diff --git a/.github/workflows/run_tests_and_deploy.yml b/.github/workflows/run_tests_and_deploy.yml index 1e6f929..3416b40 100644 --- a/.github/workflows/run_tests_and_deploy.yml +++ b/.github/workflows/run_tests_and_deploy.yml @@ -42,7 +42,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install package - run: python -m pip install .[rdkit,tf,pymatgen,test] + run: python -m pip install .[rdkit,tf,pymatgen,test,scikit] - name: Run tests run: pytest tests/ diff --git a/data/json/100_0_bd_coord.json b/data/json/100_0_bd_coord.json new file mode 100644 index 0000000..6f89400 --- /dev/null +++ b/data/json/100_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -8.22611833, "HOMO-LUMO gap/eV": 13.10109639, "electronic energy": -8.29943235, "dipole": [-0.1657503, -0.57841977, 0.45310851], "partial charges": [0.04147862, -0.43473821, 0.02547373, 0.02547373, 0.05634389, 0.28596823], "atomic dipole moments": [[0.2125321, 0.03192886, -0.03345514], [-0.15326224, -0.1500353, 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0.04581705, 0.0527928, 0.05279294, 0.05279281, 0.05279293, 0.04581704, 0.04581705, 0.02824585, 0.02824584, 0.0362213, 0.0362213, 0.03390531], "atomic dipole moments": [[0.07762422, 0.0629006, -0.01099044], [0.00971486, -0.1112633, 0.01863476], [0.00811051, 0.12863746, -0.02165087], [0.00534139, -0.08692932, 0.01457171], [0.0014317, -0.02776263, 0.00465484], [-0.00868138, 0.16834396, -0.02822824], [0.00362873, -0.08701369, 0.0145953], [-0.02130327, 0.12718846, -0.02124624], [0.00178084, -0.11165411, 0.01874413], [-0.08370186, 0.05495334, -0.00877067], [-0.10533944, 0.0638342, -0.01014421], [0.00053849, -0.08843875, -0.08680902], [0.00162252, -0.05522664, 0.11092743], [-0.0064205, 0.0545295, -0.10871766], [-0.00535856, 0.08706666, 0.08499943], [0.00667434, -0.09072722, -0.08603443], [0.00775397, -0.05765318, 0.11087784], [-0.00495305, 0.05897654, -0.11441536], [-0.00383799, 0.09312855, 0.08891575], [-0.00400878, 0.05902301, -0.11442837], [-0.00289288, 0.09317514, 0.08890271], [0.00099538, -0.057986, 0.11097089], [-8.56e-05, -0.09106032, -0.08594132], [-0.00089206, 0.08728685, 0.08493782], [-0.00195559, 0.05474925, -0.10877919], [0.0057721, -0.08818115, -0.08688082], [0.00685774, -0.05496847, 0.11085553], [0.09823849, 0.07386282, -0.0129457]], "atomic quadrupole moments": [[0.11006946, 0.16655756, 0.01549862, -0.02929135, -0.02534898, -0.12556808], [0.22169267, 0.01349994, 0.00854638, -0.00478322, -0.04135196, -0.23023905], [0.24414467, 0.02839165, 0.01185974, -0.00755405, -0.04646488, -0.2560044], [0.19673032, 0.01744621, 0.03806579, -0.00534059, -0.0472648, -0.23479611], [-0.28328608, 0.0032148, -0.30529527, 0.00438559, 0.15448493, 0.58858134], [-0.1283318, 0.00078752, -0.12595048, 0.00202736, 0.06571761, 0.25428228], [0.19883058, -0.00286592, 0.03605942, -0.00194204, -0.04681655, -0.23489], [0.24773881, -0.0063683, 0.00842622, -0.0017387, -0.04569795, -0.25616503], [0.2224176, 0.00648821, 0.00785365, -0.00361312, -0.04119776, -0.23027125], [0.14327844, 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0.77915713, 2.6448546, 2.90286802, 3.20293666, 3.28934803, 3.35091073, 3.71742412, 3.81971742, 4.0779781, 4.321977, 4.40439121, 4.96331181, 4.99263021, 5.06442768, 5.06715944, 5.12641454, 5.19661899, 6.46469555, 6.59271414, 6.73624701, 6.99562183, 7.02615854, 7.27598144, 7.66725685, 8.33725925, 8.41033948, 17.41507914], "fractional occupation": [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "program call": "xtb /tmp/scratch/tmpmp6muow1/13638_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmpmp6muow1/13638_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole module/D": 3.052, "Total charge": 0, "Transition dipole module/D": NaN, "HOMO": -10.6052, "LUMO": -6.6406, "HOMO occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [-0.08483, -0.04235, -0.03641, -0.08998, 0.40006, -0.48562, -0.08998, -0.03641, -0.04235, -0.08483, 0.02982, 0.03041, 0.03041, 0.02116, 0.02116, 0.03788, 0.03788, 0.04382, 0.04382, 0.04382, 0.04382, 0.03788, 0.03788, 0.02116, 0.02116, 0.03041, 0.03041, 0.02982], "cm5 charges": [-0.23755, -0.1557, -0.14617, -0.19306, 0.41932, -0.54042, -0.19306, -0.14617, -0.1557, -0.23755, 0.08138, 0.08263, 0.08263, 0.07634, 0.07634, 0.09618, 0.09618, 0.10067, 0.10067, 0.10067, 0.10067, 0.09618, 0.09618, 0.07634, 0.07634, 0.08263, 0.08263, 0.08138], "FUKUI+": [0.011, 0.006, 0.014, 0.031, -0.19, -0.292, 0.031, 0.014, 0.006, 0.011, -0.027, -0.014, -0.014, -0.018, -0.018, -0.021, -0.021, -0.094, -0.094, -0.094, -0.094, -0.021, -0.021, -0.018, -0.018, -0.014, -0.014, -0.027], "FUKUI-": [0.012, 0.001, 0.004, -0.007, -0.024, -0.123, -0.007, 0.004, 0.001, 0.012, -0.059, -0.049, -0.049, -0.054, -0.054, -0.038, -0.038, -0.048, -0.048, -0.048, -0.048, 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mode 100644 index 0000000..318edc5 --- /dev/null +++ b/data/json/1397_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -23.02937767, "HOMO-LUMO gap/eV": 3.85674406, "electronic energy": -23.34297822, "dipole": [0.13297763, -1.12979323, 0.56384246], "partial charges": [-0.13715105, 0.23731548, -0.35803076, 0.0059622, -0.11146551, -0.10660834, -0.10376116, 0.06953574, 0.06491982, 0.05835272, 0.04014948, 0.03664739, 0.04491532, 0.03693083, 0.05571419, 0.03983313, 0.0350184, 0.04711543, 0.04460668], "atomic dipole moments": [[-0.07697358, 0.01735559, -0.0084443], [-0.00096591, 0.0292592, -0.01236789], [0.02245698, -0.15444415, 0.07145041], [-0.00186598, -0.00155374, 0.01347901], [-0.00783891, 0.10436305, 0.01172898], [0.09197238, -0.04070836, 0.05087505], [0.01513522, -0.0185463, -0.10553594], [0.02143895, -0.0973692, -0.08728528], [0.08814231, 0.0951302, -0.02150539], [0.01679642, -0.0497359, 0.11909836], [0.09626884, -0.04622961, 0.06554754], [0.01851858, -0.02521882, -0.12184659], 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electrons": 0, "orbital energies/eV": [-19.26438775, -17.78589623, -17.18446499, -17.02230276, -16.22015983, -15.89041026, -15.39383247, -14.70283082, -14.50146656, -14.37603084, -14.02780261, -13.81188117, -13.36028867, -13.09220401, -12.94097704, -12.47338748, -12.08420134, -12.03187248, -11.90547379, -10.57590867, -6.74105427, 2.20937694, 2.35504089, 2.37635709, 2.55296198, 3.04234546, 3.39892704, 3.59101089, 4.54522869, 4.81771426, 5.27347908, 5.98850939, 6.31976764, 6.33656399, 6.94387829, 7.61312202, 8.27191869, 17.32673101], "fractional occupation": [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "program call": "xtb /tmp/scratch/tmpjwi38v9e/1572_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmpjwi38v9e/1572_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole 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newline at end of file diff --git a/data/json/15826_0_bd_coord.json b/data/json/15826_0_bd_coord.json new file mode 100644 index 0000000..fc02631 --- /dev/null +++ b/data/json/15826_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -25.31642693, "HOMO-LUMO gap/eV": 12.90845609, "electronic energy": -25.69211169, "dipole": [0.01322462, -0.01759286, 0.02042701], "partial charges": [-0.1028882, -0.01571902, -0.0580252, -0.05466665, -0.05415965, -0.05791912, -0.01661915, -0.1044326, 0.03665527, 0.03348697, 0.02990643, 0.02162557, 0.02643987, 0.02652699, 0.03296921, 0.02382297, 0.02753052, 0.02403378, 0.0321441, 0.02529441, 0.02566612, 0.03599741, 0.03156384, 0.03076613], "atomic dipole moments": [[-0.00226198, 0.07194571, -0.06608435], [-0.02868396, 0.03539863, 0.0776816], [0.05834575, 0.01229956, 0.08896056], [0.08652746, 0.02773748, -0.06287677], [0.02640132, -0.10351828, -0.00205556], [-0.06089502, -0.00920793, -0.09248339], [0.00524597, -0.05993546, 0.07338968], [-0.08851313, 0.03028606, 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/dev/null +++ b/data/json/16277_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -26.32178405, "HOMO-LUMO gap/eV": 12.91954347, "electronic energy": -26.71996615, "dipole": [0.00047061, 0.00032884, 0.01328268], "partial charges": [-0.10146713, -0.05217931, -0.06317079, -0.01548363, -0.1050573, -0.06240063, -0.05219739, -0.10129203, 0.03190286, 0.03214486, 0.03134594, 0.02663772, 0.03173701, 0.03227373, 0.03011548, 0.02448054, 0.03445128, 0.03079997, 0.03333366, 0.02981707, 0.029242, 0.03060199, 0.03147745, 0.03131854, 0.03069508, 0.03087304], "atomic dipole moments": [[-0.07928192, -0.03665219, -0.03720411], [0.04588174, -0.02576557, 0.10055816], [-0.03881522, 0.01621678, -0.10476548], [-0.02999281, 0.04172964, 0.0775389], [0.0309686, 0.06477632, -0.06390268], [0.04082236, 0.00104999, 0.10130629], [-0.04131301, -0.00497513, -0.10840006], [0.07095051, -0.04995597, 0.03444091], [0.08426451, -0.08732407, 0.0220374], [-0.02269945, 0.05849751, 0.10602614], [0.04861631, 0.08126248, 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-14.00802864, -13.54521495, -13.492562, -13.40046967, -13.27611186, -12.77729729, -12.67672442, -12.48739625, -12.24517781, -12.08415626, -12.01199181, -11.83307542, -11.59068294, -11.35612605, -11.23432152, -10.12279051, -5.01469515, 2.01528393, 2.87523148, 2.98023248, 3.38290032, 3.64984755, 4.0826206, 4.36918011, 4.55556277, 4.5853924, 5.10903012, 5.43317435, 5.58015697, 6.08655307, 6.25826104, 6.3067262, 6.48563195, 6.57440536, 7.17241977, 7.39677597, 7.87293835, 8.45929289, 10.93736177, 18.13660328], "fractional occupation": [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "program call": "xtb /tmp/scratch/tmphywgyeuh/18921_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmphywgyeuh/18921_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 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moments": [[0.15291773, -0.09314374, -0.23837243, 0.41074415, -0.15513101, 0.0854547], [0.1417292, 0.03488353, -0.16214965, 0.3392794, -0.2373668, 0.02042044], [-0.07789002, 0.06306604, 0.16568814, -0.01691241, 0.02778878, -0.08779811], [0.19225475, -0.01278071, -0.15003055, -0.02511607, -0.07676613, -0.0422242], [0.22298257, 0.00675932, -0.17794234, -0.02699743, -0.1170641, -0.04504023], [0.21857297, 0.0047016, -0.17579229, -0.03174329, -0.11053862, -0.04278068], [0.17770047, -0.06954755, -0.10460549, 0.10771197, -0.03413475, -0.07309498], [-0.02624378, 0.02356147, 0.05029369, -0.03795834, 0.01342454, -0.02404991], [-0.00647696, 0.02190051, 0.01255455, -0.05833132, 0.00254894, -0.00607758], [-0.03011859, 0.01372493, -0.0376793, 0.04488377, 0.013471, 0.06779789], [0.00640967, 0.0184629, -0.02450914, -0.06878341, -0.00960143, 0.01809947], [0.05331516, -0.0536129, -0.00358647, 0.01295119, -0.01315176, -0.04972868], [-0.01756424, -0.00681649, 0.05798037, -0.00780479, -0.00611936, 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a/data/json/23260_0_bd_coord.json b/data/json/23260_0_bd_coord.json new file mode 100644 index 0000000..f974314 --- /dev/null +++ b/data/json/23260_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -26.06000763, "HOMO-LUMO gap/eV": 4.34514821, "electronic energy": -26.3898199, "dipole": [-0.25892204, -0.40548022, 0.79394203], "partial charges": [-0.10516926, -0.03583591, -0.04082382, -0.09024504, 0.36084929, -0.40673579, -0.26144333, 0.03241196, 0.04811811, 0.04282147, 0.04845476, 0.03621528, 0.04446606, 0.07108835, 0.06233085, 0.06407359, 0.06104405, 0.06837937], "atomic dipole moments": [[0.06378598, -0.03116134, -0.00746123], [-0.121814, 0.02921063, 0.05275391], [0.16152288, -0.03626264, -0.0583863], [0.01196659, 0.0992348, 0.02676581], [0.06440684, 0.00884294, 0.14687741], [-0.05819668, -0.1400536, 