deepscreen/data/featurizers/fingerprint/pubchemfp.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Aug 25 20:29:36 2019

@author: charleshen

@Note: The code are copyed from PyBioMed, with a minor repair

https://www.ncbi.nlm.nih.gov/pubmed/29556758

these are SMARTS patterns corresponding to the PubChem fingerprints
https://astro.temple.edu/~tua87106/list_fingerprints.pdf
ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt

"""

_type = 'SMARTS-based'

import numpy as np
from rdkit import Chem
from rdkit import DataStructs
import os
import pandas as pd

smartsPatts = {
    1: ('[H]', 3),  # 1-115
    2: ('[H]', 7),
    3: ('[H]', 15),
    4: ('[H]', 31),
    5: ('[Li]', 0),
    6: ('[Li]', 1),
    7: ('[B]', 0),
    8: ('[B]', 1),
    9: ('[B]', 3),
    10: ('[C]', 1),
    11: ('[C]', 3),
    12: ('[C]', 7),
    13: ('[C]', 15),
    14: ('[C]', 31),
    15: ('[N]', 0),
    16: ('[N]', 1),
    17: ('[N]', 3),
    18: ('[N]', 7),
    19: ('[O]', 0),
    20: ('[O]', 1),
    21: ('[O]', 3),
    22: ('[O]', 7),
    23: ('[O]', 15),
    24: ('[F]', 0),
    25: ('[F]', 1),
    26: ('[F]', 3),
    27: ('[Na]', 0),
    28: ('[Na]', 1),
    29: ('[Si]', 0),
    30: ('[Si]', 1),
    31: ('[P]', 0),
    32: ('[P]', 1),
    33: ('[P]', 3),
    34: ('[S]', 0),
    35: ('[S]', 1),
    36: ('[S]', 3),
    37: ('[S]', 7),
    38: ('[Cl]', 0),
    39: ('[Cl]', 1),
    40: ('[Cl]', 3),
    41: ('[Cl]', 7),
    42: ('[K]', 0),
    43: ('[K]', 1),
    44: ('[Br]', 0),
    45: ('[Br]', 1),
    46: ('[Br]', 3),
    47: ('[I]', 0),
    48: ('[I]', 1),
    49: ('[I]', 3),
    50: ('[Be]', 0),
    51: ('[Mg]', 0),
    52: ('[Al]', 0),
    53: ('[Ca]', 0),
    54: ('[Sc]', 0),
    55: ('[Ti]', 0),
    56: ('[V]', 0),
    57: ('[Cr]', 0),
    58: ('[Mn]', 0),
    59: ('[Fe]', 0),
    60: ('[CO]', 0),
    61: ('[Ni]', 0),
    62: ('[Cu]', 0),
    63: ('[Zn]', 0),
    64: ('[Ga]', 0),
    65: ('[Ge]', 0),
    66: ('[As]', 0),
    67: ('[Se]', 0),
    68: ('[Kr]', 0),
    69: ('[Rb]', 0),
    70: ('[Sr]', 0),
    71: ('[Y]', 0),
    72: ('[Zr]', 0),
    73: ('[Nb]', 0),
    74: ('[Mo]', 0),
    75: ('[Ru]', 0),
    76: ('[Rh]', 0),
    77: ('[Pd]', 0),
    78: ('[Ag]', 0),
    79: ('[Cd]', 0),
    80: ('[In]', 0),
