 0.70412 0.50230 0.25658 1.0000 | ||
| O O101 1.0 0.80705 0.15737 0.20863 1.0000 | ||
| O O102 1.0 0.95948 0.39588 0.77098 1.0000 | ||
| O O103 1.0 0.48312 0.44200 0.79669 1.0000 | ||
| O O104 1.0 0.91700 0.37090 0.54982 1.0000 | ||
| O O105 1.0 0.53158 0.10289 0.71045 1.0000 | ||
| O O106 1.0 0.59001 0.13674 0.90626 1.0000 | ||
| O O107 1.0 0.88625 0.13064 0.02064 1.0000 | ||
| O O108 1.0 0.85968 0.37061 0.96216 1.0000 | ||
| O O109 1.0 0.87609 0.20956 0.52077 1.0000 | ||
| O O110 1.0 0.72755 0.34089 0.95513 1.0000 | ||
| O O111 1.0 0.89111 0.28285 0.59352 1.0000 | ||
| O O112 1.0 0.13077 0.56141 0.13839 1.0000 | ||
| O O113 1.0 0.36486 0.93401 0.33335 1.0000 | ||
| O O114 1.0 0.36679 0.47193 0.95124 1.0000 | ||
| O O115 1.0 0.15043 0.77288 0.25355 1.0000 | ||
| O O116 1.0 0.47419 0.50759 0.12012 1.0000 | ||
| O O117 1.0 0.29075 0.77159 0.33906 1.0000 | ||
| O O118 1.0 0.12760 0.02776 0.51858 1.0000 | ||
| O O119 1.0 0.01726 0.99438 0.35953 1.0000 | ||
| O O120 1.0 0.23993 0.74567 0.08037 1.0000 | ||
| O O121 1.0 0.24902 0.85001 0.48481 1.0000 | ||
| O O122 1.0 0.23275 0.49191 0.97548 1.0000 | ||
| O O123 1.0 0.15479 0.70345 0.41987 1.0000 | ||
| O O124 1.0 0.25878 0.00476 0.48239 1.0000 | ||
| O O125 1.0 0.49850 0.92183 0.43293 1.0000 | ||
| O O126 1.0 0.14485 0.79620 0.52319 1.0000 | ||
| O O127 1.0 0.99139 0.57256 0.06240 1.0000 | ||
| O O128 1.0 0.00537 0.91783 0.40898 1.0000 | ||
| O O129 1.0 0.47925 0.58378 0.07409 1.0000 | ||
| O O130 1.0 0.88932 0.95902 0.35999 1.0000 | ||
| O O131 1.0 0.16143 0.95090 0.52064 1.0000 | ||
| O O132 1.0 0.32676 0.54793 0.94387 1.0000 | ||
| O O133 1.0 0.60110 0.54432 0.10925 1.0000 | ||
| O O134 1.0 0.20291 0.65263 0.24910 1.0000 | ||
| O O135 1.0 0.98165 0.94277 0.18305 1.0000 | ||
| O O136 1.0 0.20119 0.99946 0.70616 1.0000 | ||
| O O137 1.0 0.29586 0.49760 0.75667 1.0000 | ||
| O O138 1.0 0.19274 0.84238 0.70777 1.0000 | ||
| O O139 1.0 0.04040 0.60406 0.27087 1.0000 | ||
| O O140 1.0 0.51691 0.55794 0.29670 1.0000 | ||
| O O141 1.0 0.08297 0.62912 0.04986 1.0000 | ||
| O O142 1.0 0.46941 0.89718 0.21113 1.0000 | ||
| O O143 1.0 0.40903 0.86353 0.40577 1.0000 | ||
| O O144 1.0 0.11446 0.86961 0.51959 1.0000 | ||
| O O145 1.0 0.13998 0.62932 0.46198 1.0000 | ||
| O O146 1.0 0.12400 0.79067 0.02045 1.0000 | ||
| O O147 1.0 0.27211 0.65893 0.45496 1.0000 | ||
| O O148 1.0 0.10925 0.71727 0.09222 1.0000 | ||
| F F1 1.0 0.59454 0.01931 0.03888 1.0000 | ||
| F F2 1.0 0.03282 0.52842 0.36063 1.0000 | ||
| F F3 1.0 0.47617 0.97356 0.12043 1.0000 | ||
| F F4 1.0 0.41305 0.51613 0.43540 1.0000 | ||
| F F5 1.0 0.40605 0.98157 0.53697 1.0000 | ||
| F F6 1.0 0.96715 0.47151 0.86070 1.0000 | ||
| F F7 1.0 0.52466 0.02671 0.61962 1.0000 | ||
| F F8 1.0 0.58697 0.48383 0.93532 1.0000 | ||
| F F9 1.0 0.09449 0.98073 0.03817 1.0000 | ||
| F F10 1.0 0.53286 0.47150 0.36075 1.0000 | ||
| F F11 1.0 0.97607 0.02672 0.11986 1.0000 | ||
| F F12 1.0 0.91305 0.48380 0.43533 1.0000 | ||
| F F13 1.0 0.90545 0.01913 0.53909 1.0000 | ||
| F F14 1.0 0.46722 0.52847 0.86074 1.0000 | ||
| F F15 1.0 0.02440 0.97339 0.61988 1.0000 | ||
| F F16 1.0 0.08695 0.51615 0.93532 1.0000 |
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