0.12165758], [0.08601091, 0.18908612, -0.12676078], [-0.169545, -0.16940575, -0.09407413], [-0.09142665, -0.08710635, -0.00643139], [-0.02296793, 0.08918731, -0.08699613], [-0.00789277, 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--pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmpnw4gzsfu/2988_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole module/D": 2.222, "Total charge": 0, "Transition dipole module/D": NaN, "HOMO": -11.1111, "LUMO": -7.2688, "HOMO occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [-0.05601, -0.0153, -0.0823, 0.57129, -0.53776, -0.42119, 0.20687, -0.09722, 0.03922, 0.05114, 0.05369, 0.03372, 0.05369, 0.03929, 0.03929, 0.03509, 0.04326, 0.04326], "cm5 charges": [-0.15541, -0.02999, -0.22656, 0.62954, -0.58851, -0.5071, 0.12459, -0.24639, 0.09354, 0.11075, 0.1084, 0.08687, 0.1084, 0.10466, 0.10466, 0.08737, 0.0976, 0.0976], "FUKUI+": [-0.091, -0.082, 0.038, -0.081, -0.192, -0.076, 0.019, 0.014, -0.119, -0.104, -0.062, -0.06, -0.062, -0.033, -0.033, -0.037, -0.02, -0.02], "FUKUI-": [-0.045, -0.053, 0.019, -0.01, -0.128, -0.071, 0.014, 0.015, -0.088, -0.068, -0.082, -0.065, -0.082, -0.08, -0.08, -0.06, -0.068, -0.068], 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occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [-0.08542, -0.03935, -0.05406, -0.01241, -0.05288, -0.04493, -0.04672, -0.04497, -0.05169, 0.02891, 0.02734, 0.02753, 0.02229, 0.02205, 0.02452, 0.02327, 0.01967, 0.0247, 0.02349, 0.02285, 0.02403, 0.02401, 0.02323, 0.0229, 0.02416, 0.02399, 0.02349], "cm5 charges": [-0.23816, -0.15324, -0.16403, -0.08341, -0.1621, -0.15568, -0.15747, -0.15568, -0.16082, 0.08046, 0.07947, 0.07971, 0.07808, 0.07739, 0.08105, 0.07989, 0.07983, 0.0809, 0.08048, 0.07899, 0.07867, 0.07862, 0.07934, 0.07902, 0.07879, 0.07946, 0.08043], "FUKUI+": [0.007, -0.014, -0.029, -0.033, 0.007, 0.006, 0.017, -0.0, -0.007, -0.073, -0.042, -0.042, -0.045, -0.051, -0.056, -0.06, -0.069, -0.039, -0.05, -0.041, -0.052, -0.06, -0.05, -0.05, -0.068, -0.047, -0.056], "FUKUI-": [0.017, 0.001, 0.008, -0.014, 0.003, -0.0, -0.0, 0.005, -0.003, -0.061, -0.063, -0.042, -0.07, -0.051, -0.064, -0.047, -0.039, -0.081, -0.043, -0.041, -0.071, -0.064, -0.04, -0.045, -0.096, 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a/data/json/41_0_bd_coord.json b/data/json/41_0_bd_coord.json new file mode 100644 index 0000000..22deda7 --- /dev/null +++ b/data/json/41_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -17.73182711, "HOMO-LUMO gap/eV": 12.18449525, "electronic energy": -17.94997438, "dipole": [0.43654752, 0.5168866, -0.24559221], "partial charges": [-0.11450851, 0.15335822, -0.12112064, -0.12112064, -0.4528302, 0.0514011, 0.03762471, 0.0514011, 0.03217921, 0.04637867, 0.03834304, 0.03834304, 0.04637867, 0.03217921, 0.281993], "atomic dipole moments": [[0.0629015, 0.07234345, 0.04695565], [-0.01828288, -0.02508584, 0.14295779], [0.03106107, -0.08368207, 0.01469383], [-0.08708034, 0.01734073, 0.01731192], [0.11571922, 0.13904955, -0.14359393], [0.03404855, -0.11813242, 0.02973684], [0.01566036, 0.02147119, -0.1218237], [-0.12118109, 0.01460459, 0.03317681], [0.06840473, 0.08141788, 0.06476977], [-0.12164805, 0.01580818, 0.03226279], [0.01436521, 0.02622262, -0.12242419], [0.02053813, 0.02094421, 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at end of file diff --git a/data/json/436081_4d1446_bd_coord.json b/data/json/436081_4d1446_bd_coord.json new file mode 100644 index 0000000..5697cf5 --- /dev/null +++ b/data/json/436081_4d1446_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -26.49174286, "HOMO-LUMO gap/eV": 3.45374329, "electronic energy": -26.98687324, "dipole": [-0.26943274, -0.10588038, -0.01619048], "partial charges": [-0.03374515, -0.04227262, 0.00903401, -0.0373304, -0.03481064, -0.03332676, -0.04097432, 0.00981461, -0.05777233, -0.05173384, 0.02596255, 0.02752723, 0.02808576, 0.02665098, 0.02713901, 0.02539658, 0.04030696, 0.03554618, 0.04120543, 0.03529677], "atomic dipole moments": [[-0.08290793, -0.10967114, 0.00387103], [0.09156226, -0.0134782, -0.00836169], [-0.03447704, 0.01936315, 0.00067263], [-0.00509344, -0.0053738, 0.00011018], [-0.00091068, -0.00300131, -0.00030395], [-0.00399983, 0.00047512, -8.054e-05], [0.00333263, 0.00454726, -0.00039917], [-0.08571217, -0.01630131, -0.01542404], [-0.00218257, 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"number of molecular orbitals": 38, "number of electrons": 42, "number of unpaired electrons": 0, "orbital energies/eV": [-20.54171872, -19.75841971, -18.6166449, -17.36248239, -16.82691947, -16.63731415, -16.26836728, -16.01709773, -15.50347737, -15.32791965, -14.64469706, -14.04182225, -13.93960081, -13.64204187, -13.11817434, -12.95652913, -12.50787894, -12.29963782, -12.23592378, -11.91842347, -11.65835301, -6.55212898, -0.24586325, 2.1421708, 2.91469971, 3.07014496, 3.65130268, 3.71369747, 4.2920016, 4.66500454, 4.72081153, 5.04581507, 6.0296025, 6.64925865, 6.90993544, 7.59059555, 8.02859828, 17.64558224], "fractional occupation": [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "program call": "xtb /tmp/scratch/tmpykddbkzb/4504_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input 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index 0000000..c47d317 --- /dev/null +++ b/data/json/4742_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -33.44142622, "HOMO-LUMO gap/eV": 5.07815866, "electronic energy": -33.85157354, "dipole": [0.10616571, -0.19053739, -0.76239023], "partial charges": [-0.10296071, -0.0532073, -0.06053482, -0.06016607, -0.05783438, -0.09113503, 0.35592142, -0.40401982, -0.26919034, 0.03331307, 0.03350402, 0.03439649, 0.03439649, 0.02907195, 0.02907196, 0.03340924, 0.03340926, 0.03124777, 0.03124777, 0.04781851, 0.04781861, 0.066184, 0.06618404, 0.0620051, 0.06804364, 0.06200514], "atomic dipole moments": [[0.07712995, -0.01904374, -0.05829796], [0.00672894, 0.02618316, 0.11050126], [0.00150818, -0.0276366, -0.11431873], [0.01668585, 0.02613073, 0.11296358], [0.01996156, -0.03229037, -0.12867263], [0.01840228, 0.02290869, 0.10004949], [0.14010092, -0.02567224, -0.06886998], [-0.01563208, -0.0441968, -0.187675], [0.0472346, 0.05307324, 0.23302562], [-0.23784496, -0.00797433, -0.09710039], 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b/data/json/508010_2af6b2_bd_coord.json new file mode 100644 index 0000000..2c737c0 --- /dev/null +++ b/data/json/508010_2af6b2_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -18.94057199, "HOMO-LUMO gap/eV": 5.26143807, "electronic energy": -19.25800033, "dipole": [0.01640089, 0.02095189, -0.10580579], "partial charges": [-0.10066662, -0.04095185, -0.04741878, -0.0078932, -0.10212454, -0.10212453, 0.04037758, 0.04037757, 0.03866446, 0.02363842, 0.02622661, 0.03095378, 0.03229004, 0.03307421, 0.03510627, 0.03510627, 0.03229005, 0.03307424], "atomic dipole moments": [[-0.03124578, -0.01427052, 0.05139677], [0.11940692, 0.03503555, -0.08223047], [-0.1221157, -0.00892906, -0.07342688], [-0.0689914, -0.02317979, 0.06470628], [0.06703115, -0.0629336, -0.01895619], [0.04117383, 0.08414217, 0.00616102], [0.09130667, -0.08511819, -0.01667023], [0.0568055, 0.11112755, 0.01684373], [-0.06495877, 0.00675508, -0.10642779], [0.06953707, -0.00870092, 0.12253441], [-0.05168982, -0.03095553, 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end of file diff --git a/data/json/508373_b19713_bd_coord.json b/data/json/508373_b19713_bd_coord.json new file mode 100644 index 0000000..6c056b4 --- /dev/null +++ b/data/json/508373_b19713_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -27.11701742, "HOMO-LUMO gap/eV": 4.9511476, "electronic energy": -27.43555417, "dipole": [0.36878651, 0.70247386, -0.42385677], "partial charges": [-0.115269, 0.08381733, -0.27036094, 0.35545064, -0.4121639, -0.0367484, -0.10727847, -0.10332924, 0.0522075, 0.05673639, 0.05856362, 0.05402233, 0.04768119, 0.05085603, 0.04506127, 0.05932248, 0.04038246, 0.04123756, 0.04895473, 0.05085643], "atomic dipole moments": [[-0.09311941, -0.08478921, 0.02531425], [-0.15463758, 0.14347285, -0.12525099], [0.00478537, -0.17955978, 0.16037164], [0.15089622, 0.04311415, -0.02311388], [0.01744438, 0.14683641, -0.12632809], [-0.02326196, -0.04366216, 0.09099788], [0.09059718, 0.07908316, 0.01928192], [0.04751133, -0.08030876, -0.07528974], [0.10428474, -0.04632455, 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"dipole": [0.0, 0.0, 2e-08], "partial charges": [-0.05431884, -0.05431884, -0.05431884, -0.05431884, -0.05431884, -0.05431884, 0.02424525, 0.0300736, 0.0300736, 0.02424524, 0.02424525, 0.0300736, 0.02424524, 0.0300736, 0.02424525, 0.0300736, 0.02424524, 0.0300736], "atomic dipole moments": [[0.01322009, 0.07199344, -0.08165283], [-0.03929332, 0.0762532, 0.06831182], [-0.09898378, -0.02120324, -0.04216211], [-0.01322011, -0.0719935, 0.08165283], [0.03929329, -0.07625316, -0.06831181], [0.09898383, 0.02120325, 0.04216209], [-0.04753215, -0.11157449, -0.01646064], [0.02714288, 0.01165316, 0.11899687], [-0.02584646, -0.0190243, -0.11833352], [0.08197301, -0.08424892, 0.03408319], [0.10068135, 0.01153184, -0.06862512], [0.0327219, 0.0162871, 0.1170333], [0.04753215, 0.11157447, 0.01646065], [-0.02714288, -0.01165315, -0.11899687], [-0.08197303, 0.08424894, -0.03408319], [0.02584646, 0.0190243, 0.11833352], [-0.10068133, -0.01153183, 0.06862512], [-0.03272191, -0.0162871, -0.1170333]], "atomic quadrupole moments": [[0.15053769, -0.119074, -0.04448913, -0.09350266, -0.08206382, -0.10604856], [0.05917603, 0.13094896, 0.06590942, -0.13547889, 0.01873847, -0.12508545], [-0.00830963, -0.03338241, 0.20745049, 0.06670119, -0.0255944, -0.19914086], [0.15053761, -0.11907393, -0.04448904, -0.09350266, -0.08206387, -0.10604857], [0.05917605, 0.13094906, 0.06590938, -0.1354789, 0.01873843, -0.12508543], [-0.00830951, -0.03338238, 0.20745039, 0.06670116, -0.0255944, -0.19914088], [-0.00698293, 0.02897953, 0.04379222, 0.00474249, 0.02017411, -0.03680929], [-0.01238112, -0.00615531, -0.03814867, 0.01970664, 0.01901006, 0.05052978], [-0.02071684, 0.017042, -0.03245986, 0.02016057, 0.00404768, 0.0531767], [0.01657401, -0.03515052, 0.01149912, 0.01930607, -0.02691143, -0.02807314], [0.02184788, 0.0028137, -0.01956486, -0.04938035, -0.00714296, -0.00228302], [-0.040763, -0.00299929, -0.01332527, 0.0196459, 0.00955183, 0.05408827], [-0.00698293, 0.02897954, 0.04379224, 0.00474249, 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"fractional occupation": [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "program call": "xtb /tmp/scratch/tmp3gnaq38r/510660_a7116d_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmp3gnaq38r/510660_a7116d_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole module/D": 0.0, "Total charge": 0, "Transition dipole module/D": NaN, "HOMO": -11.1331, "LUMO": 2.5275, "HOMO occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [-0.04634, -0.04634, -0.04634, -0.04634, -0.04634, -0.04634, 0.0235, 0.02284, 0.02284, 0.0235, 0.0235, 0.02284, 0.0235, 0.02284, 0.0235, 0.02284, 0.0235, 0.02284], "cm5 charges": [-0.15707, -0.15707, -0.15707, -0.15707, -0.15707, -0.15707, 0.07812, 0.07894, 0.07894, 0.07812, 0.07812, 0.07894, 0.07812, 0.07894, 0.07812, 0.07894, 0.07812, 0.07894], "FUKUI+": [0.011, 0.011, 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diff --git a/data/json/516760_7866b0_bd_coord.json b/data/json/516760_7866b0_bd_coord.json new file mode 100644 index 0000000..f02d04c --- /dev/null +++ b/data/json/516760_7866b0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -20.09784617, "HOMO-LUMO gap/eV": 3.97676179, "electronic energy": -20.55556755, "dipole": [-0.0968227, 0.01344136, 0.00566085], "partial charges": [-0.1004082, -0.02260148, 0.03857279, -0.02846384, -0.0282822, -0.02917905, -0.02831646, -0.02847531, 0.07513812, 0.03232546, 0.02914932, 0.02905322, 0.02915482, 0.0323328], "atomic dipole moments": [[0.3197601, -0.04459643, -0.01833635], [-0.37237858, 0.05221609, 0.02123133], [-0.00673578, 0.00096524, 0.00047286], [0.00315181, 0.00557984, -0.00149284], [-0.00369148, 0.00435488, -0.00064096], [0.00361485, -0.00058832, -0.00020583], [-0.00481879, -0.00318957, 0.00109258], [0.0016938, -0.0062969, 0.00123306], [0.20717673, -0.02941775, -0.01186782], [0.05944952, -0.13589909, 0.02426725], [-0.08868134, -0.1137091, 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--git a/data/json/5966_0_bd_coord.json b/data/json/5966_0_bd_coord.json new file mode 100644 index 0000000..64aaf39 --- /dev/null +++ b/data/json/5966_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -24.04933834, "HOMO-LUMO gap/eV": 11.12738509, "electronic energy": -24.35141799, "dipole": [-0.02091323, 0.31726232, -0.34883572], "partial charges": [-0.10647148, -0.06003642, 0.08986757, -0.32375086, 0.08986758, -0.06003642, -0.10647148, 0.03693633, 0.03693628, 0.04243689, 0.04783009, 0.04782972, 0.01327319, 0.01327325, 0.01327324, 0.01327319, 0.04783008, 0.04782973, 0.03693633, 0.03693629, 0.04243689], "atomic dipole moments": [[0.09707902, -0.03459113, 0.0337763], [0.00216493, 0.08773685, -0.0968287], [0.13936371, -0.10935527, 0.11430948], [-0.01272591, 0.19305223, -0.21227056], [-0.124816, -0.11133227, 0.1283494], [-0.01372432, 0.08761774, -0.09598444], [-0.09242534, -0.03600934, 0.04384752], [-0.00898985, 0.1225554, 0.01428015], [-0.01502633, -0.02559836, -0.12009791], [-0.09192832, 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/tmp/scratch/tmpcwipvc_k/6751_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmpcwipvc_k/6751_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole module/D": 2.619, "Total charge": 0, "Transition dipole module/D": NaN, "HOMO": -11.3164, "LUMO": -6.1419, "HOMO occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [-0.08445, -0.04305, -0.06031, 0.20059, -0.42192, 0.58663, -0.12399, -0.53121, 0.03298, 0.03048, 0.03048, 0.02572, 0.02572, 0.03738, 0.03738, 0.03841, 0.03841, 0.06111, 0.05854, 0.06111], "cm5 charges": [-0.2372, -0.15646, -0.16867, 0.11992, -0.50781, 0.63741, -0.26458, -0.5818, 0.08463, 0.0827, 0.0827, 0.08107, 0.08107, 0.09552, 0.09552, 0.1043, 0.1043, 0.1166, 0.11419, 0.1166], "FUKUI+": [0.009, 0.004, 0.004, 0.028, -0.123, -0.192, 0.05, -0.284, -0.022, -0.012, -0.012, -0.012, -0.012, -0.022, -0.022, -0.039, -0.039, -0.111, -0.084, -0.111], "FUKUI-": [0.02, 0.007, 0.009, 0.019, -0.058, -0.019, -0.003, 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b/data/json/999_0_bd_coord.json @@ -0,0 +1 @@ +{"total energy": -23.01384802, "HOMO-LUMO gap/eV": 3.85352758, "electronic energy": -23.32345865, "dipole": [-0.34832371, -0.03133894, 1.13940302], "partial charges": [-0.10299768, -0.05407995, -0.06049391, -0.05712752, -0.08335613, 0.21478791, -0.32015716, 0.03509106, 0.03385776, 0.03385768, 0.0320304, 0.03203102, 0.03081649, 0.03081634, 0.04688419, 0.04688572, 0.06416679, 0.06416739, 0.01281961], "atomic dipole moments": [[0.0788827, 0.00606183, -0.05953785], [0.00672265, -0.00010015, 0.11538635], [0.00483989, 0.00095023, -0.11611013], [0.02522253, 0.0011822, 0.12911074], [0.00133339, 0.00056369, -0.08990098], [-0.05396282, -0.00368543, -0.05420632], [0.00202629, -0.00072539, 0.16971596], [-0.10304065, -0.0071711, -0.06845227], [-0.00917935, 0.09910254, 0.07298102], [0.00536439, -0.10012087, 0.07196687], [0.00462034, -0.09841539, -0.07301231], [-0.0097776, 0.09878091, -0.07200124], [-0.00626096, 0.09769452, 0.07274414], [0.0080534, 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0000000..d4e6f42 --- /dev/null +++ b/data/ysi_xtb.csv @@ -0,0 +1,235 @@ +Species,CAS,Ref,Type,YSI,YSI_err,SMILES,xtbjson +"1-ethynyl-2,5-dimethylbenzene",74331-70-7,1.0,aromatic,512.7,19.6,C#Cc1cc(C)ccc1C,519175_3342b2_bd_coord.json +2-methylindene,2177-47-1,1.0,aromatic,500.1,19.1,CC1=Cc2ccccc2C1,437628_fd0a51_bd_coord.json +azulene,275-51-4,2.0,aromatic,492.3,19.0,c1ccc2cccc-2cc1,435907_1c36e8_bd_coord.json +1-ethynyl-2-methylbenzene,766-47-2,1.0,aromatic,485.0,18.5,C#Cc1ccccc1C,22307_0_bd_coord.json +"1-ethenyl-2,5-dimethylbenzene",2039-89-6,1.0,aromatic,469.3,17.8,C=Cc1cc(C)ccc1C,509114_ad5711_bd_coord.json +indene,95-13-6,1.0,aromatic,467.7,17.8,C1=Cc2ccccc2C1,2739_0_bd_coord.json +"1,2-dihydronaphthalene",447-53-0,1.0,aromatic,466.1,17.8,C1=Cc2ccccc2CC1,436081_4d1446_bd_coord.json +naphthalene,91-20-3,1.0,aromatic,466.1,8.4,c1ccc2ccccc2c1,509122_3d4389_bd_coord.json +(2-propynyl)-benzene,10147-11-2,1.0,aromatic,443.7,17.1,C#CCc1ccccc1,83340_0_bd_coord.json +1-ethynyl-4-ethylbenzene,40307-11-7,1.0,aromatic,442.6,17.1,C#Cc1ccc(CC)cc1,445913_b31cd3_bd_coord.json +(2-methyl-1-propenyl)-benzene,768-49-0,1.0,aromatic,436.9,16.6,CC(C)=Cc1ccccc1,436609_6062ff_bd_coord.json +(1-propynyl)-benzene,673-32-5,1.0,aromatic,427.5,16.5,CC#Cc1ccccc1,507886_d77d00_bd_coord.json +1-ethenyl-2-methylbenzene,611-15-4,1.0,aromatic,408.1,15.9,C=Cc1ccccc1C,17240_0_bd_coord.json +"1,2,3,4-tetramethylbenzene",488-23-3,1.0,aromatic,393.0,15.3,Cc1ccc(C)c(C)c1C,12952_0_bd_coord.json +"1,2,4,5-tetramethylbenzene",95-93-2,2.0,aromatic,393.0,15.3,Cc1cc(C)c(C)cc1C,2645_0_bd_coord.json +1-ethynyl-3-methylbenzene,766-82-5,1.0,aromatic,384.6,14.7,C#Cc1cccc(C)c1,22120_0_bd_coord.json +"1,2-diethylbenzene",135-01-3,1.0,aromatic,376.3,14.7,CCc1ccccc1CC,6949_0_bd_coord.json +1-ethynyl-4-methylbenzene,766-97-2,1.0,aromatic,374.7,14.7,C#Cc1ccc(C)cc1,516874_12f22e_bd_coord.json +(1-propenyl)-benzene,637-50-3,1.0,aromatic,352.2,13.5,C/C=C/c1ccccc1,436414_8f7071_bd_coord.json +cyclopropylbenzene,873-49-4,1.0,aromatic,343.9,13.5,c1ccc(C2CC2)cc1,24482_0_bd_coord.json +tetralin,119-64-2,1.0,aromatic,336.0,13.4,c1ccc2c(c1)CCCC2,435498_a67883_bd_coord.json +1-ethenyl-3-methylbenzene,100-80-1,1.0,aromatic,322.4,12.8,C=Cc1cccc(C)c1,435556_a65113_bd_coord.json +"1,3-diethylbenzene",141-93-5,1.0,aromatic,320.9,12.8,CCc1cccc(CC)c1,7241_0_bd_coord.json +(2-propenyl)-benzene,300-57-2,1.0,aromatic,310.9,12.3,C=CCc1ccccc1,507901_578e4a_bd_coord.json +"1,2,4-trimethylbenzene",95-63-6,1.0,aromatic,308.3,12.2,Cc1ccc(C)c(C)c1,509215_fbb763_bd_coord.json +(3-butynyl)-benzene,16520-62-0,1.0,aromatic,298.9,11.7,C#CCCc1ccccc1,517734_a2fee2_bd_coord.json +"(1,1-dimethylethyl)-benzene",98-06-6,1.0,aromatic,291.1,11.6,CC(C)(C)c1ccccc1,509245_ccc722_bd_coord.json +1-ethyl-3-methylbenzene,620-14-4,1.0,aromatic,278.0,11.1,CCc1cccc(C)c1,17913_0_bd_coord.json +(3-butenyl)-benzene,768-56-9,1.0,aromatic,275.9,11.1,C=CCCc1ccccc1,436600_1e570e_bd_coord.json +"1,4-diethylbenzene",105-05-5,1.0,aromatic,270.7,11.0,CCc1ccc(CC)cc1,4436_0_bd_coord.json +1-ethyl-2-methylbenzene,611-14-3,1.0,aromatic,267.0,11.0,CCc1ccccc1C,509282_69ff97_bd_coord.json +(2-methylpropyl)-benzene,538-93-2,1.0,aromatic,257.6,10.5,CC(C)Cc1ccccc1,509290_4d0288_bd_coord.json +1-ethyl-4-methylbenzene,622-96-8,1.0,aromatic,257.1,10.5,CCc1ccc(C)cc1,509295_b8887e_bd_coord.json +n-butylbenzene,104-51-8,1.0,aromatic,245.1,9.9,CCCCc1ccccc1,3966_0_bd_coord.json +ethylbenzene,100-41-4,1.0,aromatic,223.7,9.3,CCc1ccccc1,3607_0_bd_coord.json +phenylacetylene,536-74-3,1.0,aromatic,216.3,9.3,C#Cc1ccccc1,516760_7866b0_bd_coord.json +"1,2-dimethylbenzene",95-47-6,1.0,aromatic,204.8,8.8,Cc1ccccc1C,2663_0_bd_coord.json +isopropylbenzene,98-82-8,1.0,aromatic,187.6,8.2,CC(C)c1ccccc1,509355_6ae0b0_bd_coord.json +"1-methyl-1,4-cyclohexadiene",4313-57-9,1.0,aliphatic,175.6,7.7,CC1=CCC=CC1,12560_0_bd_coord.json +styrene,100-42-5,1.0,aromatic,174.0,7.7,C=Cc1ccccc1,509356_d2560a_bd_coord.json +methoxybenzene,100-66-3,1.0,aromatic,107.1,5.8,COc1ccccc1,508480_3cbc9b_bd_coord.json +cis + trans decahydronaphthalene,91-17-8,2.0,aromatic,105.5,5.8,C1CCC2CCCCC2C1,2194_0_bd_coord.json +"1,4-cyclohexadiene",628-41-1,1.0,aliphatic,101.4,5.8,C1=CCC=CC1,510632_cfd2f3_bd_coord.json +benzene,71-43-2,1.0,aromatic,100.3,5.8,c1ccccc1,509365_083657_bd_coord.json +"1,3-cyclohexadiene",592-57-4,1.0,aliphatic,98.8,5.8,C1=CCCC=C1,16666_0_bd_coord.json +1-methylcyclopentene,693-89-0,3.0,cyclic alkenes,96.5,2.8,CC1=CCCC1,20492_0_bd_coord.json +"2,4,4-trimethyl-2-pentene",107-40-4,3.0,alkenes,89.3,2.6,CC(C)=CC(C)(C)C,5011_0_bd_coord.json +"2,3,4-trimethyl-2-pentene",565-77-5,3.0,alkenes,87.0,2.5,CC(C)=C(C)C(C)C,15694_0_bd_coord.json +butylcyclohexane,1678-93-9,3.0,cyclic alkanes,76.8,2.2,CCCCC1CCCCC1,34777_0_bd_coord.json +1-decene,872-05-9,3.0,alkenes,74.8,2.2,C=CCCCCCCCC,5800_0_bd_coord.json +isopropylcyclohexane,696-29-7,3.0,cyclic alkanes,74.7,2.2,CC(C)C1CCCCC1,3160_0_bd_coord.json +1-octyne,629-05-0,3.0,alkynes/alkadienes,74.1,2.2,C#CCCCCCC,516826_340bac_bd_coord.json +cyclopentene,142-29-0,3.0,cyclic alkenes,70.2,2.1,C1=CCCC1,510166_c8f1dc_bd_coord.json +propylcyclohexane,1678-92-8,3.0,cyclic alkanes,69.2,2.1,CCCC1CCCCC1,34801_0_bd_coord.json +"2,4,4-trimethyl-1-pentene",107-39-1,3.0,alkenes,68.5,2.1,C=C(C)CC(C)(C)C,4921_0_bd_coord.json +"1,1-dimethylcyclohexane",590-66-9,3.0,cyclic alkanes,67.9,2.1,CC1(C)CCCCC1,16326_0_bd_coord.json +"2-methyl-1,5-hexadiene",4049-81-4,3.0,alkynes/alkadienes,67.7,2.1,C=CCCC(=C)C,53344_0_bd_coord.json +"2,2,4,4-tetramethyl-3-pentanone",815-24-7,3.0,saturated alkanone,65.8,2.0,CC(C)(C)C(=O)C(C)(C)C,22895_0_bd_coord.json +"cis 1,2-dimethylcyclohexane",2207-01-4,3.0,cyclic alkanes,65.2,2.0,C[C@H]1CCCC[C@H]1C,15826_0_bd_coord.json +2-methyl-2-heptene,627-97-4,3.0,alkenes,64.5,2.0,CCCCC=C(C)C,18921_0_bd_coord.json +"2,3-dimethyl-2-butene",563-79-1,3.0,alkenes,62.4,2.0,CC(C)=C(C)C,15548_0_bd_coord.json +methyl cyclopentyl ether,5614-37-9,3.0,saturated ethers,62.3,2.0,COC1CCCC1,38145_0_bd_coord.json +"2,2,4-trimethylpentane",540-84-1,3.0,linear alkanes,61.7,2.0,CC(C)CC(C)(C)C,14930_0_bd_coord.json +"4,4-dimethyl-1-pentene",762-62-9,3.0,alkenes,61.4,2.0,C=CCC(C)(C)C,21727_0_bd_coord.json +"2,3,4-trimethylpentane",565-75-3,3.0,linear alkanes,60.9,2.0,CC(C)C(C)C(C)C,15667_0_bd_coord.json +ethylcyclohexane,1678-91-7,3.0,cyclic alkanes,60.7,2.0,CCC1CCCCC1,34800_0_bd_coord.json +3-ethyl-2-pentene,816-79-5,3.0,alkenes,59.8,2.0,CC=C(CC)CC,436620_9743f0_bd_coord.json +trans 4-octene,14850-23-8,3.0,alkenes,59.8,2.0,CCC/C=C/CCC,16625_0_bd_coord.json +trans 3-octene,14919-01-8,3.0,alkenes,58.8,2.0,CC/C=C/CCCC,16582_0_bd_coord.json +ethylcyclopentane,1640-89-7,3.0,cyclic alkanes,58.6,2.0,CCC1CCCC1,509449_ec0877_bd_coord.json +cyclooctane,292-64-8,3.0,cyclic alkanes,57.7,2.0,C1CCCCCCC1,510259_4d2078_bd_coord.json +n-decane,124-18-5,3.0,linear alkanes,57.2,2.0,CCCCCCCCCC,6799_0_bd_coord.json +trans 2-octene,13389-42-9,3.0,alkenes,56.7,2.0,C/C=C/CCCCC,5895_0_bd_coord.json +"2,5-dimethylhexane",592-13-2,3.0,linear alkanes,56.1,2.0,CC(C)CCC(C)C,16548_0_bd_coord.json +1-octene,111-66-0,3.0,alkenes,56.0,2.0,C=CCCCCCC,6123_0_bd_coord.json +"2,6-dimethyl-4-heptanone",108-83-8,3.0,saturated alkanone,55.8,2.0,CC(C)CC(=O)CC(C)C,5151_0_bd_coord.json +"2,2,3-trimethylbutane",464-06-2,3.0,linear alkanes,55.3,2.0,CC(C)C(C)(C)C,508003_846a96_bd_coord.json +2-pentyne,627-21-4,3.0,alkynes/alkadienes,54.7,2.0,CC#CCC,18995_0_bd_coord.json +cis 4-methyl-2-pentene,691-38-3,3.0,alkenes,54.1,2.0,C/C=C\C(C)C,508010_2af6b2_bd_coord.json +3-methyl-2-pentene,922-61-2,3.0,alkenes,53.7,2.0,C/C=C(\C)CC,508020_186d6d_bd_coord.json +2-methyl-2-pentene,625-27-4,3.0,alkenes,53.6,2.0,CCC=C(C)C,509489_e96a4f_bd_coord.json +methylcyclohexane,108-87-2,3.0,cyclic alkanes,53.6,2.0,CC1CCCCC1,5193_0_bd_coord.json +trans 3-heptene,14686-14-7,3.0,alkenes,53.5,2.0,CC/C=C/CCC,16605_0_bd_coord.json +"3,3-dimethyl-1-butene",558-37-2,3.0,alkenes,53.1,2.0,C=CC(C)(C)C,15444_0_bd_coord.json +"2,2-dimethylhexane",590-73-8,3.0,linear alkanes,52.8,2.0,CCCCC(C)(C)C,16305_0_bd_coord.json +cis 2-heptene,6443-92-1,3.0,alkenes,50.8,2.0,C/C=C\CCCC,508031_6f74a8_bd_coord.json +2-propyl-1-pentanol,58175-57-8,3.0,saturated alcohols,50.5,2.0,CCCC(CO)CCC,181010_0_bd_coord.json +methylcyclopentane,96-37-7,3.0,cyclic alkanes,50.3,2.0,CC1CCCC1,2763_0_bd_coord.json +cycloheptane,291-64-5,3.0,cyclic alkanes,50.0,2.0,C1CCCCCC1,510274_74e3ef_bd_coord.json +"2,4-dimethylpentane",108-08-7,3.0,linear alkanes,49.6,2.0,CC(C)CC(C)C,5265_0_bd_coord.json +2-methylheptane,592-27-8,3.0,linear alkanes,49.4,2.0,CCCCCC(C)C,6700_0_bd_coord.json +2-methyl-1-hexene,6094-02-6,3.0,alkenes,49.1,2.0,C=C(C)CCCC,21813_0_bd_coord.json +1-heptene,592-76-7,3.0,alkenes,48.4,2.0,C=CCCCCC,508067_b0a965_bd_coord.json +4-methylheptane,589-53-7,3.0,linear alkanes,48.1,2.0,CCCC(C)CCC,16277_0_bd_coord.json +"3,3-dimethylpentane",562-49-2,3.0,linear alkanes,47.7,2.0,CCC(C)(C)CC,15502_0_bd_coord.json +"2,2-dimethylpentane",590-35-2,3.0,linear alkanes,47.4,2.0,CCCC(C)(C)C,16322_0_bd_coord.json +trans 3-hexene,13269-52-8,3.0,alkenes,47.2,2.0,CC/C=C/CC,16673_0_bd_coord.json +trans 2-hexene,4050-45-7,3.0,alkenes,45.8,2.0,C/C=C/CCC,16535_0_bd_coord.json +2-ethyl-1-butene,760-21-4,3.0,alkenes,45.6,2.0,C=C(CC)CC,21586_0_bd_coord.json +methyl-3-hexenoate,2396-78-3,4.0,unsaturated esters,45.3,2.0,CC/C=C/CC(=O)OC,40275_0_bd_coord.json +cis 2-hexene,7688-21-3,3.0,alkenes,44.7,2.0,C/C=C\CCC,509612_94d550_bd_coord.json +"2,3-dimethylbutane",79-29-8,3.0,linear alkanes,44.0,2.0,CC(C)C(C)C,1732_0_bd_coord.json +nonanal,124-19-6,3.0,saturated aldehyde,43.7,2.0,CCCCCCCCC=O,6770_0_bd_coord.json +isopentyl acetate,123-92-2,3.0,saturated esters,43.6,2.0,CC(=O)OCCC(C)C,6574_0_bd_coord.json +2-methyl-2-butene,513-35-9,3.0,alkenes,43.5,2.0,CC=C(C)C,14097_0_bd_coord.json +butyl propionate,590-01-2,3.0,saturated esters,43.3,2.0,CCCCOC(=O)CC,16364_0_bd_coord.json +"4,4-dimethyl-2-pentanone",590-50-1,3.0,saturated alkanone,42.7,2.0,CC(=O)CC(C)(C)C,16359_0_bd_coord.json +cyclohexane,110-82-7,3.0,cyclic alkanes,42.7,2.0,C1CCCCC1,510660_a7116d_bd_coord.json +"2,4-dimethyl-3-pentanone",565-80-0,3.0,saturated alkanone,42.6,2.0,CC(C)C(=O)C(C)C,15692_0_bd_coord.json +n-octane,111-65-9,3.0,linear alkanes,42.6,2.0,CCCCCCCC,6131_0_bd_coord.json +2-methylhexane,591-76-4,3.0,linear alkanes,42.4,2.0,CCCCC(C)C,16405_0_bd_coord.json +cyclohexanol,108-93-0,3.0,saturated alcohols,42.3,2.0,OC1CCCCC1,4204_0_bd_coord.json +"2,4-dimethyl-3-pentanol",600-36-2,3.0,saturated alcohols,41.9,2.1,CC(C)C(O)C(C)C,16908_0_bd_coord.json +2-methyl-2-hexanol,625-23-0,3.0,saturated alcohols,41.8,2.1,CCCCC(C)(C)O,18686_0_bd_coord.json +5-nonanone,502-56-7,3.0,saturated alkanone,41.8,2.1,CCCCC(=O)CCCC,13638_0_bd_coord.json +2-ethyl-1-butanol,97-95-0,3.0,saturated alcohols,41.7,2.1,CCC(CC)CO,2929_0_bd_coord.json +ethyl-4-pentenoate,1968-40-7,4.0,unsaturated esters,41.2,2.1,C=CCCC(=O)OCC,37200_0_bd_coord.json +1-octanol,111-87-5,3.0,saturated alcohols,41.1,2.1,CCCCCCCCO,508200_f2b6b1_bd_coord.json +isobutyl propionate,540-42-1,3.0,saturated esters,41.1,2.1,CCC(=O)OCC(C)C,508201_81286f_bd_coord.json +"3,3-dimethyl-1-butanol",624-95-3,3.0,saturated alcohols,40.9,2.1,CC(C)(C)CCO,508202_78e26e_bd_coord.json +"2,3-dimethyl-2-butanol",594-60-5,3.0,saturated alcohols,40.6,2.1,CC(C)C(C)(C)O,16689_0_bd_coord.json +"3,3-dimethyl-2-butanone",75-97-8,3.0,saturated alkanone,40.6,2.1,CC(=O)C(C)(C)C,1397_0_bd_coord.json +3-ethyl-3-pentanol,597-49-9,3.0,saturated alcohols,40.5,2.1,CCC(O)(CC)CC,16770_0_bd_coord.json +tert-butyl propionate,20487-40-5,3.0,saturated esters,40.5,2.1,CCC(=O)OC(C)(C)C,110758_0_bd_coord.json +cis 2-pentene,627-20-3,3.0,alkenes,39.8,2.1,C/C=C\CC,509706_bb2796_bd_coord.json +ethyl-3-methyl-2-butenoate,638-10-8,4.0,unsaturated esters,39.5,2.1,CCOC(=O)C=C(C)C,19599_0_bd_coord.json +methyl-5-hexenoate,2396-80-7,4.0,unsaturated esters,39.2,2.1,C=CCCCC(=O)OC,40291_0_bd_coord.json +methyl-3-pentenoate,818-58-6,4.0,unsaturated esters,38.8,2.1,C/C=C/CC(=O)OC,23260_0_bd_coord.json +dibutyl ether,142-96-1,3.0,saturated ethers,38.7,2.1,CCCCOCCCC,7284_0_bd_coord.json +diisopropyl ether,108-20-3,3.0,saturated ethers,38.7,2.1,CC(C)OC(C)C,5212_0_bd_coord.json +4-heptanol,589-55-9,3.0,saturated alcohols,38.5,2.1,CCCC(O)CCC,16132_0_bd_coord.json +"3,3-dimethylbutanal",2987-16-8,3.0,saturated aldehyde,38.4,2.1,CC(C)(C)CC=O,45102_0_bd_coord.json +3-methylpentane,96-14-0,3.0,linear alkanes,38.2,2.1,CCC(C)CC,2861_0_bd_coord.json +methyl tert-amyl ether,994-05-8,3.0,saturated ethers,38.1,2.1,CCC(C)(C)OC,26827_0_bd_coord.json +methyl-2-methyl-2-butenoate,6622-76-0,4.0,unsaturated esters,38.0,2.1,C/C=C(/C)C(=O)OC,439760_3a05a4_bd_coord.json +tert-butyl ethyl ether,637-92-3,3.0,saturated ethers,37.9,2.1,CCOC(C)(C)C,19570_0_bd_coord.json +octanal,124-13-0,3.0,saturated aldehyde,37.5,2.1,CCCCCCCC=O,6805_0_bd_coord.json +propyl butyrate,105-66-8,3.0,saturated esters,37.3,2.1,CCCOC(=O)CCC,4467_0_bd_coord.json +propyl-2-methyl-2-propenoate,2210-28-8,4.0,unsaturated esters,37.1,2.1,C=C(C)C(=O)OCCC,39144_0_bd_coord.json +ethyl isopentanoate,108-64-5,3.0,saturated esters,36.6,2.1,CCOC(=O)CC(C)C,508255_871758_bd_coord.json +2-methyl-2-pentanol,590-36-3,3.0,saturated alcohols,36.4,2.1,CCCC(C)(C)O,16318_0_bd_coord.json +methyl-3-methyl-2-butenoate,924-50-5,4.0,unsaturated esters,36.4,2.1,COC(=O)C=C(C)C,509763_ca3e69_bd_coord.json +isopropyl butyrate,638-11-9,3.0,saturated esters,36.3,2.1,CCCC(=O)OC(C)C,19577_0_bd_coord.json +3-octanone,106-68-3,3.0,saturated alkanone,36.0,2.2,CCCCCC(=O)CC,4525_0_bd_coord.json +butyl acetate,123-86-4,3.0,saturated esters,36.0,2.2,CCCCOC(C)=O,6751_0_bd_coord.json +n-heptane,142-82-5,3.0,linear alkanes,36.0,2.2,CCCCCCC,7248_0_bd_coord.json +2-methyl-3-hexanone,7379-12-6,3.0,saturated alkanone,35.9,2.2,CCCC(=O)C(C)C,80219_0_bd_coord.json +pentyl formate,638-49-3,3.0,saturated esters,35.7,2.2,CCCCCOC=O,508276_af34ab_bd_coord.json +4-methyl-1-pentanol,626-89-1,3.0,saturated alcohols,35.6,2.2,CC(C)CCCO,18730_0_bd_coord.json +1-heptanol,111-70-6,3.0,saturated alcohols,34.7,2.2,CCCCCCCO,5942_0_bd_coord.json +dipropyl carbonate,623-96-1,3.0,other multi-oxygen compounds,34.5,2.2,CCCOC(=O)OCCC,18327_0_bd_coord.json +cyclohexanone,108-94-1,3.0,saturated alkanone,34.3,2.2,O=C1CCCCC1,1572_0_bd_coord.json +ethyl-2-methyl-2-butenoate,5837-78-5,4.0,unsaturated esters,34.0,2.2,C/C=C(\C)C(=O)OCC,508292_8673ea_bd_coord.json +heptanal,111-71-7,3.0,saturated aldehyde,33.8,2.2,CCCCCCC=O,6034_0_bd_coord.json +methyl-2-pentenoate,15790-88-2,4.0,unsaturated esters,33.6,2.2,CC/C=C/C(=O)OC,23138_0_bd_coord.json +3-methoxy-3-methyl-1-butanol,56539-66-3,3.0,other multi-oxygen compounds,33.2,2.2,COC(C)(C)CCO,176748_0_bd_coord.json +2-methyl-2-butanol,75-85-4,3.0,saturated alcohols,32.9,2.2,CCC(C)(C)O,1402_0_bd_coord.json +4-methyl-2-pentanone,108-10-1,3.0,saturated alkanone,32.8,2.2,CC(=O)CC(C)C,5069_0_bd_coord.json +methyl heptanoate,106-73-0,3.0,saturated esters,32.5,2.2,CCCCCCC(=O)OC,4742_0_bd_coord.json +propyl propionate,106-36-5,3.0,saturated esters,31.9,2.2,CCCOC(=O)CC,4698_0_bd_coord.json +butyl formate,592-84-7,3.0,saturated esters,31.0,2.3,CCCCOC=O,4504_0_bd_coord.json +2-methyl-3-pentanone,565-69-5,3.0,saturated alkanone,30.7,2.3,CCC(=O)C(C)C,15664_0_bd_coord.json +3-heptanone,106-35-4,3.0,saturated alkanone,30.7,2.3,CCCCC(=O)CC,4612_0_bd_coord.json +isobutyl formate,542-55-2,3.0,saturated esters,30.4,2.3,CC(C)COC=O,15081_0_bd_coord.json +ethyl-2-butenoate,623-70-1,4.0,unsaturated esters,30.3,2.3,C/C=C/C(=O)OCC,18248_0_bd_coord.json +1-hexanol,111-27-3,3.0,saturated alcohols,30.0,2.3,CCCCCCO,5929_0_bd_coord.json +"2,2-dimethylbutyric acid",595-37-9,3.0,saturated esters,30.0,2.3,CCC(C)(C)C(=O)O,3033_0_bd_coord.json +3-pentanol,584-02-1,3.0,saturated alcohols,29.1,2.3,CCC(O)CC,15915_0_bd_coord.json +2-ethylbutanal,97-96-1,3.0,saturated aldehyde,29.0,2.3,CCC(C=O)CC,2904_0_bd_coord.json +methyl-2-methyl-2-propenoate,80-62-6,4.0,unsaturated esters,29.0,2.3,C=C(C)C(=O)OC,1850_0_bd_coord.json +4-heptanone,123-19-3,3.0,saturated alkanone,28.5,2.3,CCCC(=O)CCC,6667_0_bd_coord.json +ethyl pentanoate,539-82-2,3.0,saturated esters,28.4,2.3,CCCCC(=O)OCC,14802_0_bd_coord.json +methyl isopentanoate,556-24-1,3.0,saturated esters,28.4,2.3,COC(=O)CC(C)C,15377_0_bd_coord.json +dipropyl ether,111-43-3,3.0,saturated ethers,28.0,2.3,CCCOCCC,5966_0_bd_coord.json +tert-butanol,75-65-0,3.0,saturated alcohols,27.5,2.3,CC(C)(C)O,41_0_bd_coord.json +"1,1-diethoxypropane",4744-08-5,3.0,other multi-oxygen compounds,27.3,2.4,CCOC(CC)OCC,59717_0_bd_coord.json +methyl-2-butenoate,623-43-8,4.0,unsaturated esters,27.3,2.4,C/C=C/C(=O)OC,17710_0_bd_coord.json +hexanal,66-25-1,3.0,saturated aldehyde,26.7,2.4,CCCCCC=O,999_0_bd_coord.json +3-methyl-2-butanone,563-80-4,3.0,saturated alkanone,26.6,2.4,CC(=O)C(C)C,15567_0_bd_coord.json +tetrahydropyran,142-68-7,3.0,cyclic saturated ethers,26.5,2.4,C1CCOCC1,7323_0_bd_coord.json +ethyl isobutyrate,97-62-1,3.0,saturated esters,26.1,2.4,CCOC(=O)C(C)C,508373_b19713_bd_coord.json +2-ethylbutyric acid,88-09-5,3.0,saturated esters,25.9,2.4,CCC(CC)C(=O)O,2010_0_bd_coord.json +2-hexanone,591-78-6,3.0,saturated alkanone,25.6,2.4,CCCCC(C)=O,5138_0_bd_coord.json +2-isopropoxyethanol,109-59-1,3.0,other multi-oxygen compounds,25.5,2.4,CC(C)OCCO,5503_0_bd_coord.json +3-hexanone,589-38-8,3.0,saturated alkanone,25.5,2.4,CCCC(=O)CC,509886_04ffd9_bd_coord.json +ethyl butyrate,105-54-4,3.0,saturated esters,25.5,2.4,CCCC(=O)OCC,4420_0_bd_coord.json +1-pentanol,71-41-0,3.0,saturated alcohols,25.4,2.4,CCCCCO,1200_0_bd_coord.json +ethyl-2-methyl-2-propenoate,97-63-2,4.0,unsaturated esters,25.4,2.4,C=C(C)C(=O)OCC,2988_0_bd_coord.json +2-butoxyethanol,111-76-2,3.0,other multi-oxygen compounds,25.3,2.4,CCCCOCCO,1640_0_bd_coord.json +propyl acetate,109-60-4,3.0,saturated esters,24.4,2.4,CCCOC(C)=O,5508_0_bd_coord.json +isopropyl acetate,108-21-4,3.0,saturated esters,23.7,2.5,CC(=O)OC(C)C,5067_0_bd_coord.json +methyl butyl ether,628-28-4,3.0,saturated ethers,23.0,2.5,CCCCOC,19021_0_bd_coord.json +methyl pentanoate,624-24-8,3.0,saturated esters,22.3,2.5,CCCCC(=O)OC,18431_0_bd_coord.json +methyl isobutyrate,547-63-7,3.0,saturated esters,22.2,2.5,COC(=O)C(C)C,15213_0_bd_coord.json +1-butanol,71-36-3,3.0,saturated alcohols,22.0,2.5,CCCCO,1195_0_bd_coord.json +ethyl-2-propenoate,140-88-5,4.0,unsaturated esters,22.0,2.5,C=CC(=O)OCC,508399_56fa16_bd_coord.json +isobutanal,78-84-2,3.0,saturated aldehyde,21.2,2.5,CC(C)C=O,1669_0_bd_coord.json +2-pentanone,107-87-9,3.0,saturated alkanone,21.1,2.5,CCCC(C)=O,4875_0_bd_coord.json +"1,2-diethoxyethane",629-14-1,3.0,other multi-oxygen compounds,20.4,2.6,CCOCCOCC,19297_0_bd_coord.json +isopropyl formate,625-55-8,3.0,saturated esters,20.3,2.6,CC(C)OC=O,18574_0_bd_coord.json +tetrahydrofuran,109-99-9,3.0,cyclic saturated ethers,20.3,2.6,C1CCOC1,5461_0_bd_coord.json +methyl-2-propenoate,96-33-3,4.0,unsaturated esters,19.4,2.6,C=CC(=O)OC,2884_0_bd_coord.json +isobutyric acid,79-31-2,3.0,saturated esters,18.8,2.6,CC(C)C(=O)O,1736_0_bd_coord.json +diethoxymethane,462-95-3,3.0,other multi-oxygen