    81: ('[Sn]', 0),
    82: ('[Sb]', 0),
    83: ('[Te]', 0),
    84: ('[Xe]', 0),
    85: ('[Cs]', 0),
    86: ('[Ba]', 0),
    87: ('[Lu]', 0),
    88: ('[Hf]', 0),
    89: ('[Ta]', 0),
    90: ('[W]', 0),
    91: ('[Re]', 0),
    92: ('[Os]', 0),
    93: ('[Ir]', 0),
    94: ('[Pt]', 0),
    95: ('[Au]', 0),
    96: ('[Hg]', 0),
    97: ('[Tl]', 0),
    98: ('[Pb]', 0),
    99: ('[Bi]', 0),
    100: ('[La]', 0),
    101: ('[Ce]', 0),
    102: ('[Pr]', 0),
    103: ('[Nd]', 0),
    104: ('[Pm]', 0),
    105: ('[Sm]', 0),
    106: ('[Eu]', 0),
    107: ('[Gd]', 0),
    108: ('[Tb]', 0),
    109: ('[Dy]', 0),
    110: ('[Ho]', 0),
    111: ('[Er]', 0),
    112: ('[Tm]', 0),
    113: ('[Yb]', 0),
    114: ('[Tc]', 0),
    115: ('[U]', 0),
    116: ('[Li&!H0]', 0),  # 264-881
    117: ('[Li]~[Li]', 0),
    118: ('[Li]~[#5]', 0),
    119: ('[Li]~[#6]', 0),
    120: ('[Li]~[#8]', 0),
    121: ('[Li]~[F]', 0),
    122: ('[Li]~[#15]', 0),
    123: ('[Li]~[#16]', 0),
    124: ('[Li]~[Cl]', 0),
    125: ('[#5&!H0]', 0),
    126: ('[#5]~[#5]', 0),
    127: ('[#5]~[#6]', 0),
    128: ('[#5]~[#7]', 0),
    129: ('[#5]~[#8]', 0),
    130: ('[#5]~[F]', 0),
    131: ('[#5]~[#14]', 0),
    132: ('[#5]~[#15]', 0),
    133: ('[#5]~[#16]', 0),
    134: ('[#5]~[Cl]', 0),
    135: ('[#5]~[Br]', 0),
    136: ('[#6&!H0]', 0),
    137: ('[#6]~[#6]', 0),
    138: ('[#6]~[#7]', 0),
    139: ('[#6]~[#8]', 0),
    140: ('[#6]~[F]', 0),
    141: ('[#6]~[Na]', 0),
    142: ('[#6]~[Mg]', 0),
    143: ('[#6]~[Al]', 0),
    144: ('[#6]~[#14]', 0),
    145: ('[#6]~[#15]', 0),
    146: ('[#6]~[#16]', 0),
    147: ('[#6]~[Cl]', 0),
    148: ('[#6]~[#33]', 0),
    149: ('[#6]~[#34]', 0),
    150: ('[#6]~[Br]', 0),
    151: ('[#6]~[I]', 0),
    152: ('[#7&!H0]', 0),
    153: ('[#7]~[#7]', 0),
    154: ('[#7]~[#8]', 0),
    155: ('[#7]~[F]', 0),
    156: ('[#7]~[#14]', 0),
    157: ('[#7]~[#15]', 0),
    158: ('[#7]~[#16]', 0),
    159: ('[#7]~[Cl]', 0),
    160: ('[#7]~[Br]', 0),
    161: ('[#8&!H0]', 0),
    162: ('[#8]~[#8]', 0),
    163: ('[#8]~[Mg]', 0),
    164: ('[#8]~[Na]', 0),
    165: ('[#8]~[Al]', 0),
    166: ('[#8]~[#14]', 0),
    167: ('[#8]~[#15]', 0),
    168: ('[#8]~[K]', 0),
    169: ('[F]~[#15]', 0),
