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ndonyapourndonyapour
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Add UFF force fields parameters
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-15
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9 files changed

+498
-15
lines changed

‎examples/cgenffgsg/create_datasets.py renamed to ‎examples/cgenffgsg/extract_features.py

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@@ -17,7 +17,6 @@
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('NonStar', 'test'), ('Huuskonen', 'test')]
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FILES_PATH = '../../'
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‎examples/cgenffgsg/test_models.py

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@@ -22,7 +22,7 @@
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DEVICE = 'cpu'
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def run_tests(results_save_path):
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def run_tests(results_save_path, test_sets):
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params = product(GSG_PARAMS['wavelet_scale'],
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GSG_PARAMS['scattering_operators'])
@@ -48,11 +48,18 @@ def run_tests(results_save_path):
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data_loader = DataLoader(TRAIN_DATASET, dataset_path)
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51-
ChEMBL_data = data_loader.load_data()
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DCL_data = data_loader.load_data()
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53-
test_sets = {'ChEMBL': ChEMBL_data['ChEMBL_test']}
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x_train = DCL_data[f'{TRAIN_DATASET}_training'][0]
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test_sets = {}
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for test_set_name, path in test_set_paths.items():
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data_loader = DataLoader(test_set_name,
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osp.join(path, dataset_path))
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test_data = data_loader.load_data()[f'{test_set_name}_test']
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test_sets.update({test_set_name: test_data})
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x_train = ChEMBL_data['ChEMBL_training'][0]
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scaler = StandardScaler()
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scaler.fit(x_train)
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@@ -101,4 +108,5 @@ def run_tests(results_save_path):
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if not osp.exists(results_save_path):
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os.makedirs(results_save_path)
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run_tests(results_save_path)
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test_set_paths = {'ChEMBL': './'}
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run_tests(results_save_path, test_set_paths)

‎examples/cgenffgsg/train_models.py

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -75,15 +75,14 @@ def create_model(wavelet_scale, scattering_operators):
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split_dataset(wavelet_scale, scattering_operators)
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data_loader = DataLoader(DATASET,
79-
f'data_{wavelet_scale}_'
80-
f'{scop_to_str(scattering_operators)}')
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model_save_path = osp.join(MODELS_SAVE_PATH,
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f'model_{wavelet_scale}_'
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f'{scop_to_str(scattering_operators)}.pkl')
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if not osp.exists(model_save_path):
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data_loader = DataLoader(DATASET,
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f'data_{wavelet_scale}_'
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f'{scop_to_str(scattering_operators)}')
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data = data_loader.load_data()
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‎src/classicalgsg/atomic_attr/forcefields_params/UFF.prm

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#
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# Open Babel file: UFF.prm
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#
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# Force field parameters for UFF, the Universal Force Field
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# Used by OBForceField and OBUFFForceField
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#
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# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
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# The parameters in this file are taken from the UFF implementation in RDKit
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# http://rdkit.org/
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#
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# Atom typing rules are based on UFF published atom descriptions