compounds,18.5,2.6,CCOCOCC,12471_0_bd_coord.json +butyric acid,107-92-6,3.0,saturated esters,18.1,2.6,CCCC(=O)O,824_0_bd_coord.json +methyl propyl ether,557-17-5,3.0,saturated ethers,18.0,2.6,CCCOC,15398_0_bd_coord.json +3-methoxy-1-propanol,1589-49-7,3.0,other multi-oxygen compounds,17.9,2.6,COCCCO,508422_58c103_bd_coord.json +butanal,123-72-8,3.0,saturated aldehyde,17.6,2.6,CCCC=O,6745_0_bd_coord.json +2-butanone,78-93-3,3.0,saturated alkanone,17.2,2.7,CCC(C)=O,508423_49e42c_bd_coord.json +diethyl ether,60-29-7,3.0,saturated ethers,16.8,2.7,CCOCC,829_0_bd_coord.json +"2,2-dimethoxypropane",77-76-9,3.0,other multi-oxygen compounds,16.4,2.7,COC(C)(C)OC,1479_0_bd_coord.json +1-propanol,71-23-8,3.0,saturated alcohols,16.2,2.7,CCCO,1183_0_bd_coord.json +diglyme,111-96-6,3.0,other multi-oxygen compounds,16.1,2.7,COCCOCCOC,509932_5dfdc8_bd_coord.json +diethyl carbonate,105-58-8,3.0,other multi-oxygen compounds,15.3,2.7,CCOC(=O)OCC,4327_0_bd_coord.json +2-(2-methoxyethoxy)-ethanol,111-77-3,3.0,other multi-oxygen compounds,15.0,2.7,COCCOCCO,6087_0_bd_coord.json +methyl propionate,554-12-1,3.0,saturated esters,15.0,2.7,CCC(=O)OC,11574_0_bd_coord.json +"1,1-dimethoxy-2-propanone",6342-56-9,3.0,other multi-oxygen compounds,14.8,2.7,COC(OC)C(C)=O,508431_6a2cc4_bd_coord.json +propanal (propionaldehyde),123-38-6,3.0,saturated aldehyde,13.9,2.8,CCC=O,6559_0_bd_coord.json +ethyl acetate,141-78-6,3.0,saturated esters,13.4,2.8,CCOC(C)=O,7187_0_bd_coord.json +2-propanone (acetone),67-64-1,3.0,saturated alkanone,13.0,2.8,CC(C)=O,575_0_bd_coord.json +trimethoxymethane,149-73-5,3.0,other multi-oxygen compounds,12.8,2.8,COC(OC)OC,508437_3bdd6d_bd_coord.json +"1,1,1-trimethoxyethane",1445-45-0,3.0,other multi-oxygen compounds,12.7,2.8,COC(C)(OC)OC,14518_0_bd_coord.json +dimethoxymethane,109-87-5,3.0,other multi-oxygen compounds,10.9,2.9,COCOC,5420_0_bd_coord.json +dimethyl carbonate,616-38-6,3.0,other multi-oxygen compounds,10.5,2.9,COC(=O)OC,17608_0_bd_coord.json +ethanol,64-17-5,3.0,saturated alcohols,10.3,2.9,CCO,900_0_bd_coord.json +2-hydroxy-methylpropionate,27871-49-4,3.0,other multi-oxygen compounds,9.6,2.9,COC(=O)[C@H](C)O,15209_0_bd_coord.json +methanol,67-56-1,3.0,saturated alcohols,6.6,3.0,CO,100_0_bd_coord.json +1-methyl-1-cyclohexene,591-49-1,,cyclic alkenes,62.0,3.0,CC1=CCCCC1,16461_0_bd_coord.json +1-tert-butyl-1-cyclohexene,3419-66-7,,cyclic alkenes,161.0,5.0,CC(C)(C)C1=CCCCC1,48556_0_bd_coord.json +cyclooctene,931-88-4,,cyclic alkenes,78.0,4.0,C1=C\CCCCCC/1,508442_9f6d62_bd_coord.json +cycloheptene,628-92-2,,cyclic alkenes,79.0,4.0,C1=CCCCCC1,19128_0_bd_coord.json +cyclopentanone,120-92-3,,cyclic ketone,22.0,4.0,O=C1CCCC1,6427_0_bd_coord.json +"2,5-dimethylfuran",625-86-5,,furan,55.0,4.0,Cc1ccc(C)o1,508464_2b8c12_bd_coord.json +2-methyl-3-buten-2-ol,115-18-4,,unsaturated alcohol,25.0,4.0,C=CC(C)(C)O,6313_0_bd_coord.json diff --git a/examples/creating_and_training_a_model_xtb.ipynb b/examples/creating_and_training_a_model_xtb.ipynb new file mode 100644 index 0000000..e17ba4c --- /dev/null +++ b/examples/creating_and_training_a_model_xtb.ipynb @@ -0,0 +1,998 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2022-02-01 14:48:44.517500: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /nopt/slurm/current/lib:\n", + "2022-02-01 14:48:44.517539: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "tensorflow 2.4.1\n", + "nfp 0.3.8\n" + ] + } + ], + "source": [ + "import numpy as np\n", + "import pandas as pd\n", + "\n", + "import tensorflow as tf\n", + "import nfp\n", + "\n", + "from tqdm import tqdm\n", + "tqdm.pandas()\n", + "\n", + "print(f\"tensorflow {tf.__version__}\")\n", + "print(f\"nfp {nfp.__version__}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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SpeciesCASRefTypeYSIYSI_errSMILESxtbjson
01-ethynyl-2,5-dimethylbenzene74331-70-71.0aromatic512.719.6C#Cc1cc(C)ccc1C519175_3342b2_bd_coord.json
12-methylindene2177-47-11.0aromatic500.119.1CC1=Cc2ccccc2C1437628_fd0a51_bd_coord.json
2azulene275-51-42.0aromatic492.319.0c1ccc2cccc-2cc1435907_1c36e8_bd_coord.json
31-ethynyl-2-methylbenzene766-47-21.0aromatic485.018.5C#Cc1ccccc1C22307_0_bd_coord.json
41-ethenyl-2,5-dimethylbenzene2039-89-61.0aromatic469.317.8C=Cc1cc(C)ccc1C509114_ad5711_bd_coord.json
\n", + "
" + ], + "text/plain": [ + " Species CAS Ref Type YSI YSI_err \\\n", + "0 1-ethynyl-2,5-dimethylbenzene 74331-70-7 1.0 aromatic 512.7 19.6 \n", + "1 2-methylindene 2177-47-1 1.0 aromatic 500.1 19.1 \n", + "2 azulene 275-51-4 2.0 aromatic 492.3 19.0 \n", + "3 1-ethynyl-2-methylbenzene 766-47-2 1.0 aromatic 485.0 18.5 \n", + "4 1-ethenyl-2,5-dimethylbenzene 2039-89-6 1.0 aromatic 469.3 17.8 \n", + "\n", + " SMILES xtbjson \n", + "0 C#Cc1cc(C)ccc1C 519175_3342b2_bd_coord.json \n", + "1 CC1=Cc2ccccc2C1 437628_fd0a51_bd_coord.json \n", + "2 c1ccc2cccc-2cc1 435907_1c36e8_bd_coord.json \n", + "3 C#Cc1ccccc1C 22307_0_bd_coord.json \n", + "4 C=Cc1cc(C)ccc1C 509114_ad5711_bd_coord.json " + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Load the input data, here YSI (10.1016/j.combustflame.2017.12.005)\n", + "ysi = pd.read_csv('../data/ysi_xtb.csv')\n", + "ysi.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(134, 50, 50)" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Split the data into training, validation, and test sets\n", + "valid, test, train = np.split(ysi[['SMILES','xtbjson']].sample(frac=1., random_state=1), [50, 100])\n", + "len(train), len(valid), len(test)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "# Define how to featurize the input molecules\n", + "from nfp.preprocessing.xtb_preprocessor import xTBSmilesPreprocessor\n", + "from nfp.preprocessing.features import get_ring_size\n", + "\n", + "\n", + "def atom_featurizer(atom):\n", + " \"\"\" Return an string representing the atom type\n", + " \"\"\"\n", + "\n", + " return str((\n", + " atom.GetSymbol(),\n", + " atom.GetIsAromatic(),\n", + " get_ring_size(atom, max_size=6),\n", + " atom.GetDegree(),\n", + " atom.GetTotalNumHs(includeNeighbors=True)\n", + " ))\n", + "\n", + "\n", + "def bond_featurizer(bond, flipped=False):\n", + " \"\"\" Get a similar classification of the bond type.\n", + " Flipped indicates which 'direction' the bond edge is pointing. \"\"\"\n", + " \n", + " if not flipped:\n", + " atoms = \"{}-{}\".format(\n", + " *tuple((bond.GetBeginAtom().GetSymbol(),\n", + " bond.GetEndAtom().GetSymbol())))\n", + " else:\n", + " atoms = \"{}-{}\".format(\n", + " *tuple((bond.GetEndAtom().GetSymbol(),\n", + " bond.GetBeginAtom().GetSymbol())))\n", + " \n", + " btype = str(bond.GetBondType())\n", + " ring = 'R{}'.format(get_ring_size(bond, max_size=6)) if bond.IsInRing() else ''\n", + " \n", + " return \" \".join([atoms, btype, ring]).strip()\n", + "\n", + "\n", + "preprocessor = xTBSmilesPreprocessor(atom_features=atom_featurizer, bond_features=bond_featurizer)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "before pre-allocating\n", + "{'unk': 1}\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2022-02-01 14:48:58.336917: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set\n", + "2022-02-01 14:48:58.337520: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /nopt/slurm/current/lib:\n", + "2022-02-01 14:48:58.337550: W tensorflow/stream_executor/cuda/cuda_driver.cc:326] failed call to cuInit: UNKNOWN ERROR (303)\n", + "2022-02-01 14:48:58.337590: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (el1): /proc/driver/nvidia/version does not exist\n", + "2022-02-01 14:48:58.338118: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F FMA\n", + "To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.\n", + "2022-02-01 14:48:58.339728: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "after pre-allocating\n", + "{'unk': 1, \"('C', False, 0, 3, 2)\": 2, \"('C', False, 0, 3, 0)\": 3, \"('C', False, 0, 4, 3)\": 4, \"('C', False, 0, 4, 2)\": 5, \"('C', False, 0, 4, 0)\": 6, \"('H', False, 0, 1, 0)\": 7, \"('O', False, 0, 2, 1)\": 8, \"('O', False, 0, 2, 0)\": 9, \"('O', False, 0, 1, 0)\": 10, \"('C', False, 0, 3, 1)\": 11, \"('C', False, 0, 4, 1)\": 12, \"('C', True, 'max', 3, 0)\": 13, \"('C', True, 'max', 3, 1)\": 14, \"('C', False, 'max', 3, 0)\": 15, \"('C', False, 'max', 4, 2)\": 16, \"('C', False, 'max', 4, 1)\": 17, \"('C', False, 5, 3, 0)\": 18, \"('C', False, 5, 3, 1)\": 19, \"('C', False, 5, 4, 2)\": 20, \"('C', True, 5, 3, 0)\": 21, \"('C', True, 5, 3, 1)\": 22, \"('O', True, 5, 2, 0)\": 23, \"('C', False, 'max', 3, 1)\": 24, \"('C', False, 0, 2, 0)\": 25, \"('C', False, 5, 4, 1)\": 26, \"('C', False, 0, 2, 1)\": 27, \"('O', False, 5, 2, 0)\": 28}\n" + ] + } + ], + "source": [ + "# Initially, the preprocessor has no data on atom types, so we have to loop over the \n", + "# training set once to pre-allocate these mappings\n", + "print(\"before pre-allocating\")\n", + "print(preprocessor.atom_tokenizer._data)\n", + "\n", + "for row in train.index:\n", + " smiles = train.at[row,'SMILES']\n", + " jsonfile = train.at[row,'xtbjson']\n", + " input_dict = preprocessor(smiles, jsonfile='../data/json/'+jsonfile,train=True)\n", + " \n", + "print()\n", + "print(\"after pre-allocating\")\n", + "print(preprocessor.atom_tokenizer._data)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([2, 3, 4, 5, 6, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,\n", + " 7, 7], dtype=int32)" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Main input types for a SMILES-based prediction\n", + "smiles = 'C=C(C)CC(C)(C)C'\n", + "jsonfile = '../data/json/4921_0_bd_coord.json'\n", + "\n", + "# Atom types, as integer classes\n", + "preprocessor(smiles, jsonfile=jsonfile, train=True)['atom']" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([2, 3, 3, 2, 2, 2, 2, 3, 3, 3, 2, 2, 3, 3, 2, 2, 2, 2, 2, 3, 3, 3,\n", + " 2, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,\n", + " 3, 3], dtype=int32)" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Bond types, as integer classes\n", + "preprocessor(smiles, jsonfile=jsonfile, train=True)['bond']" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[ 0, 1],\n", + " [ 0, 8],\n", + " [ 0, 9],\n", + " [ 1, 0],\n", + " [ 1, 2],\n", + " [ 1, 3],\n", + " [ 2, 1],\n", + " [ 2, 10],\n", + " [ 2, 11],\n", + " [ 2, 12],\n", + " [ 3, 1],\n", + " [ 3, 4],\n", + " [ 3, 13],\n", + " [ 3, 14],\n", + " [ 4, 3],\n", + " [ 4, 5],\n", + " [ 4, 6],\n", + " [ 4, 7],\n", + " [ 5, 4],\n", + " [ 5, 15],\n", + " [ 5, 16],\n", + " [ 5, 17],\n", + " [ 6, 4],\n", + " [ 6, 18],\n", + " [ 6, 19],\n", + " [ 6, 20],\n", + " [ 7, 4],\n", + " [ 7, 21],\n", + " [ 7, 22],\n", + " [ 7, 23],\n", + " [ 8, 0],\n", + " [ 9, 0],\n", + " [10, 2],\n", + " [11, 2],\n", + " [12, 2],\n", + " [13, 3],\n", + " [14, 3],\n", + " [15, 5],\n", + " [16, 5],\n", + " [17, 5],\n", + " [18, 6],\n", + " [19, 6],\n", + " [20, 6],\n", + " [21, 7],\n", + " [22, 7],\n", + " [23, 7]], dtype=int32)" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# A connectivity array, where row i indicates bond i connects atom j to atom k\n", + "preprocessor(smiles, jsonfile=jsonfile, train=True)['connectivity']" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[-1.1438e-01, -2.1724e-01, -1.1700e-01, -7.1000e-02, -9.4000e-02,\n", + " 1.0410e+00, 3.0730e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 3.0767e+01, 9.0910e+00],\n", + " [ 2.3920e-02, -3.7200e-03, -1.7400e-01, -5.7000e-02, -1.1600e-01,\n", + " 1.0910e+00, 2.8850e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.7551e+01, 8.6080e+00],\n", + " [-9.1840e-02, -2.3884e-01, 