    170: ('[F]~[#16]', 0),
    171: ('[Al&!H0]', 0),
    172: ('[Al]~[Cl]', 0),
    173: ('[#14&!H0]', 0),
    174: ('[#14]~[#14]', 0),
    175: ('[#14]~[Cl]', 0),
    176: ('[#15&!H0]', 0),
    177: ('[#15]~[#15]', 0),
    178: ('[#33&!H0]', 0),
    179: ('[#33]~[#33]', 0),
    180: ('[#6](~Br)(~[#6])', 0),
    181: ('[#6](~Br)(~[#6])(~[#6])', 0),
    182: ('[#6&!H0]~[Br]', 0),
    183: ('[#6](~[Br])(:[c])', 0),
    184: ('[#6](~[Br])(:[n])', 0),
    185: ('[#6](~[#6])(~[#6])', 0),
    186: ('[#6](~[#6])(~[#6])(~[#6])', 0),
    187: ('[#6](~[#6])(~[#6])(~[#6])(~[#6])', 0),
    188: ('[#6H1](~[#6])(~[#6])(~[#6])', 0),
    189: ('[#6](~[#6])(~[#6])(~[#6])(~[#7])', 0),
    190: ('[#6](~[#6])(~[#6])(~[#6])(~[#8])', 0),
    191: ('[#6H1](~[#6])(~[#6])(~[#7])', 0),
    192: ('[#6H1](~[#6])(~[#6])(~[#8])', 0),
    193: ('[#6](~[#6])(~[#6])(~[#7])', 0),
    194: ('[#6](~[#6])(~[#6])(~[#8])', 0),
    195: ('[#6](~[#6])(~[Cl])', 0),
    196: ('[#6&!H0](~[#6])(~[Cl])', 0),
    197: ('[#6H,#6H2,#6H3,#6H4]~[#6]', 0),
    198: ('[#6&!H0](~[#6])(~[#7])', 0),
    199: ('[#6&!H0](~[#6])(~[#8])', 0),
    200: ('[#6H1](~[#6])(~[#8])(~[#8])', 0),
    201: ('[#6&!H0](~[#6])(~[#15])', 0),
    202: ('[#6&!H0](~[#6])(~[#16])', 0),
    203: ('[#6](~[#6])(~[I])', 0),
    204: ('[#6](~[#6])(~[#7])', 0),
    205: ('[#6](~[#6])(~[#8])', 0),
    206: ('[#6](~[#6])(~[#16])', 0),
    207: ('[#6](~[#6])(~[#14])', 0),
    208: ('[#6](~[#6])(:c)', 0),
    209: ('[#6](~[#6])(:c)(:c)', 0),
    210: ('[#6](~[#6])(:c)(:n)', 0),
    211: ('[#6](~[#6])(:n)', 0),
    212: ('[#6](~[#6])(:n)(:n)', 0),
    213: ('[#6](~[Cl])(~[Cl])', 0),
    214: ('[#6&!H0](~[Cl])', 0),
    215: ('[#6](~[Cl])(:c)', 0),
    216: ('[#6](~[F])(~[F])', 0),
    217: ('[#6](~[F])(:c)', 0),
    218: ('[#6&!H0](~[#7])', 0),
    219: ('[#6&!H0](~[#8])', 0),
    220: ('[#6&!H0](~[#8])(~[#8])', 0),
    221: ('[#6&!H0](~[#16])', 0),
    222: ('[#6&!H0](~[#14])', 0),
    223: ('[#6&!H0]:c', 0),
    224: ('[#6&!H0](:c)(:c)', 0),
    225: ('[#6&!H0](:c)(:n)', 0),
    226: ('[#6&!H0](:n)', 0),
    227: ('[#6H3]', 0),
    228: ('[#6](~[#7])(~[#7])', 0),
    229: ('[#6](~[#7])(:c)', 0),
    230: ('[#6](~[#7])(:c)(:c)', 0),
    231: ('[#6](~[#7])(:c)(:n)', 0),
