kaggle-champs/constants.py at master · robinniesert/kaggle-champs · GitHub

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import os
import numpy as np
from rdkit import Chem, RDConfig


TYPES          = np.array(['1JHC', '2JHH', '1JHN', '2JHN', '2JHC', '3JHH',
                           '3JHC', '3JHN'])
TYPES_MAP      = {t: i for i, t in enumerate(TYPES)}
SYMBOLS        = ['H', 'C', 'N', 'O', 'F']
DEGREES        = [1, 2, 3, 4, 5]
HYBRIDIZATIONS = [Chem.rdchem.HybridizationType.SP,
                  Chem.rdchem.HybridizationType.SP2,
                  Chem.rdchem.HybridizationType.SP3,
                  Chem.rdchem.HybridizationType.UNSPECIFIED]
ATOMIC_RADIUS  = {'H': 0.38, 'C': 0.77, 'N': 0.75, 'O': 0.73, 'F': 0.71}
ELECTRO_NEG    = {'H': 2.2, 'C': 2.55, 'N': 3.04, 'O': 3.44, 'F': 3.98}


# feature definition file
FDEF = os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef')


SC_EDGE_FEATS = ['type_0', 'type_1', 'type_2', 'type_3', 'type_4', 'type_5',
                 'type_6', 'type_7', 'dist', 'dist_min_rad',
                 'dist_electro_neg_adj', 'normed_dist', 'diangle', 'cos_angle',
                 'cos_angle0', 'cos_angle1']
SC_MOL_FEATS  = ['type_0', 'type_1', 'type_2', 'type_3', 'type_4', 'type_5',
                 'type_6', 'type_7', 'dist', 'dist_min_rad',
                 'dist_electro_neg_adj', 'normed_dist', 'diangle', 'cos_angle',
                 'cos_angle0', 'cos_angle1', 'num_atoms', 'num_C_atoms',
                 'num_F_atoms', 'num_H_atoms', 'num_N_atoms', 'num_O_atoms',
                 'std_bond_length', 'ave_bond_length', 'ave_atom_weight']
ATOM_FEATS    = ['type_H', 'type_C', 'type_N', 'type_O', 'type_F', 'degree_1',
                 'degree_2', 'degree_3', 'degree_4', 'degree_5', 'SP', 'SP2',
                 'SP3', 'hybridization_unspecified', 'aromatic',
                 'formal_charge', 'atomic_num', 'ave_bond_length',
                 'ave_neighbor_weight', 'donor', 'acceptor']
BOND_FEATS    = ['single', 'double', 'triple', 'aromatic', 'conjugated',
                 'in_ring', 'dist', 'normed_dist']


TARGET_COL   = 'scalar_coupling_constant'
CONTRIB_COLS = ['fc', 'sd', 'pso', 'dso']


N_TYPES            = 8
N_SC_EDGE_FEATURES = 16
N_SC_MOL_FEATURES  = 25
N_ATOM_FEATURES    = 21
N_BOND_FEATURES    = 8
MAX_N_ATOMS        = 29
MAX_N_SC           = 135
BATCH_PAD_VAL      = -999
N_SC_TRAIN         = 4658147
N_MOLS             = 130775


N_FOLDS = 8


SC_MEAN             = 16
SC_STD              = 35
SC_FEATS_TO_SCALE   = ['dist', 'dist_min_rad', 'dist_electro_neg_adj',
                       'num_atoms', 'num_C_atoms', 'num_F_atoms', 'num_H_atoms',
                       'num_N_atoms', 'num_O_atoms', 'ave_bond_length',
                       'std_bond_length', 'ave_atom_weight']
ATOM_FEATS_TO_SCALE = ['atomic_num', 'ave_bond_length', 'ave_neighbor_weight']
BOND_FEATS_TO_SCALE = ['dist']


RAW_DATA_PATH  = 'data/'
PATH           = 'tmp/'
PROC_DATA_PATH = 'proc_data/'
SUB_PATH       = 'submissions/'
OOF_PATH       = 'oofs/'