4.7000e-02, 2.7000e-02, 3.7000e-02,\n", + " 1.0080e+00, 3.0840e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.2643e+01, 6.7840e+00],\n", + " [-6.6130e-02, -1.6850e-01, 2.6000e-02, -0.0000e+00, 1.3000e-02,\n", + " 1.0370e+00, 3.0290e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.1883e+01, 6.6580e+00],\n", + " [ 4.2450e-02, 5.1000e-03, -1.2000e-02, -2.6000e-02, -1.9000e-02,\n", + " 1.0810e+00, 2.8770e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 1.9968e+01, 6.3520e+00],\n", + " [-9.9180e-02, -2.4876e-01, 1.9000e-02, 2.2000e-02, 2.1000e-02,\n", + " 1.0150e+00, 3.0840e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.2623e+01, 6.7800e+00],\n", + " [-9.9770e-02, -2.4904e-01, 1.9000e-02, 1.5000e-02, 1.7000e-02,\n", + " 1.0130e+00, 3.0860e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.2641e+01, 6.7830e+00],\n", + " [-9.9470e-02, -2.4877e-01, 1.9000e-02, 1.9000e-02, 1.9000e-02,\n", + " 1.0140e+00, 3.0860e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.2574e+01, 6.7730e+00],\n", + " [ 3.0180e-02, 8.5080e-02, -1.3900e-01, -8.0000e-02, -1.1000e-01,\n", + " 9.7000e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5760e+00, 2.5100e+00],\n", + " [ 2.9980e-02, 8.4230e-02, -1.3800e-01, -8.9000e-02, -1.1300e-01,\n", + " 9.7000e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.6560e+00, 2.5490e+00],\n", + " [ 3.7540e-02, 8.9870e-02, -9.0000e-02, -8.3000e-02, -8.7000e-02,\n", + " 9.6200e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.4460e+00, 2.4460e+00],\n", + " [ 3.4440e-02, 8.7390e-02, -6.1000e-02, -5.5000e-02, -5.8000e-02,\n", + " 9.6600e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.4910e+00, 2.4680e+00],\n", + " [ 3.5130e-02, 8.8600e-02, -8.6000e-02, -7.2000e-02, -7.9000e-02,\n", + " 9.6500e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.3580e+00, 2.4010e+00],\n", + " [ 3.3330e-02, 9.1040e-02, -6.0000e-02, -6.8000e-02, -6.4000e-02,\n", + " 9.6700e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.4720e+00, 2.4590e+00],\n", + " [ 2.8670e-02, 8.6550e-02, -6.8000e-02, -6.1000e-02, -6.5000e-02,\n", + " 9.7100e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.4920e+00, 2.4690e+00],\n", + " [ 3.1100e-02, 8.4260e-02, -3.7000e-02, -6.8000e-02, -5.2000e-02,\n", + " 9.6900e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5180e+00, 2.4810e+00],\n", + " [ 3.0300e-02, 8.3440e-02, -2.1000e-02, -4.2000e-02, -3.2000e-02,\n", + " 9.7000e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5450e+00, 2.4950e+00],\n", + " [ 2.9660e-02, 8.2760e-02, -2.3000e-02, -4.9000e-02, -3.6000e-02,\n", + " 9.7000e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5530e+00, 2.4990e+00],\n", + " [ 3.0120e-02, 8.3360e-02, -4.2000e-02, -5.3000e-02, -4.8000e-02,\n", + " 9.7000e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5380e+00, 2.4920e+00],\n", + " [ 2.9860e-02, 8.3240e-02, -1.8000e-02, -4.0000e-02, -2.9000e-02,\n", + " 9.7000e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5450e+00, 2.4950e+00],\n", + " [ 3.1690e-02, 8.6520e-02, 1.2000e-02, -2.8000e-02, -8.0000e-03,\n", + " 9.6800e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.4480e+00, 2.4470e+00],\n", + " [ 3.2330e-02, 8.6770e-02, 4.0000e-03, -2.7000e-02, -1.2000e-02,\n", + " 9.6800e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.4920e+00, 2.4680e+00],\n", + " [ 3.0980e-02, 8.4200e-02, -3.9000e-02, -7.1000e-02, -5.5000e-02,\n", + " 9.6900e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5450e+00, 2.4950e+00],\n", + " [ 2.9070e-02, 8.2460e-02, -2.0000e-02, -4.3000e-02, -3.1000e-02,\n", + " 9.7100e-01, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,\n", + " 0.0000e+00, 0.0000e+00, 2.5610e+00, 2.5030e+00]],\n", + " dtype=float32)" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "preprocessor(smiles, jsonfile=jsonfile, train=True)['atom_xtb']" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([[1.9268622 , 1.3242947 ],\n", + " [0.9755401 , 1.0764849 ],\n", + " [0.976035 , 1.0775048 ],\n", + " [1.9268622 , 1.3242947 ],\n", + " [1.0250528 , 1.4998841 ],\n", + " [1.0109937 , 1.5060523 ],\n", + " [1.0250528 , 1.4998841 ],\n", + " [0.96929526, 1.0907905 ],\n", + " [0.9851119 , 1.0871836 ],\n", + " [0.9720007 , 1.0873462 ],\n", + " [1.0109937 , 1.5060523 ],\n", + " [0.9652852 , 1.5472038 ],\n", + " [0.9695576 , 1.0925564 ],\n", + " [0.9729345 , 1.0923398 ],\n", + " [0.9652852 , 1.5472038 ],\n", + " [0.9969557 , 1.5319772 ],\n", + " [1.0006814 , 1.5286028 ],\n", + " [0.9998898 , 1.5291462 ],\n", + " [0.9969557 , 1.5319772 ],\n", + " [0.98522764, 1.0879004 ],\n", + " [0.9861606 , 1.0879096 ],\n", + " [0.98609173, 1.0880784 ],\n", + " [1.0006814 , 1.5286028 ],\n", + " [0.98516583, 1.0881023 ],\n", + " [0.9858648 , 1.0878273 ],\n", + " [0.982679 , 1.0868458 ],\n", + " [0.9998898 , 1.5291462 ],\n", + " [0.98415387, 1.0871557 ],\n", + " [0.9851873 , 1.0883454 ],\n", + " [0.98518836, 1.0881969 ],\n", + " [0.9755401 , 1.0764849 ],\n", + " [0.976035 , 1.0775048 ],\n", + " [0.96929526, 1.0907905 ],\n", + " [0.9851119 , 1.0871836 ],\n", + " [0.9720007 , 1.0873462 ],\n", + " [0.9695576 , 1.0925564 ],\n", + " [0.9729345 , 1.0923398 ],\n", + " [0.98522764, 1.0879004 ],\n", + " [0.9861606 , 1.0879096 ],\n", + " [0.98609173, 1.0880784 ],\n", + " [0.98516583, 1.0881023 ],\n", + " [0.9858648 , 1.0878273 ],\n", + " [0.982679 , 1.0868458 ],\n", + " [0.98415387, 1.0871557 ],\n", + " [0.9851873 , 1.0883454 ],\n", + " [0.98518836, 1.0881969 ]], dtype=float32)" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "preprocessor(smiles, jsonfile=jsonfile, train=True)['bond_xtb']" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([-25.27425892, -25.68649081, -10.3364 , -5.1588 ])" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "preprocessor(smiles, jsonfile=jsonfile, train=True)['mol_xtb']" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "# Construct the tf.data pipeline. There's a lot of specifying data types and\n", + "# expected shapes for tensorflow to pre-allocate the necessary arrays. But \n", + "# essentially, this is responsible for calling the input constructor, batching \n", + "# together multiple molecules, and padding the resulting molecules so that all\n", + "# molecules in the same batch have the same number of atoms (we pad with zeros,\n", + "# hence why the atom and bond types above start with 1 as the unknown class)\n", + "\n", + "train_dataset = tf.data.Dataset.from_generator(\n", + " lambda: ((preprocessor(row.SMILES, '../data/json/'+row.xtbjson, train=True), row.YSI)\n", + " for i, row in ysi[ysi.SMILES.isin(train.SMILES)].iterrows()),\n", + " output_signature=(preprocessor.output_signature, tf.TensorSpec((), dtype=tf.float32)))\\\n", + " .cache().shuffle(buffer_size=200)\\\n", + " .padded_batch(batch_size=64)\\\n", + " .prefetch(tf.data.experimental.AUTOTUNE)\n", + "\n", + "\n", + "valid_dataset = tf.data.Dataset.from_generator(\n", + " lambda: ((preprocessor(row.SMILES, '../data/json/'+row.xtbjson, train=False), row.YSI)\n", + " for i, row in ysi[ysi.SMILES.isin(valid.SMILES)].iterrows()),\n", + " output_signature=(preprocessor.output_signature, tf.TensorSpec((), dtype=tf.float32)))\\\n", + " .cache()\\\n", + " .padded_batch(batch_size=64)\\\n", + " .prefetch(tf.data.experimental.AUTOTUNE)" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2022-02-01 14:49:06.063810: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)\n", + "2022-02-01 14:49:06.067276: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2300000000 Hz\n" + ] + } + ], + "source": [ + "inputs, outputs = next(train_dataset.as_numpy_iterator())" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[TensorShape([None, None, 8]), TensorShape([None, None, 8]), TensorShape([None, None, 2]), TensorShape([None, 8])]\n", + "[TensorShape([None, None, 8]), TensorShape([None, None, 8]), TensorShape([None, None, 2]), TensorShape([None, 8])]\n", + "[TensorShape([None, None, 8]), TensorShape([None, None, 8]), TensorShape([None, None, 2]), TensorShape([None, 8])]\n" + ] + } + ], + "source": [ + "## Define the keras model\n", + "from tensorflow.keras import layers\n", + "\n", + "# Input layers\n", + "atom = layers.Input(shape=[None], dtype=tf.int64, name='atom')\n", + "bond = layers.Input(shape=[None], dtype=tf.int64, name='bond')\n", + "connectivity = layers.Input(shape=[None, 2], dtype=tf.int64, name='connectivity')\n", + "atom_xtb = layers.Input(shape=[None,None], dtype=tf.float64, name=\"atom_xtb\")\n", + "bond_xtb = layers.Input(shape=[None,None], dtype=tf.float64, name=\"bond_xtb\")\n", + "\n", + "num_features = 8 # Controls the size of the model\n", + "\n", + "# Convert from a single integer defining the atom state to a vector\n", + "# of weights associated with that class\n", + "atom_state = layers.Embedding(preprocessor.atom_classes, num_features,\n", + " name='atom_embedding', mask_zero=True)(atom)\n", + "\n", + "# Ditto with the bond state\n", + "bond_state = layers.Embedding(preprocessor.bond_classes, num_features,\n", + " name='bond_embedding', mask_zero=True)(bond)\n", + "\n", + "# Here we use our first nfp layer. This is an attention layer that looks at\n", + "# the atom and bond states and reduces them to a single, graph-level vector. \n", + "# mum_heads * units has to be the same dimension as the atom / bond dimension\n", + "global_state = nfp.GlobalUpdate(units=8, num_heads=1)([atom_state, bond_state, connectivity])\n", + "\n", + "for _ in range(3): # Do the message passing\n", + " new_bond_state = nfp.EdgeUpdate()([atom_state, bond_state, connectivity, global_state])\n", + " bond_state = layers.Add()([bond_state, new_bond_state])\n", + " \n", + " new_atom_state = nfp.NodeUpdate()([atom_state, bond_state, connectivity, global_state])\n", + " atom_state = layers.Add()([atom_state, new_atom_state])\n", + " \n", + " new_global_state = nfp.GlobalUpdate(units=8, num_heads=1)(\n", + " [atom_state, bond_state, connectivity, global_state]) \n", + " global_state = layers.Add()([global_state, new_global_state])\n", + "\n", + " \n", + "# Since the final prediction is a single, molecule-level property (YSI), we \n", + "# reduce the last global state to a single prediction.\n", + "ysi_prediction = layers.Dense(1)(global_state)\n", + "\n", + "# Construct the tf.keras model\n", + "model = tf.keras.Model([atom, bond, connectivity, atom_xtb, bond_xtb], [ysi_prediction])" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Epoch 1/100\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/projects/rlmolecule/svss/envs/tf27_gpu/lib/python3.8/site-packages/tensorflow/python/keras/engine/functional.py:592: UserWarning: Input dict contained keys ['bond_indices', 'mol_xtb'] which did not match any model input. They will be ignored by the model.