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# atom [SMARTS] [atomtype] [description]
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# These must be sorted according to the element and complexity
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# of the type rule (i.e., generic rules first, more specific rules later)
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#
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# Parameters follow later
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# param Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
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#atom [#0] Du Dummy atom (e.g., ligand attachment point)
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atom [#1] H_ Generic hydrogen
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atom [#1D2] H_b Bridging hydrogen
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atom [#2] He4+4 Helium
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atom [#3] Li Lithium
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atom [#4] Be3+2 Generic Be
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atom [#5] B_2 Trigonal planar boron
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atom [#5D4] B_3 Tetrahedral boron
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atom [#6] C_3 Generic sp3 C
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atom [C^2] C_2 sp2 non-aromatic C
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atom [C^1] C_1 sp hybridized C
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atom [c] C_R aromatic C
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atom [#6H1D3r5] C_R aromatic C (cyclopentadienyl ring)
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atom [#7] N_3 Generic sp3 N
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atom [N^2] N_2 sp2 non-aromatic N
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atom [N^1] N_1 sp hybridized N
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atom [n] N_R aromatic N
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atom [#8] O_3 generic, sp3 hybridized O
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atom [#8][#14] O_3_z sp3 hybridized O for zeolites
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atom [O^2] O_2 sp2 hybridized O
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atom [O^1] O_1 sp hybridized O
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atom [o] O_R aromatic O
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atom [#9] F_ generic F
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atom [#10] Ne4+4
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atom [#11] Na
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atom [#12] Mg3+2
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atom [#13] Al3
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atom [#14] Si3
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#atom [#15] P_3+q Organometallic phosphine ligands
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atom [#15] P_3+3 generic phosphorus
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atom [#15D5] P_3+5 formal charge +5
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atom [#16] S_3+2 generic S
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atom [#16+4] S_3+4 S+4 ( SO2 )
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atom [#16+6] S_3+6 S+6 ( SO3 / H2SO4 )
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atom [S^2] S_2 non-aromatic sp2 S
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atom [s] S_R aromatic S
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atom [#17] Cl
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atom [#18] Ar4+4
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atom [#19] K_
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atom [#20] Ca6+2
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atom [#21] Sc3+3
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atom [#22] Ti6+4 generic Ti (6-valent)
61+
atom [#22D3] Ti3+4
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atom [#23] V_3+5
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atom [#24] Cr6+3
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atom [#25] Mn6+2
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atom [#26] Fe6+2 generic Fe (6-valent)
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atom [#26D3] Fe3+2
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atom [#27] Co6+3
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atom [#28] Ni4+2
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atom [#29] Cu3+1
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atom [#30] Zn3+2
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atom [#31] Ga3+3
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atom [#32] Ge3
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atom [#33] As3+3
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atom [#34] Se3+2
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atom [#35] Br
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atom [#36] Kr4+4
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atom [#37] Rb
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atom [#38] Sr6+2
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atom [#39] Y_3+3
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atom [#40] Zr3+4