    232: ('[#6](~[#7])(:n)', 0),
    233: ('[#6](~[#8])(~[#8])', 0),
    234: ('[#6](~[#8])(:c)', 0),
    235: ('[#6](~[#8])(:c)(:c)', 0),
    236: ('[#6](~[#16])(:c)', 0),
    237: ('[#6](:c)(:c)', 0),
    238: ('[#6](:c)(:c)(:c)', 0),
    239: ('[#6](:c)(:c)(:n)', 0),
    240: ('[#6](:c)(:n)', 0),
    241: ('[#6](:c)(:n)(:n)', 0),
    242: ('[#6](:n)(:n)', 0),
    243: ('[#7](~[#6])(~[#6])', 0),
    244: ('[#7](~[#6])(~[#6])(~[#6])', 0),
    245: ('[#7&!H0](~[#6])(~[#6])', 0),
    246: ('[#7&!H0](~[#6])', 0),
    247: ('[#7&!H0](~[#6])(~[#7])', 0),
    248: ('[#7](~[#6])(~[#8])', 0),
    249: ('[#7](~[#6])(:c)', 0),
    250: ('[#7](~[#6])(:c)(:c)', 0),
    251: ('[#7&!H0](~[#7])', 0),
    252: ('[#7&!H0](:c)', 0),
    253: ('[#7&!H0](:c)(:c)', 0),
    254: ('[#7](~[#8])(~[#8])', 0),
    255: ('[#7](~[#8])(:o)', 0),
    256: ('[#7](:c)(:c)', 0),
    257: ('[#7](:c)(:c)(:c)', 0),
    258: ('[#8](~[#6])(~[#6])', 0),
    259: ('[#8&!H0](~[#6])', 0),
    260: ('[#8](~[#6])(~[#15])', 0),
    261: ('[#8&!H0](~[#16])', 0),
    262: ('[#8](:c)(:c)', 0),
    263: ('[#15](~[#6])(~[#6])', 0),
    264: ('[#15](~[#8])(~[#8])', 0),
    265: ('[#16](~[#6])(~[#6])', 0),
    266: ('[#16&!H0](~[#6])', 0),
    267: ('[#16](~[#6])(~[#8])', 0),
    268: ('[#14](~[#6])(~[#6])', 0),
    269: ('[#6]=,:[#6]', 0),
    270: ('[#6]#[#6]', 0),
    271: ('[#6]=,:[#7]', 0),
    272: ('[#6]#[#7]', 0),
    273: ('[#6]=,:[#8]', 0),
    274: ('[#6]=,:[#16]', 0),
    275: ('[#7]=,:[#7]', 0),
    276: ('[#7]=,:[#8]', 0),
    277: ('[#7]=,:[#15]', 0),
    278: ('[#15]=,:[#8]', 0),
    279: ('[#15]=,:[#15]', 0),
    280: ('[#6](#[#6])(-,:[#6])', 0),
    281: ('[#6&!H0](#[#6])', 0),
    282: ('[#6](#[#7])(-,:[#6])', 0),
    283: ('[#6](-,:[#6])(-,:[#6])(=,:[#6])', 0),
    284: ('[#6](-,:[#6])(-,:[#6])(=,:[#7])', 0),
    285: ('[#6](-,:[#6])(-,:[#6])(=,:[#8])', 0),
    286: ('[#6](-,:[#6])([Cl])(=,:[#8])', 0),
    287: ('[#6&!H0](-,:[#6])(=,:[#6])', 0),
    288: ('[#6&!H0](-,:[#6])(=,:[#7])', 0),
    289: ('[#6&!H0](-,:[#6])(=,:[#8])', 0),
    290: ('[#6](-,:[#6])(-,:[#7])(=,:[#6])', 0),
    291: ('[#6](-,:[#6])(-,:[#7])(=,:[#7])', 0),
    292: ('[#6](-,:[#6])(-,:[#7])(=,:[#8])', 0),
    293: ('[#6](-,:[#6])(-,:[#8])(=,:[#8])', 0),