\n", + " warnings.warn(\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "3/3 [==============================] - 7s 1s/step - loss: 89.6957 - val_loss: 104.1403\n", + "Epoch 2/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 90.0728 - val_loss: 103.8789\n", + "Epoch 3/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 87.5763 - val_loss: 103.4945\n", + "Epoch 4/100\n", + "3/3 [==============================] - 0s 30ms/step - loss: 89.2564 - val_loss: 102.8956\n", + "Epoch 5/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 92.3957 - val_loss: 101.8961\n", + "Epoch 6/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 91.9479 - val_loss: 100.0637\n", + "Epoch 7/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 86.0807 - val_loss: 95.5032\n", + "Epoch 8/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 80.6203 - val_loss: 83.5468\n", + "Epoch 9/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 68.8767 - val_loss: 78.0933\n", + "Epoch 10/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 64.4152 - val_loss: 81.0304\n", + "Epoch 11/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 66.5636 - val_loss: 81.1164\n", + "Epoch 12/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 70.7887 - val_loss: 77.6578\n", + "Epoch 13/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 62.3534 - val_loss: 78.6554\n", + "Epoch 14/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 66.7106 - val_loss: 79.3879\n", + "Epoch 15/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 66.4846 - val_loss: 78.0953\n", + "Epoch 16/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 64.5384 - val_loss: 77.2566\n", + "Epoch 17/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 65.2349 - val_loss: 77.4973\n", + "Epoch 18/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 63.1854 - val_loss: 77.5039\n", + "Epoch 19/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 62.0618 - val_loss: 76.8574\n", + "Epoch 20/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 59.5350 - val_loss: 76.9440\n", + "Epoch 21/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 60.3808 - val_loss: 76.7679\n", + "Epoch 22/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 59.3118 - val_loss: 76.6795\n", + "Epoch 23/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 60.6851 - val_loss: 76.8553\n", + "Epoch 24/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 64.9050 - val_loss: 77.3786\n", + "Epoch 25/100\n", + "3/3 [==============================] - 0s 30ms/step - loss: 63.0165 - val_loss: 77.6968\n", + "Epoch 26/100\n", + "3/3 [==============================] - 0s 30ms/step - loss: 68.3085 - val_loss: 77.0120\n", + "Epoch 27/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 60.8650 - val_loss: 75.8382\n", + "Epoch 28/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 59.2354 - val_loss: 75.5865\n", + "Epoch 29/100\n", + "3/3 [==============================] - 0s 34ms/step - loss: 58.7827 - val_loss: 76.2220\n", + "Epoch 30/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 61.2479 - val_loss: 75.3012\n", + "Epoch 31/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 57.6180 - val_loss: 74.2274\n", + "Epoch 32/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 61.5462 - val_loss: 74.1011\n", + "Epoch 33/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 59.8214 - val_loss: 73.1256\n", + "Epoch 34/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 60.0742 - val_loss: 72.2864\n", + "Epoch 35/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 55.5559 - val_loss: 71.3521\n", + "Epoch 36/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 55.4260 - val_loss: 69.8589\n", + "Epoch 37/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 56.1927 - val_loss: 67.8273\n", + "Epoch 38/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 57.9371 - val_loss: 65.4359\n", + "Epoch 39/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 53.2332 - val_loss: 62.1518\n", + "Epoch 40/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 51.6943 - val_loss: 58.1403\n", + "Epoch 41/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 42.7877 - val_loss: 53.5165\n", + "Epoch 42/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 43.6861 - val_loss: 48.0897\n", + "Epoch 43/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 39.0778 - val_loss: 41.2808\n", + "Epoch 44/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 34.2861 - val_loss: 36.9258\n", + "Epoch 45/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 30.7535 - val_loss: 32.1651\n", + "Epoch 46/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 24.4201 - val_loss: 34.2050\n", + "Epoch 47/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 24.3964 - val_loss: 39.9840\n", + "Epoch 48/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 26.6450 - val_loss: 36.7720\n", + "Epoch 49/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 26.0261 - val_loss: 32.2325\n", + "Epoch 50/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 19.7276 - val_loss: 31.0926\n", + "Epoch 51/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 20.7063 - val_loss: 30.7724\n", + "Epoch 52/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 21.2172 - val_loss: 30.6167\n", + "Epoch 53/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 20.5296 - val_loss: 31.8409\n", + "Epoch 54/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.6064 - val_loss: 31.7600\n", + "Epoch 55/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 19.1202 - val_loss: 30.8431\n", + "Epoch 56/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.8930 - val_loss: 29.1852\n", + "Epoch 57/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.3020 - val_loss: 29.3147\n", + "Epoch 58/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 20.2255 - val_loss: 29.3093\n", + "Epoch 59/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 17.7891 - val_loss: 29.7951\n", + "Epoch 60/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 19.3988 - val_loss: 31.9735\n", + "Epoch 61/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 19.0405 - val_loss: 31.2371\n", + "Epoch 62/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.0995 - val_loss: 28.9266\n", + "Epoch 63/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 17.5320 - val_loss: 30.0275\n", + "Epoch 64/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.7064 - val_loss: 34.7176\n", + "Epoch 65/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 19.7782 - val_loss: 32.0842\n", + "Epoch 66/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 21.4557 - val_loss: 29.7688\n", + "Epoch 67/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 18.7506 - val_loss: 32.1488\n", + "Epoch 68/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 18.3865 - val_loss: 36.3625\n", + "Epoch 69/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 21.7615 - val_loss: 29.2937\n", + "Epoch 70/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 15.3927 - val_loss: 33.3881\n", + "Epoch 71/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.7074 - val_loss: 39.4471\n", + "Epoch 72/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 22.9105 - val_loss: 34.4473\n", + "Epoch 73/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 19.7357 - val_loss: 30.1155\n", + "Epoch 74/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 15.8764 - val_loss: 29.6672\n", + "Epoch 75/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.1005 - val_loss: 28.2699\n", + "Epoch 76/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 16.7261 - val_loss: 28.0326\n", + "Epoch 77/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.1611 - val_loss: 28.7118\n", + "Epoch 78/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 18.0240 - val_loss: 29.4046\n", + "Epoch 79/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.2178 - val_loss: 28.8814\n", + "Epoch 80/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 15.2737 - val_loss: 28.4953\n", + "Epoch 81/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 15.9951 - val_loss: 28.1290\n", + "Epoch 82/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 17.0696 - val_loss: 27.5496\n", + "Epoch 83/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.6385 - val_loss: 28.6073\n", + "Epoch 84/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.5023 - val_loss: 28.5329\n", + "Epoch 85/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 15.6316 - val_loss: 29.1235\n", + "Epoch 86/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.0495 - val_loss: 27.3807\n", + "Epoch 87/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 16.3476 - val_loss: 26.3223\n", + "Epoch 88/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 15.3556 - val_loss: 26.6821\n", + "Epoch 89/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 14.6263 - val_loss: 29.0494\n", + "Epoch 90/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.8060 - val_loss: 28.3243\n", + "Epoch 91/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.4821 - val_loss: 27.3747\n", + "Epoch 92/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 17.3160 - val_loss: 30.0814\n", + "Epoch 93/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.6148 - val_loss: 27.0652\n", + "Epoch 94/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 15.7225 - val_loss: 27.2585\n", + "Epoch 95/100\n", + "3/3 [==============================] - 0s 34ms/step - loss: 16.0970 - val_loss: 26.4869\n", + "Epoch 96/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 15.3523 - val_loss: 26.0890\n", + "Epoch 97/100\n", + "3/3 [==============================] - 0s 32ms/step - loss: 16.2900 - val_loss: 26.5539\n", + "Epoch 98/100\n", + "3/3 [==============================] - 0s 31ms/step - loss: 13.7786 - val_loss: 28.4712\n", + "Epoch 99/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 16.6781 - val_loss: 32.7345\n", + "Epoch 100/100\n", + "3/3 [==============================] - 0s 33ms/step - loss: 18.4583 - val_loss: 28.7672\n" + ] + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model.compile(loss='mae', optimizer=tf.keras.optimizers.Adam(1E-3))\n", + "\n", + "# Fit the model. The first epoch is slower, since it needs to cache\n", + "# the preprocessed molecule inputs\n", + "model.fit(train_dataset, validation_data=valid_dataset, epochs=100)" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "# Here, we create a test dataset that doesn't assume we know the values for the YSI\n", + "\n", + "test_dataset = tf.data.Dataset.from_generator(\n", + " lambda: (preprocessor(row.SMILES, '../data/json/'+row.xtbjson, train=False)\n", + " for i, row in test.iterrows()),\n", + " output_signature=preprocessor.output_signature)\\\n", + " .padded_batch(batch_size=64)\\\n", + " .prefetch(tf.data.experimental.AUTOTUNE)" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "16.83903667831421" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Here are the predictions on the test set\n", + "test_predictions = model.predict(test_dataset)\n", + "test_db_values = ysi.set_index('SMILES').reindex(test.SMILES).YSI.values\n", + "\n", + "np.abs(test_db_values - test_predictions.flatten()).mean()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "tf27_gpu", + "language": "python", + "name": "tf27_gpu" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.12" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/nfp/preprocessing/features.py b/nfp/preprocessing/features.py index 8d90783..3c0018c 100644 --- a/nfp/preprocessing/features.py +++ b/nfp/preprocessing/features.py @@ -104,11 +104,3 @@ def bond_features_v3(bond, flipped=False): end_atom, ) ) - - -def bond_features_wbo(start_atom, end_atom, bondatoms): - - start_atom_symbol = bondatoms[0].GetSymbol() - end_atom_symbol = bondatoms[1].GetSymbol() - - return str((start_atom_symbol, end_atom_symbol)) diff --git a/nfp/preprocessing/xtb_preprocessor.py b/nfp/preprocessing/xtb_preprocessor.py index f337770..8b4614c 100644 --- a/nfp/preprocessing/xtb_preprocessor.py +++ b/nfp/preprocessing/xtb_preprocessor.py @@ -1,5 +1,8 @@ import json from typing import Callable, Dict, Hashable, Optional, List +from sklearn.preprocessing import StandardScaler +from rdkit.Geometry import Point3D +from rdkit.Chem import AllChem import networkx as nx import numpy as np @@ -11,7 +14,10 @@ tf = None from nfp.preprocessing import features -from nfp.preprocessing.mol_preprocessor import MolPreprocessor, SmilesPreprocessor +from nfp.preprocessing.mol_preprocessor import ( + MolPreprocessor, + SmilesPreprocessor, +) class xTBPreprocessor(MolPreprocessor): @@ -22,15 +28,15 @@ def __init__( xtb_atom_features: Optional[List[str]] = None, xtb_bond_features: Optional[List[str]] = None, xtb_mol_features: Optional[List[str]] = None, - cutoff: float = 0.3, + scaler: bool = True, **kwargs ): super(xTBPreprocessor, self).