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atom [#41] Nb3+5
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atom [#42] Mo6+6 generic Mo (6-valent)
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atom [#42D3] Mo3+6 trivalent Mo
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atom [#43] Tc6+5
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atom [#44] Ru6+2
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atom [#45] Rh6+3
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atom [#46] Pd4+2
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atom [#47] Ag1+1
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atom [#48] Cd3+2
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atom [#49] In3+3
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atom [#50] Sn3
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atom [#51] Sb3+3
93+
atom [#52] Te3+2
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atom [#53] I_
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atom [#54] Xe4+4
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atom [#55] Cs
97+
atom [#56] Ba6+2
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atom [#57] La3+3
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atom [#58] Ce6+3
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atom [#59] Pr6+3
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atom [#60] Nd6+3
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atom [#61] Pm6+3
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atom [#62] Sm6+3
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atom [#63] Eu6+3
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atom [#64] Gd6+3
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atom [#65] Tb6+3
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atom [#66] Dy6+3
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atom [#67] Ho6+3
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atom [#68] Er6+3
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atom [#69] Tm6+3
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atom [#70] Yb6+3
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atom [#71] Lu6+3
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atom [#72] Hf3+4
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atom [#73] Ta3+5
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atom [#74] W_6+6 generic W (6-valent)
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atom [#74D3+4] W_3+4
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atom [#74D3+6] W_3+6
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atom [#75] Re6+5 generic Re (6-valent)
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atom [#75D3] Re3+7 trivalent Re
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atom [#76] Os6+6
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atom [#77] Ir6+3
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atom [#78] Pt4+2
123+
atom [#79] Au4+3
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atom [#80] Hg1+2
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atom [#81] Tl3+3
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atom [#82] Pb3
127+
atom [#83] Bi3+3
128+
atom [#84] Po3+2
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atom [#85] At
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atom [#86] Rn4+4
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atom [#87] Fr
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atom [#88] Ra6+2
133+
atom [#89] Ac6+3
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atom [#90] Th6+4
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atom [#91] Pa6+4
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atom [#92] U_6+4
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atom [#93] Np6+4
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atom [#94] Pu6+4
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atom [#95] Am6+4
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atom [#96] Cm6+3
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atom [#97] Bk6+3
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atom [#98] Cf6+3
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atom [#99] Es6+3
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atom [#100] Fm6+3
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atom [#101] Md6+3
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atom [#102] No6+3
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atom [#103] Lw6+3
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149+
# Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
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param Du 0.01 180 0.4 5000 12 10.0 0 0 9.66 14.92 0.7
151+
param H_ 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
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param D 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
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param H_b 0.46 83.5 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371
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param He4+4 0.849 90 2.362 0.056 15.24 0.098 0 0 9.66 14.92 1.3
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param Li 1.336 180 2.451 0.025 12 1.026 0 2 3.006 2.386 1.557
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param Be3+2 1.074 109.47 2.745 0.085 12 1.565 0 2 4.877 4.443 1.24
