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Shree changes #18

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33bcc8b
1. xtb_preprocessing : creates a graph object with xtb features
shreesowndarya Jan 3, 2022
4d0a4b0
1. xtb_preprocessing : creates a graph object with xtb features 2. fe…
shreesowndarya Jan 3, 2022
e115dd8
Merge branch 'shree_changes' of https://github.com/shreesowndarya/nfp…
shreesowndarya Jan 3, 2022
b52589b
1. adding in examples for xtb json file
shreesowndarya Jan 3, 2022
6d95c46
1. updated to Mol Preprossor
shreesowndarya Jan 4, 2022
d58f690
Merge branch 'master' into shree_changes
pstjohn Jan 4, 2022
b238a14
1. making different classes.
shreesowndarya Jan 4, 2022
df5c9dd
edits to the xtb test, a couple minor edits to the xtb and preprocess…
pstjohn Jan 4, 2022
4b5ce64
Updating mol features, adding in bond distance and other features
shreesowndarya Jan 6, 2022
452b416
Corrections to if else block
shreesowndarya Jan 6, 2022
8ee0e54
Corrections to if else block
shreesowndarya Jan 6, 2022
ced8ab4
Merge branch 'shree_changes' of https://github.com/shreesowndarya/nfp…
shreesowndarya Jan 6, 2022
c6e60c8
Correct test_1 for test
shreesowndarya Jan 6, 2022
f5abca0
Correct test_1
shreesowndarya Jan 6, 2022
2f9b73c
I think I removed >>>>>> Head
shreesowndarya Jan 6, 2022
bc04dc6
test corrections
shreesowndarya Jan 6, 2022
2c85d55
As an array graph_features
shreesowndarya Jan 6, 2022
4a97653
Update test_xtb_preprocessor.py
pstjohn Jan 6, 2022
d9b34fd
Merge branch 'NREL:master' into shree_changes
shreesowndarya Jan 31, 2022
11010db
bond index for xtb preprocessing
shreesowndarya Jan 31, 2022
debfc3c
Merge branches 'shree_changes', 'shree_changes', 'shree_changes' and …
shreesowndarya Jan 31, 2022
88c27d5
bond index for xTB
shreesowndarya Jan 31, 2022
69fd693
Adding in example with xtb json
shreesowndarya Feb 1, 2022
3b5a0d4
Preprocessing based on 3D distances from xTB. Graphs created based on…
shreesowndarya Mar 7, 2022
56e5567
Tokenizing only bonds with are actually there. Other 0
shreesowndarya Mar 7, 2022
d2852b1
Directly taking in bond_distance.
shreesowndarya Mar 7, 2022
86c91c9
Fixing tests for scikit learn
shreesowndarya Mar 8, 2022
732fd8d
reworking Rdkit, WBO and 3D
shreesowndarya Mar 8, 2022
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2 changes: 1 addition & 1 deletion .github/workflows/run_tests_and_deploy.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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/
Expand Down
1 change: 1 addition & 0 deletions data/json/100_0_bd_coord.json
Original file line number Diff line number Diff line change
@@ -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, 0.12210884], [-0.02040957, 0.01014487, 0.11756452], [-0.02688531, -0.11019066, -0.03841985], [-0.06568327, 0.08547965, -0.06321717], [0.03927454, -0.05421878, 0.04019709]], "atomic quadrupole moments": [[0.45073569, 0.13488674, -0.2253818, -0.13313573, -0.024311, -0.22535389], [0.15212817, 0.05202112, -0.06668243, -0.05153045, -0.04516526, -0.08544574], [-0.01035342, 0.01239493, -0.0550147, -0.00928806, 0.01155733, 0.06536813], [-0.0102008, 0.01665969, 0.05078307, -0.0096492, 0.03925908, -0.04058226], [0.01397615, -0.03782355, 0.00743307, 0.02618576, -0.04900991, -0.02140922], [0.02485391, -0.06855809, 0.01051792, 0.04801844, -0.07661588, -0.03537183]], "number of molecular orbitals": 12, "number of electrons": 14, "number of unpaired electrons": 0, "orbital energies/eV": [-18.74525139, -16.82362327, -15.4445109, -14.27070539, -14.12950699, -12.43762235, -11.31476501, 1.78633138, 3.50205074, 4.61751069, 5.35926582, 6.65546839], "fractional occupation": [2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0, 0.0], "program call": "xtb /tmp/scratch/tmprdcriv1z/100_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmprdcriv1z/100_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole module/D": 1.915, "Total charge": 0, "Transition dipole module/D": NaN, "HOMO": -11.3148, "LUMO": 1.7863, "HOMO occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [0.17511, -0.56235, 0.00888, 0.00888, 0.03301, 0.33647], "cm5 charges": [0.04962, -0.78428, 0.06653, 0.06653, 0.09348, 