    294: ('[#6](-,:[#6])(=,:[#6])', 0),
    295: ('[#6](-,:[#6])(=,:[#7])', 0),
    296: ('[#6](-,:[#6])(=,:[#8])', 0),
    297: ('[#6]([Cl])(=,:[#8])', 0),
    298: ('[#6&!H0](-,:[#7])(=,:[#6])', 0),
    299: ('[#6&!H0](=,:[#6])', 0),
    300: ('[#6&!H0](=,:[#7])', 0),
    301: ('[#6&!H0](=,:[#8])', 0),
    302: ('[#6](-,:[#7])(=,:[#6])', 0),
    303: ('[#6](-,:[#7])(=,:[#7])', 0),
    304: ('[#6](-,:[#7])(=,:[#8])', 0),
    305: ('[#6](-,:[#8])(=,:[#8])', 0),
    306: ('[#7](-,:[#6])(=,:[#6])', 0),
    307: ('[#7](-,:[#6])(=,:[#8])', 0),
    308: ('[#7](-,:[#8])(=,:[#8])', 0),
    309: ('[#15](-,:[#8])(=,:[#8])', 0),
    310: ('[#16](-,:[#6])(=,:[#8])', 0),
    311: ('[#16](-,:[#8])(=,:[#8])', 0),
    312: ('[#16](=,:[#8])(=,:[#8])', 0),
    313: ('[#6]-,:[#6]-,:[#6]#[#6]', 0),
    314: ('[#8]-,:[#6]-,:[#6]=,:[#7]', 0),
    315: ('[#8]-,:[#6]-,:[#6]=,:[#8]', 0),
    316: ('[#7]:[#6]-,:[#16&!H0]', 0),
    317: ('[#7]-,:[#6]-,:[#6]=,:[#6]', 0),
    318: ('[#8]=,:[#16]-,:[#6]-,:[#6]', 0),
    319: ('[#7]#[#6]-,:[#6]=,:[#6]', 0),
    320: ('[#6]=,:[#7]-,:[#7]-,:[#6]', 0),
    321: ('[#8]=,:[#16]-,:[#6]-,:[#7]', 0),
    322: ('[#16]-,:[#16]-,:[#6]:[#6]', 0),
    323: ('[#6]:[#6]-,:[#6]=,:[#6]', 0),
    324: ('[#16]:[#6]:[#6]:[#6]', 0),
    325: ('[#6]:[#7]:[#6]-,:[#6]', 0),
    326: ('[#16]-,:[#6]:[#7]:[#6]', 0),
    327: ('[#16]:[#6]:[#6]:[#7]', 0),
    328: ('[#16]-,:[#6]=,:[#7]-,:[#6]', 0),
    329: ('[#6]-,:[#8]-,:[#6]=,:[#6]', 0),
    330: ('[#7]-,:[#7]-,:[#6]:[#6]', 0),
    331: ('[#16]-,:[#6]=,:[#7&!H0]', 0),
    332: ('[#16]-,:[#6]-,:[#16]-,:[#6]', 0),
    333: ('[#6]:[#16]:[#6]-,:[#6]', 0),
    334: ('[#8]-,:[#16]-,:[#6]:[#6]', 0),
    335: ('[#6]:[#7]-,:[#6]:[#6]', 0),
    336: ('[#7]-,:[#16]-,:[#6]:[#6]', 0),
    337: ('[#7]-,:[#6]:[#7]:[#6]', 0),
    338: ('[#7]:[#6]:[#6]:[#7]', 0),
    339: ('[#7]-,:[#6]:[#7]:[#7]', 0),
    340: ('[#7]-,:[#6]=,:[#7]-,:[#6]', 0),
    341: ('[#7]-,:[#6]=,:[#7&!H0]', 0),
    342: ('[#7]-,:[#6]-,:[#16]-,:[#6]', 0),
    343: ('[#6]-,:[#6]-,:[#6]=,:[#6]', 0),
    344: ('[#6]-,:[#7]:[#6&!H0]', 0),
    345: ('[#7]-,:[#6]:[#8]:[#6]', 0),
    346: ('[#8]=,:[#6]-,:[#6]:[#6]', 0),
    347: ('[#8]=,:[#6]-,:[#6]:[#7]', 0),
    348: ('[#6]-,:[#7]-,:[#6]:[#6]', 0),