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param B_3 0.838 109.47 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822
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param B_2 0.828 120 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822
159+
param C_3 0.757 109.47 3.851 0.105 12.73 1.912 2.119 2 5.343 5.063 0.759
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param C_R 0.729 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
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param C_2 0.732 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
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param C_1 0.706 180 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759
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param N_3 0.7 106.7 3.66 0.069 13.407 2.544 0.45 2 6.899 5.88 0.715
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param N_R 0.699 120 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
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param N_2 0.685 111.2 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
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param N_1 0.656 180 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715
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param O_3 0.658 104.51 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669
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param O_3_z 0.528 146 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669
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param O_R 0.68 110 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
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param O_2 0.634 120 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
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param O_1 0.639 180 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669
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param F_ 0.668 180 3.364 0.05 14.762 1.735 0 2 10.874 7.474 0.706
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param Ne4+4 0.92 90 3.243 0.042 15.44 0.194 0 2 11.04 10.55 1.768
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param Na 1.539 180 2.983 0.03 12 1.081 0 1.25 2.843 2.296 2.085
175+
param Mg3+2 1.421 109.47 3.021 0.111 12 1.787 0 1.25 3.951 3.693 1.5
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param Al3 1.244 109.47 4.499 0.505 11.278 1.792 0 1.25 4.06 3.59 1.201
177+
param Si3 1.117 109.47 4.295 0.402 12.175 2.323 1.225 1.25 4.168 3.487 1.176
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param P_3+3 1.101 93.8 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
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param P_3+5 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
180+
param P_3+q 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102
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param S_3+2 1.064 92.1 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
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param S_3+4 1.049 103.2 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
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param S_3+6 1.027 109.47 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047
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param S_R 1.077 92.2 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047
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param S_2 0.854 120 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047
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param Cl 1.044 180 3.947 0.227 14.866 2.348 0 1.25 8.564 4.946 0.994
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param Ar4+4 1.032 90 3.868 0.185 15.763 0.3 0 1.25 9.465 6.355 2.108
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param K_ 1.953 180 3.812 0.035 12 1.165 0 0.7 2.421 1.92 2.586
189+
param Ca6+2 1.761 90 3.399 0.238 12 2.141 0 0.7 3.231 2.88 2
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param Sc3+3 1.513 109.47 3.295 0.019 12 2.592 0 0.7 3.395 3.08 1.75
191+
param Ti3+4 1.412 109.47 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607
192+
param Ti6+4 1.412 90 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607
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param V_3+5 1.402 109.47 3.144 0.016 12 2.679 0 0.7 3.65 3.41 1.47
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param Cr6+3 1.345 90 3.023 0.015 12 2.463 0 0.7 3.415 3.865 1.402
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param Mn6+2 1.382 90 2.961 0.013 12 2.43 0 0.7 3.325 4.105 1.533
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param Fe3+2 1.27 109.47 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393
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param Fe6+2 1.335 90 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393
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param Co6+3 1.241 90 2.872 0.014 12 2.43 0 0.7 4.105 4.175 1.406
199+
param Ni4+2 1.164 90 2.834 0.015 12 2.43 0 0.7 4.465 4.205 1.398
200+
param Cu3+1 1.302 109.47 3.495 0.005 12 1.756 0 0.7 4.2 4.22 1.434
201+
param Zn3+2 1.193 109.47 2.763 0.124 12 1.308 0 0.7 5.106 4.285 1.4
202+
param Ga3+3 1.26 109.47 4.383 0.415 11 1.821 0 0.7 3.641 3.16 1.211
203+
param Ge3 1.197 109.47 4.28 0.379 12 2.789 0.701 0.7 4.051 3.438 1.189
204+