0.50812], "FUKUI+": [-0.001, -0.269, -0.145, -0.145, -0.159, -0.281], "FUKUI-": [0.043, -0.311, -0.239, -0.239, -0.14, -0.113], "FUKUIrad": [0.021, -0.29, -0.192, -0.192, -0.149, -0.197], "s proportion": [0.963, 1.685, 0.991, 0.991, 0.967, 0.664], "p proportion": [2.862, 4.877, 0.0, 0.0, 0.0, 0.0], "d proportion": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "Fermi-level/eV": -4.7642, "Coordination numbers": [3.623, 1.655, 0.924, 0.924, 0.925, 0.805], "Dispersion coefficient C6": [20.312, 21.535, 2.652, 2.652, 2.242, 0.765], "Total dispersion C6": 216.956274, "Total dispersion C8": 4156.459374, "Polarizability alpha": [6.496, 6.264, 2.547, 2.547, 2.342, 1.374], "Total polarizability alpha": 21.569032, "Wiberg matrix": [[0.0, 1.0104095712218268, 0.980986802719205, 0.9809867987816954, 0.9833139260953622, 0.0], [1.0104095712218268, 0.0, 0.0, 0.0, 0.0, 0.9066229827655317], [0.980986802719205, 0.0, 0.0, 0.0, 0.0, 0.0], [0.9809867987816954, 0.0, 0.0, 0.0, 0.0, 0.0], [0.9833139260953622, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.9066229827655317, 0.0, 0.0, 0.0, 0.0]], "Born radii": [], "Atomic SASAs": [], "Solvent H bonds": [], "Total SASA": NaN, "Total FOD": 0.0, "FOD": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "FOD s proportion": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "FOD p proportion": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "FOD d proportion": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "coordinates": [["-0.36156098405244", "0.03241861135337", "-0.00999961121014"], ["0.97602946096338", "0.34725736674979", "-0.30841528842192"], ["-0.56727117735480", "0.11339347100597", "1.06295456465381"], ["-0.62586435571286", "-0.97541463364512", "-0.34840787729957"], ["-0.97617832386686", "0.75576701890605", "-0.54251712413124"], ["1.55484538002358", "-0.27342383437007", "0.14638533640907"]], "bond_dist": [[0.0, 1.4061733737000397, 1.0954927087973432, 1.0954927094932705, 1.0883759895721818, 1.9469486910853686], [1.4061733737000397, 0.0, 2.0777691055289873, 2.077769098744945, 2.0081830196819945, 0.9628689578170828], [1.0954927087973432, 2.0777691055289873, 0.0, 1.7835022264804177, 1.7769040978625414, 2.3437374983139656], [1.0954927094932705, 2.077769098744945, 1.7835022264804177, 0.0, 1.7769041026794776, 2.343737689703061], [1.0883759895721818, 2.0081830196819945, 1.7769040978625414, 1.7769041026794776, 0.0, 2.817783065152639], [1.9469486910853686, 0.9628689578170828, 2.3437374983139656, 2.343737689703061, 2.817783065152639, 0.0]]}
1 change: 1 addition & 0 deletions data/json/110758_0_bd_coord.json

Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions data/json/11574_0_bd_coord.json
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"total energy": -20.78343624, "HOMO-LUMO gap/eV": 5.12578821, "electronic energy": -21.00687926, "dipole": [0.17038058, 0.78624238, -0.061013], "partial charges": [-0.10464474, -0.08649046, 0.35580053, -0.40166845, -0.27071411, 0.03365612, 0.05317237, 0.05317236, 0.04387092, 0.06609532, 0.0660953, 0.06787604, 0.06188945, 0.06188934], "atomic dipole moments": [[0.10270816, 0.0767844, -0.01156068], [0.01334163, -0.10313698, 0.00568029], [0.14311391, 0.06893269, -0.01369237], [-0.00925613, 0.19255032, -0.01162352], [0.04026734, -0.23953563, 0.01258836], [-0.23446949, 0.10459536, 0.00862047], [0.00682079, -0.06946187, 0.106053], [-0.0063598, -0.0823195, -0.09644566], [-0.1016467, 0.07000985, 0.00217089], [0.00873312, 0.08413323, 0.09889386], [-0.0047984, 0.07093332, -0.10899586], [0.08107744, 0.09604843, -0.01137642], [-6.386e-05, -0.08102022, -0.09931531], [0.01342422, -0.06786239, 0.10789946]], "atomic quadrupole moments": [[0.14853063, 0.18109087, -0.00562168, -0.03068372, -0.02071453, -0.14290895], [0.21665435, -0.00316123, 0.03128658, -0.0302411, -0.01772019, -0.24794092], [-0.13728146, 0.14996111, -0.32058406, 0.02950661, 0.03994987, 0.45786551], [-0.11265375, 0.01270188, -0.08516344, 0.01955642, 0.01729173, 0.19781719], [0.07727169, -0.03611433, 0.00862408, -0.00837834, -0.00370043, -0.08589577], [0.42693927, -0.30141819, -0.13760545, -0.02755973, 0.00991144, -0.28933382], [-0.03265749, 0.00447207, -0.0164605, 0.01601381, -0.05376602, 0.04911799], [-0.03558012, 0.01044519, -0.00202581, -0.00681173, 0.05953668, 0.03760593], [0.04400619, -0.05768024, 