    349: ('[#7]:[#7]-,:[#6&!H0]', 0),
    350: ('[#8]-,:[#6]:[#6]:[#7]', 0),
    351: ('[#8]-,:[#6]=,:[#6]-,:[#6]', 0),
    352: ('[#7]-,:[#6]:[#6]:[#7]', 0),
    353: ('[#6]-,:[#16]-,:[#6]:[#6]', 0),
    354: ('[Cl]-,:[#6]:[#6]-,:[#6]', 0),
    355: ('[#7]-,:[#6]=,:[#6&!H0]', 0),
    356: ('[Cl]-,:[#6]:[#6&!H0]', 0),
    357: ('[#7]:[#6]:[#7]-,:[#6]', 0),
    358: ('[Cl]-,:[#6]:[#6]-,:[#8]', 0),
    359: ('[#6]-,:[#6]:[#7]:[#6]', 0),
    360: ('[#6]-,:[#6]-,:[#16]-,:[#6]', 0),
    361: ('[#16]=,:[#6]-,:[#7]-,:[#6]', 0),
    362: ('[Br]-,:[#6]:[#6]-,:[#6]', 0),
    363: ('[#7&!H0]-,:[#7&!H0]', 0),
    364: ('[#16]=,:[#6]-,:[#7&!H0]', 0),
    365: ('[#6]-,:[#33]-[#8&!H0]', 0),
    366: ('[#16]:[#6]:[#6&!H0]', 0),
    367: ('[#8]-,:[#7]-,:[#6]-,:[#6]', 0),
    368: ('[#7]-,:[#7]-,:[#6]-,:[#6]', 0),
    369: ('[#6H,#6H2,#6H3]=,:[#6H,#6H2,#6H3]', 0),
    370: ('[#7]-,:[#7]-,:[#6]-,:[#7]', 0),
    371: ('[#8]=,:[#6]-,:[#7]-,:[#7]', 0),
    372: ('[#7]=,:[#6]-,:[#7]-,:[#6]', 0),
    373: ('[#6]=,:[#6]-,:[#6]:[#6]', 0),
    374: ('[#6]:[#7]-,:[#6&!H0]', 0),
    375: ('[#6]-,:[#7]-,:[#7&!H0]', 0),
    376: ('[#7]:[#6]:[#6]-,:[#6]', 0),
    377: ('[#6]-,:[#6]=,:[#6]-,:[#6]', 0),
    378: ('[#33]-,:[#6]:[#6&!H0]', 0),
    379: ('[Cl]-,:[#6]:[#6]-,:[Cl]', 0),
    380: ('[#6]:[#6]:[#7&!H0]', 0),
    381: ('[#7&!H0]-,:[#6&!H0]', 0),
    382: ('[Cl]-,:[#6]-,:[#6]-,:[Cl]', 0),
    383: ('[#7]:[#6]-,:[#6]:[#6]', 0),
    384: ('[#16]-,:[#6]:[#6]-,:[#6]', 0),
    385: ('[#16]-,:[#6]:[#6&!H0]', 0),
    386: ('[#16]-,:[#6]:[#6]-,:[#7]', 0),
    387: ('[#16]-,:[#6]:[#6]-,:[#8]', 0),
    388: ('[#8]=,:[#6]-,:[#6]-,:[#6]', 0),
    389: ('[#8]=,:[#6]-,:[#6]-,:[#7]', 0),
    390: ('[#8]=,:[#6]-,:[#6]-,:[#8]', 0),
    391: ('[#7]=,:[#6]-,:[#6]-,:[#6]', 0),
    392: ('[#7]=,:[#6]-,:[#6&!H0]', 0),
    393: ('[#6]-,:[#7]-,:[#6&!H0]', 0),
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    660: ('[#8][#6]1[#6][#6](Br)[#6][#6][#6]1', 0),
    661: ('[#16][#6]1[#6][#6]([#16])[#6][#6][#6]1', 0),
    662: ('[#16][#6]1[#6][#6]([#7])[#6][#6][#6]1', 0),
    663: ('[#16][#6]1[#6][#6](Cl)[#6][#6][#6]1', 0),
    664: ('[#16][#6]1[#6][#6](Br)[#6][#6][#6]1', 0),
    665: ('[#7][#6]1[#6][#6]([#7])[#6][#6][#6]1', 0),