param As3+3 1.211 92.1 4.23 0.309 13 2.864 1.5 0.7 5.188 3.809 1.204
205+
param Se3+2 1.19 90.6 4.205 0.291 14 2.764 0.335 0.7 6.428 4.131 1.224
206+
param Br 1.192 180 4.189 0.251 15 2.519 0 0.7 7.79 4.425 1.141
207+
param Kr4+4 1.147 90 4.141 0.22 16 0.452 0 0.7 8.505 5.715 2.27
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param Rb 2.26 180 4.114 0.04 12 1.592 0 0.2 2.331 1.846 2.77
209+
param Sr6+2 2.052 90 3.641 0.235 12 2.449 0 0.2 3.024 2.44 2.415
210+
param Y_3+3 1.698 109.47 3.345 0.072 12 3.257 0 0.2 3.83 2.81 1.998
211+
param Zr3+4 1.564 109.47 3.124 0.069 12 3.667 0 0.2 3.4 3.55 1.758
212+
param Nb3+5 1.473 109.47 3.165 0.059 12 3.618 0 0.2 3.55 3.38 1.603
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param Mo6+6 1.467 90 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53
214+
param Mo3+6 1.484 109.47 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53
215+
param Tc6+5 1.322 90 2.998 0.048 12 3.4 0 0.2 3.29 3.99 1.5
216+
param Ru6+2 1.478 90 2.963 0.056 12 3.4 0 0.2 3.575 4.015 1.5
217+
param Rh6+3 1.332 90 2.929 0.053 12 3.5 0 0.2 3.975 4.005 1.509
218+
param Pd4+2 1.338 90 2.899 0.048 12 3.21 0 0.2 4.32 4 1.544
219+
param Ag1+1 1.386 180 3.148 0.036 12 1.956 0 0.2 4.436 3.134 1.622
220+
param Cd3+2 1.403 109.47 2.848 0.228 12 1.65 0 0.2 5.034 3.957 1.6
221+
param In3+3 1.459 109.47 4.463 0.599 11 2.07 0 0.2 3.506 2.896 1.404
222+
param Sn3 1.398 109.47 4.392 0.567 12 2.961 0.199 0.2 3.987 3.124 1.354
223+
param Sb3+3 1.407 91.6 4.42 0.449 13 2.704 1.1 0.2 4.899 3.342 1.404
224+
param Te3+2 1.386 90.25 4.47 0.398 14 2.882 0.3 0.2 5.816 3.526 1.38
225+
param I_ 1.382 180 4.5 0.339 15 2.65 0 0.2 6.822 3.762 1.333
226+
param Xe4+4 1.267 90 4.404 0.332 12 0.556 0 0.2 7.595 4.975 2.459
227+
param Cs 2.57 180 4.517 0.045 12 1.573 0 0.1 2.183 1.711 2.984
228+
param Ba6+2 2.277 90 3.703 0.364 12 2.727 0 0.1 2.814 2.396 2.442
229+
param La3+3 1.943 109.47 3.522 0.017 12 3.3 0 0.1 2.8355 2.7415 2.071
230+
param Ce6+3 1.841 90 3.556 0.013 12 3.3 0 0.1 2.774 2.692 1.925
231+
param Pr6+3 1.823 90 3.606 0.01 12 3.3 0 0.1 2.858 2.564 2.007
232+
param Nd6+3 1.816 90 3.575 0.01 12 3.3 0 0.1 2.8685 2.6205 2.007
233+
param Pm6+3 1.801 90 3.547 0.009 12 3.3 0 0.1 2.881 2.673 2
234+
param Sm6+3 1.78 90 3.52 0.008 12 3.3 0 0.1 2.9115 2.7195 1.978
235+
param Eu6+3 1.771 90 3.493 0.008 12 3.3 0 0.1 2.8785 2.7875 2.227
236+
param Gd6+3 1.735 90 3.368 0.009 12 3.3 0 0.1 3.1665 2.9745 1.968
237+
param Tb6+3 1.732 90 3.451 0.007 12 3.3 0 0.1 3.018 2.834 1.954
238+
param Dy6+3 1.71 90 3.428 0.007 12 3.3 0 0.1 3.0555 2.8715 1.934
239+
param Ho6+3 1.696 90 3.409 0.007 12 3.416 0 0.1 3.127 2.891 1.925
240+
param Er6+3 1.673 90 3.391 0.007 12 3.3 0 0.1 3.1865 2.9145 1.915
241+
param Tm6+3 1.66 90 3.374 0.006 12 3.3 0 0.1 3.2514 2.9329 2
242+
param Yb6+3 1.637 90 3.355 0.228 12 2.618 0 0.1 3.2889 2.965 2.158
243+
param Lu6+3 1.671 90 3.64 0.041 12 3.271 0 0.1 2.9629 2.4629 1.896
244+
param Hf3+4 1.611 109.47 3.141 0.072 12 3.921 0 0.1 3.7 3.4 1.759
245+
param Ta3+5 1.511 109.47 3.17 0.081 12 4.075 0 0.1 5.1 2.85 1.605
246+
param W_6+6 1.392 90 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
247+
param W_3+4 1.526 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
248+
param W_3+6 1.38 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538
249+
param Re6+5 1.372 90 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6
250+
param Re3+7 1.314 109.47 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6
251+
param Os6+6 1.372 90 3.12 0.037 12 3.7 0 0.1 5.14 3.63 1.7
252+
param Ir6+3 1.371 90 2.84 0.073 12 3.731 0 0.1 5 4 1.866
253+
param Pt4+2 1.364 90 2.754 0.08 12 3.382 0 0.1 4.79 4.43 1.557
254+
param Au4+3 1.262 90 3.293 0.039 12 2.625 0 0.1 4.894 2.586 1.618
255+
param Hg1+2 1.34 180 2.705 0.385 12 1.75 0 0.1 6.27 4.16 1.6
256+
param Tl3+3 1.518 120 4.347 0.68 11 2.068 0 0.1 3.2 2.9 1.53
257+
param Pb3 1.459 109.47 4.297 0.663 12 2.846 0.1 0.1 3.9 3.53 1.444
258+
param Bi3+3 1.512 90 4.37 0.518 13 2.47 1 0.1 4.69 3.74 1.514
259+
param Po3+2 1.5 90 4.709 0.325 14 2.33 0.3 0.1 4.21 4.21 1.48
260+
param At 1.545 180 4.75 0.284 15 2.24 0 0.1 4.75 4.75 1.47
261+
param Rn4+4 1.42 90 4.765 0.248 16 0.583 0 0.1 5.37 5.37 2.2
262+
param Fr 2.88 180 4.9 0.05 12 1.847 0 0 2 2 2.3
263+
param Ra6+2 2.512 90 3.677 0.404 12 2.92 0 0 2.843 2.434 2.2
264+
param Ac6+3 1.983 90 3.478 0.033 12 3.9 0 0 2.835 2.835 2.108
265+
param Th6+4 1.721 90 3.396 0.026 12 4.202 0 0 3.175 2.905 2.018
266+
param Pa6+4 1.711 90 3.424 0.022 12 3.9 0 0 2.985 2.905 1.8
267+
param U_6+4 1.684 90 3.395 0.022 12 3.9 0 0 3.341 2.853 1.713
268+
param Np6+4 1.666 90 3.424 0.019 12 3.9 0 0 3.549 2.717 1.8
269+
param Pu6+4 1.657 90 3.424 0.016 12 3.9 0 0 3.243 2.819 1.84
270+
param Am6+4 1.66 90 3.381 0.014 12 3.9 0 0 2.9895 3.0035 1.942
271+
param Cm6+3 1.801 90 3.326 0.013 12 3.9 0 0 2.8315 3.1895 1.9
272+
param Bk6+3 1.761 90 3.339 0.013 12 3.9 0 0 3.1935 3.0355 1.9
273+
param Cf6+3 1.75 90 3.313 0.013 12 3.9 0 0 3.197 3.101 1.9
274+
param Es6+3 1.724 90 3.299 0.012 12 3.9 0 0 3.333 3.089 1.9
275+
param Fm6+3 1.712 90 3.286 0.012 12 3.9 0 0 3.4 3.1 1.9
276+
param Md6+3 1.689 90 3.274 0.011 12 3.9 0 0 3.47 3.11 1.9
277+
param No6+3 1.679 90 3.248 0.011 12 3.9 0 0 3.475 3.175 1.9
278+
param Lw6+3 1.698 90 3.236 0.011 12 3.9 0 0 3.5 3.2 1.9

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