0.01285213, -0.00291806, -0.0006867, -0.05685832], [-0.01445402, 0.01517102, -0.00948362, -0.00960489, 0.05380672, 0.02393764], [-0.01148704, 0.00986145, -0.02266569, 0.01351875, -0.04967356, 0.03415273], [0.03532887, 0.05078012, 0.02258043, -0.00936826, -0.00848933, -0.0579093], [-0.01414294, -0.01565237, -0.01210371, 0.00562701, 0.05320757, 0.02624666], [-0.01454324, -0.02221432, -0.02452556, 0.00296983, -0.04419763, 0.0390688]], "number of molecular orbitals": 32, "number of electrons": 36, "number of unpaired electrons": 0, "orbital energies/eV": [-20.24455005, -19.45746053, -18.40306258, -17.25400699, -16.56025525, -16.01649371, -16.00691849, -15.35708937, -15.10296457, -14.27468412, -13.89025785, -13.53456632, -13.04784206, -12.95954747, -12.54066892, -12.28324671, -12.0958153, -11.30503111, -6.1792429, 0.29795349, 3.22896859, 3.36528531, 3.61245017, 4.1862497, 4.20971681, 4.95450376, 5.20105691, 5.23438553, 6.97890549, 7.43294112, 7.68823733, 17.97668708], "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], "program call": "xtb /tmp/scratch/tmp5luy_533/11574_0_xyzopt.xyz --pop --wbo --acc 0.2 --gfn 2 --chrg 0 --uhf 0 --etemp 300 --input /tmp/scratch/tmp5luy_533/11574_0_xtb.inp", "method": "GFN2-xTB", "xtb version": "6.3.3 (7355c4f)", "Dipole module/D": 2.051, "Total charge": 0, "Transition dipole module/D": NaN, "HOMO": -11.305, "LUMO": -6.1792, "HOMO occupancy": 2.0, "LUMO occupancy": 0, "mulliken charges": [-0.07883, -0.07602, 0.57929, -0.52927, -0.41872, 0.17579, 0.04303, 0.04303, 0.03067, 0.05346, 0.05346, 0.0372, 0.04345, 0.04345], "cm5 charges": [-0.22919, -0.17745, 0.63147, -0.5812, -0.50895, 0.05516, 0.09736, 0.09736, 0.08253, 0.11203, 0.11203, 0.09806, 0.10539, 0.10539], "FUKUI+": [0.032, 0.028, -0.19, -0.285, -0.125, 0.047, -0.033, -0.033, -0.064, -0.101, -0.101, -0.076, -0.05, -0.05], "FUKUI-": [0.017, -0.011, -0.02, -0.173, -0.108, 0.027, -0.092, -0.092, -0.118, -0.097, -0.097, -0.082, -0.078, -0.078], "FUKUIrad": [0.025, 0.008, -0.105, -0.229, -0.116, 0.037, -0.062, -0.062, -0.091, -0.099, -0.099, -0.079, -0.064, -0.064], "s proportion": [1.002, 1.034, 0.981, 1.72, 1.686, 0.973, 0.957, 0.957, 0.969, 0.947, 0.947, 0.963, 0.957, 0.957], "p proportion": [3.076, 3.042, 2.44, 4.809, 4.732, 2.852, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "d proportion": [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], "Fermi-level/eV": -8.7421, "Coordination numbers": [3.753, 3.802, 2.722, 0.856, 1.704, 3.655, 0.925, 0.925, 0.925, 0.924, 0.924, 0.925, 0.924, 0.924], "Dispersion coefficient C6": [22.558, 22.149, 20.96, 21.715, 18.489, 20.301, 2.281, 2.281, 2.398, 2.129, 2.129, 2.109, 2.177, 2.177], "Total dispersion C6": 1542.730529, "Total dispersion C8": 32696.934133, "Polarizability alpha": [6.773, 6.7, 7.495, 6.248, 5.805, 6.468, 2.362, 2.362, 2.422, 2.282, 2.282, 2.271, 2.307, 2.307], "Total polarizability alpha": 58.083671, "Wiberg matrix": [[0.0, 1.0202071843480722, 0.0, 0.0, 0.0, 0.0, 0.9863665229097803, 0.9863665233606033, 0.986927822489732, 0.0, 0.0, 0.0, 0.0, 0.0], [1.0202071843480722, 0.0, 0.9719514812994723, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.9555776255195927, 0.9555776596047553, 0.0, 0.0, 0.0], [0.0, 0.9719514812994723, 0.0, 1.7673723029267627, 1.1176349746048295, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 1.7673723029267627, 0.0, 0.16949995566066683, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 1.1176349746048295, 0.16949995566066683, 0.0, 0.958408471097539, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.958408471097539, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.9819756017640767, 0.9775453940378007, 0.9775453931559673], [0.9863665229097803, 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], [0.9863665233606033, 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], [0.986927822489732, 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, 0.9555776255195927, 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, 0.9555776596047553, 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, 0.9819756017640767, 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, 0.9775453940378007, 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, 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