    666: ('[#7][#6]1[#6][#6](Cl)[#6][#6][#6]1', 0),
    667: ('[#7][#6]1[#6][#6](Br)[#6][#6][#6]1', 0),
    668: ('Cl[#6]1[#6][#6](Cl)[#6][#6][#6]1', 0),
    669: ('Cl[#6]1[#6][#6](Br)[#6][#6][#6]1', 0),
    670: ('Br[#6]1[#6][#6](Br)[#6][#6][#6]1', 0),
    671: ('[#6][#6]1[#6]([#6])[#6][#6][#6][#6]1', 0),
    672: ('[#6][#6]1[#6]([#8])[#6][#6][#6][#6]1', 0),
    673: ('[#6][#6]1[#6]([#16])[#6][#6][#6][#6]1', 0),
    674: ('[#6][#6]1[#6]([#7])[#6][#6][#6][#6]1', 0),
    675: ('[#6][#6]1[#6](Cl)[#6][#6][#6][#6]1', 0),
    676: ('[#6][#6]1[#6](Br)[#6][#6][#6][#6]1', 0),
    677: ('[#8][#6]1[#6]([#8])[#6][#6][#6][#6]1', 0),
    678: ('[#8][#6]1[#6]([#16])[#6][#6][#6][#6]1', 0),
    679: ('[#8][#6]1[#6]([#7])[#6][#6][#6][#6]1', 0),
    680: ('[#8][#6]1[#6](Cl)[#6][#6][#6][#6]1', 0),
    681: ('[#8][#6]1[#6](Br)[#6][#6][#6][#6]1', 0),
    682: ('[#16][#6]1[#6]([#16])[#6][#6][#6][#6]1', 0),
    683: ('[#16][#6]1[#6]([#7])[#6][#6][#6][#6]1', 0),
    684: ('[#16][#6]1[#6](Cl)[#6][#6][#6][#6]1', 0),
    685: ('[#16][#6]1[#6](Br)[#6][#6][#6][#6]1', 0),
    686: ('[#7][#6]1[#6]([#7])[#6][#6][#6][#6]1', 0),
    687: ('[#7][#6]1[#6](Cl)[#6][#6][#6][#6]1', 0),
    688: ('[#7][#6]1[#6](Br)[#6][#6][#6][#6]1', 0),
    689: ('Cl[#6]1[#6](Cl)[#6][#6][#6][#6]1', 0),
    690: ('Cl[#6]1[#6](Br)[#6][#6][#6][#6]1', 0),
    691: ('Br[#6]1[#6](Br)[#6][#6][#6][#6]1', 0),
    692: ('[#6][#6]1[#6][#6]([#6])[#6][#6]1', 0),
    693: ('[#6][#6]1[#6][#6]([#8])[#6][#6]1', 0),
    694: ('[#6][#6]1[#6][#6]([#16])[#6][#6]1', 0),
    695: ('[#6][#6]1[#6][#6]([#7])[#6][#6]1', 0),
    696: ('[#6][#6]1[#6][#6](Cl)[#6][#6]1', 0),
    697: ('[#6][#6]1[#6][#6](Br)[#6][#6]1', 0),
    698: ('[#8][#6]1[#6][#6]([#8])[#6][#6]1', 0),
    699: ('[#8][#6]1[#6][#6]([#16])[#6][#6]1', 0),
    700: ('[#8][#6]1[#6][#6]([#7])[#6][#6]1', 0),
    701: ('[#8][#6]1[#6][#6](Cl)[#6][#6]1', 0),
    702: ('[#8][#6]1[#6][#6](Br)[#6][#6]1', 0),
    703: ('[#16][#6]1[#6][#6]([#16])[#6][#6]1', 0),
    704: ('[#16][#6]1[#6][#6]([#7])[#6][#6]1', 0),
    705: ('[#16][#6]1[#6][#6](Cl)[#6][#6]1', 0),
    706: ('[#16][#6]1[#6][#6](Br)[#6][#6]1', 0),
    707: ('[#7][#6]1[#6][#6]([#7])[#6][#6]1', 0),
    708: ('[#7][#6]1[#6][#6](Cl)[#6][#6]1', 0),
    709: ('[#7][#6]1[#6][#6](Br)[#6][#6]1', 0),