__init__(*args, **kwargs) self.explicit_hs = explicit_hs - self.cutoff = cutoff + self.scaler = scaler # update only bond features as we dont use rdkit - self.bond_features = features.bond_features_wbo + self.bond_features = features.bond_features_v3 if xtb_atom_features is None: self.xtb_atom_features = [ @@ -81,59 +87,76 @@ def create_nx_graph( for atom in mol.GetAtoms(): atom_data = { "atom": atom, + "atom_index": atom.GetIdx(), "atom_xtb": [ json_data[prop][atom.GetIdx()] for prop in self.xtb_atom_features ], } g.add_node(atom.GetIdx(), **atom_data) - # add edges based on wilberg bond orders. - wbo = np.array(json_data["Wiberg matrix"]) - edges_to_add = ( - (i, j) - for i in range(len(wbo)) - for j in range(len(wbo)) - if wbo[i][j] > self.cutoff - ) - - for i, j in edges_to_add: - + for bond in mol.GetBonds(): edge_data = { - "bondatoms": (mol.GetAtomWithIdx(i), mol.GetAtomWithIdx(j)), - "bond_xtb": [json_data[prop][i][j] for prop in self.xtb_bond_features], + "bondatoms": (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()), + "bond": bond, + "bond_index": bond.GetIdx(), + "bond_xtb": [ + json_data[prop][bond.GetBeginAtomIdx()][bond.GetEndAtomIdx()] + for prop in self.xtb_bond_features + ], } - - g.add_edge(i, j, **edge_data) + g.add_edge(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), **edge_data) return nx.DiGraph(g) def get_edge_features( self, edge_data: list, max_num_edges ) -> Dict[str, np.ndarray]: - + bond_indices = np.zeros(max_num_edges, dtype=self.output_dtype) + bond_atom_indices = np.zeros((max_num_edges, 2), dtype=self.output_dtype) bond_feature_matrix = np.zeros(max_num_edges, dtype=self.output_dtype) bond_feature_matrix_xtb = np.zeros( (max_num_edges, len(self.xtb_bond_features)), dtype="float32" ) for n, (start_atom, end_atom, bond_dict) in enumerate(edge_data): - bond_feature_matrix[n] = self.bond_tokenizer( - self.bond_features(start_atom, end_atom, bond_dict["bondatoms"]) - ) + bond_indices[n] = bond_dict["bond_index"] + bond_atom_indices[n] = (start_atom, end_atom) + if bond_dict["bond"] is not None: + bond_feature_matrix[n] = self.bond_tokenizer( + self.bond_features(bond_dict["bond"]) + ) + else: + bond_feature_matrix[n] = 0 bond_feature_matrix_xtb[n] = bond_dict["bond_xtb"] - return {"bond": bond_feature_matrix, "bond_xtb": bond_feature_matrix_xtb} + if self.scaler: + scaler = StandardScaler() + bond_feature_matrix_xtb = scaler.fit_transform(bond_feature_matrix_xtb) + return { + "bond": bond_feature_matrix, + "bond_xtb": bond_feature_matrix_xtb, + "bond_indices": bond_indices, + "bond_atom_indices": bond_atom_indices, + } def get_node_features( self, node_data: list, max_num_nodes: int ) -> Dict[str, np.ndarray]: + atom_indices = np.zeros(max_num_nodes, dtype=self.output_dtype) node_features = super().get_node_features(node_data, max_num_nodes) node_features["atom_xtb"] = np.zeros( [max_num_nodes, len(self.xtb_atom_features)], dtype="float32" ) + for n, atom_dict in node_data: + atom_indices[n] = atom_dict["atom_index"] node_features["atom_xtb"][n] = atom_dict["atom_xtb"] - return node_features + + if self.scaler: + scaler = StandardScaler() + node_features["atom_xtb"] = scaler.fit_transform(node_features["atom_xtb"]) + + return {"atom_indices": atom_indices, **node_features} def get_graph_features(self, graph_data: dict) -> Dict[str, np.ndarray]: return {"mol_xtb": np.asarray(graph_data["mol_xtb"])} @@ -147,15 +170,27 @@ def output_signature(self) -> Dict[str, tf.TensorSpec]: output_signature["bond_xtb"] = tf.TensorSpec( shape=(None, None), dtype="float32" ) + output_signature["bond_indices"] = tf.TensorSpec( + shape=(None,), dtype=self.output_dtype + ) + output_signature["bond_atom_indices"] = tf.TensorSpec( + shape=(None, None), dtype=self.output_dtype + ) + output_signature["atom_indices"] = tf.TensorSpec( + shape=(None,), dtype=self.output_dtype + ) output_signature["mol_xtb"] = tf.TensorSpec(shape=(None,), dtype="float32") return output_signature @property def padding_values(self) -> Dict[str, tf.constant]: padding_values = super().padding_values - padding_values["atom_xtb"] = tf.constant(np.nan, dtype="float32") - padding_values["bond_xtb"] = tf.constant(np.nan, dtype="float32") - padding_values["mol_xtb"] = tf.constant(np.nan, dtype="float32") + padding_values["atom_xtb"] = tf.constant(0, dtype="float32") + padding_values["bond_xtb"] = tf.constant(0, dtype="float32") + padding_values["bond_indices"] = tf.constant(0, dtype=self.output_dtype) + padding_values["bond_atom_indices"] = tf.constant(0, dtype=self.output_dtype) + padding_values["atom_indices"] = tf.constant(0, dtype=self.output_dtype) + padding_values["mol_xtb"] = tf.constant(0, dtype="float32") return padding_values @property @@ -169,13 +204,31 @@ def tfrecord_features(self) -> Dict[str, tf.io.FixedLenFeature]: ) tfrecord_features["bond_xtb"] = tf.io.FixedLenFeature( [], - dtype=self.output_dtype + dtype="float32" if len(self.output_signature["bond_xtb"].shape) == 0 else tf.string, ) - tfrecord_features["mol_xtb"] = tf.io.FixedLenFeature( + tfrecord_features["bond_indices"] = tf.io.FixedLenFeature( + [], + dtype=self.output_dtype + if len(self.output_signature["bond_indices"].shape) == 0 + else tf.string, + ) + tfrecord_features["bond_atom_indices"] = tf.io.FixedLenFeature( + [], + dtype=self.output_dtype + if len(self.output_signature["bond_atom_indices"].shape) == 0 + else tf.string, + ) + tfrecord_features["atom_indices"] = tf.io.FixedLenFeature( [], dtype=self.output_dtype + if len(self.output_signature["atom_indices"].shape) == 0 + else tf.string, + ) + tfrecord_features["mol_xtb"] = tf.io.FixedLenFeature( + [], + dtype="float32" if len(self.output_signature["mol_xtb"].shape) == 0 else tf.string, ) @@ -184,3 +237,134 @@ def tfrecord_features(self) -> Dict[str, tf.io.FixedLenFeature]: class xTBSmilesPreprocessor(SmilesPreprocessor, xTBPreprocessor): pass + + +class xTBWBOPreprocessor(xTBPreprocessor): + def __init__(self, cutoff: int = 0.3, **kwargs): + self.cutoff = cutoff + super(xTBWBOPreprocessor, self).__init__(**kwargs) + + def create_nx_graph( + self, mol: rdkit.Chem.Mol, jsonfile: str, **kwargs + ) -> nx.DiGraph: + + with open(jsonfile, "r") as f: + json_data = json.load(f) + + # add hydrogens as wbo contains hydrogens and add xtb features to the graphs + mol_data = {"mol_xtb": [json_data[prop] for prop in self.xtb_mol_features]} + + g = nx.Graph(mol=mol, **mol_data) + for atom in mol.GetAtoms(): + atom_data = { + "atom": atom, + "atom_index": atom.GetIdx(), + "atom_xtb": [ + json_data[prop][atom.GetIdx()] for prop in self.xtb_atom_features + ], + } + g.add_node(atom.GetIdx(), **atom_data) + + # add edges based on wilberg bond orders. + wbo = np.array(json_data["Wiberg matrix"]) + edges_to_add = ( + (i, j) + for i in range(len(wbo)) + for j in range(len(wbo)) + if wbo[i][j] > self.cutoff and j > i + ) + + max_bonds = len(mol.GetBonds()) - 1 + for i, j in edges_to_add: + if mol.GetBondBetweenAtoms(i, j) is not None: + idx = mol.GetBondBetweenAtoms(i, j).GetIdx() + else: + max_bonds += 1 + idx = max_bonds + edge_data = { + "bondatoms": (mol.GetAtomWithIdx(i), mol.GetAtomWithIdx(j)), + "bond": mol.GetBondBetweenAtoms(i, j), + "bond_index": idx, + "bond_xtb": [json_data[prop][i][j] for prop in self.xtb_bond_features], + } + + g.add_edge(i, j, **edge_data) + + return nx.DiGraph(g) + + +class xTBSmilesWBOPreprocessor(SmilesPreprocessor, xTBWBOPreprocessor): + pass + + +class xTB3DPreprocessor(xTBPreprocessor): + def __init__(self, n_neighbors: int = 100, distcutoff: int = 5, **kwargs): + self.n_neighbors = n_neighbors + self.distcutoff = distcutoff + super(xTB3DPreprocessor, self).__init__(**kwargs) + + def create_nx_graph( + self, mol: rdkit.Chem.Mol, jsonfile: str, **kwargs + ) -> nx.DiGraph: + + with open(jsonfile, "r") as f: + json_data = json.load(f) + + # add hydrogens as wbo contains hydrogens and add xtb features to the graphs + mol_data = {"mol_xtb": [json_data[prop] for prop in self.xtb_mol_features]} + + g = nx.Graph(mol=mol, **mol_data) + for atom in mol.GetAtoms(): + atom_data = { + "atom": atom, + "atom_index": atom.GetIdx(), + "atom_xtb": [ + json_data[prop][atom.GetIdx()] for prop in self.xtb_atom_features + ], + } + g.add_node(atom.GetIdx(), **atom_data) + + # add edges based on neighbours from coordinates. + distance_matrix = np.array(json_data["bond_dist"]) + + edges_to_add = [] + for n, atom in enumerate(mol.GetAtoms()): + # if n_neighbors is greater than total atoms, then each atom is a + # neighbor. + if (self.n_neighbors + 1) > len(mol.GetAtoms()): + neighbor_end_index = len(mol.GetAtoms()) + else: + neighbor_end_index = self.n_neighbors + 1 + + distance_atom = distance_matrix[n, :] + cutoff_end_index = distance_atom[distance_atom < self.distcutoff].size + + end_index = min(neighbor_end_index, cutoff_end_index) + neighbor_inds = distance_matrix[n, :].argsort()[1:end_index] + + if len(neighbor_inds) == 0: + neighbor_inds = [n] + for neighbor in neighbor_inds: + edges_to_add.append((int(n), int(neighbor))) + + max_bonds = len(mol.GetBonds()) - 1 + for i, j in edges_to_add: + if mol.GetBondBetweenAtoms(i, j) is not None: + idx = mol.GetBondBetweenAtoms(i, j).GetIdx() + else: + max_bonds += 1 + idx = max_bonds + edge_data = { + "bondatoms": (mol.GetAtomWithIdx(i), mol.GetAtomWithIdx(j)), + "bond": mol.GetBondBetweenAtoms(i, j), + "bond_index": idx, + "bond_xtb": [json_data[prop][i][j] for prop in self.xtb_bond_features], + } + + g.add_edge(i, j, **edge_data) + + return nx.DiGraph(g) + + +class xTBSmiles3DPreprocessor(SmilesPreprocessor, xTB3DPreprocessor): + pass diff --git a/setup.cfg b/setup.cfg index 21924e0..aceca77 100644 --- a/setup.cfg +++ b/setup.cfg @@ -15,4 +15,5 @@ install_requires = pymatgen = pymatgen tf = tensorflow>=2.4 rdkit = rdkit-pypi -test = pytest \ No newline at end of file +test = pytest +scikit = scikit-learn diff --git a/tests/preprocessing/test_xtb_preprocessor.py b/tests/preprocessing/test_xtb_preprocessor.py index 040841a..de0a03c 100644 --- a/tests/preprocessing/test_xtb_preprocessor.py +++ b/tests/preprocessing/test_xtb_preprocessor.py @@ -2,7 +2,7 @@ import pytest import tensorflow as tf -from nfp.preprocessing.xtb_preprocessor import xTBSmilesPreprocessor +from nfp.preprocessing.xtb_preprocessor import xTBSmilesWBOPreprocessor dir_path = os.path.dirname(os.path.realpath(__file__)) @@ -28,7 +28,7 @@ def get_2d_smiles_json(): def test_xtb_smiles_preprocessor(get_2d_smiles_json): train, train_json, test, test_json = get_2d_smiles_json - preprocessor = xTBSmilesPreprocessor(explicit_hs=True) + preprocessor = xTBSmilesWBOPreprocessor(explicit_hs=True) inputs = [ preprocessor(smiles, jsonfile, train=True) for smiles, jsonfile in zip(train, train_json) @@ -67,7 +67,7 @@ def test_xtb_batching(get_2d_smiles_json): train, train_json, test, test_json = get_2d_smiles_json - preprocessor = xTBSmilesPreprocessor(explicit_hs=True) + preprocessor = xTBSmilesWBOPreprocessor(explicit_hs=True) inputs = ( preprocessor(smiles, jsonfile, train=True)