    710: ('Cl[#6]1[#6][#6](Cl)[#6][#6]1', 0),
    711: ('Cl[#6]1[#6][#6](Br)[#6][#6]1', 0),
    712: ('Br[#6]1[#6][#6](Br)[#6][#6]1', 0),
    713: ('[#6][#6]1[#6]([#6])[#6][#6][#6]1', 0),
    714: ('[#6][#6]1[#6]([#8])[#6][#6][#6]1', 0),
    715: ('[#6][#6]1[#6]([#16])[#6][#6][#6]1', 0),
    716: ('[#6][#6]1[#6]([#7])[#6][#6][#6]1', 0),
    717: ('[#6][#6]1[#6](Cl)[#6][#6][#6]1', 0),
    718: ('[#6][#6]1[#6](Br)[#6][#6][#6]1', 0),
    719: ('[#8][#6]1[#6]([#8])[#6][#6][#6]1', 0),
    720: ('[#8][#6]1[#6]([#16])[#6][#6][#6]1', 0),
    721: ('[#8][#6]1[#6]([#7])[#6][#6][#6]1', 0),
    722: ('[#8][#6]1[#6](Cl)[#6][#6][#6]1', 0),
    723: ('[#8][#6]1[#6](Br)[#6][#6][#6]1', 0),
    724: ('[#16][#6]1[#6]([#16])[#6][#6][#6]1', 0),
    725: ('[#16][#6]1[#6]([#7])[#6][#6][#6]1', 0),
    726: ('[#16][#6]1[#6](Cl)[#6][#6][#6]1', 0),
    727: ('[#16][#6]1[#6](Br)[#6][#6][#6]1', 0),
    728: ('[#7][#6]1[#6]([#7])[#6][#6][#6]1', 0),
    729: ('[#7][#6]1[#6](Cl)[#6][#6]1', 0),
    730: ('[#7][#6]1[#6](Br)[#6][#6][#6]1', 0),
    731: ('Cl[#6]1[#6](Cl)[#6][#6][#6]1', 0),
    732: ('Cl[#6]1[#6](Br)[#6][#6][#6]1', 0),
    733: ('Br[#6]1[#6](Br)[#6][#6][#6]1', 0)}

PubchemKeys = None


def InitKeys(keyList, keyDict):
    """ *Internal Use Only*
    generates SMARTS patterns for the keys, run once
    """
    assert len(keyList) == len(keyDict.keys()), 'length mismatch'
    for key in keyDict.keys():
        patt, count = keyDict[key]
        if patt != '?':
            sma = Chem.MolFromSmarts(patt)
            if not sma:
                print('SMARTS parser error for key #%d: %s' % (key, patt))
            else:
                keyList[key - 1] = sma, count


def calcPubChemFingerPart1(mol, **kwargs):
    """  Calculate PubChem Fingerprints （1-115; 263-881)
    **Arguments**
     - mol: the molecule to be fingerprinted
     - any extra keyword arguments are ignored
    **Returns**
      a _DataStructs.SparseBitVect_ containing the fingerprint.
    >>> m = Chem.MolFromSmiles('CNO')
    >>> bv = PubChemFingerPart1(m)
    >>> tuple(bv.GetOnBits())
    (24, 68, 69, 71, 93, 94, 102, 124, 131, 139, 151, 158, 160, 161, 164)
    >>> bv = PubChemFingerPart1(Chem.MolFromSmiles('CCC'))
    >>> tuple(bv.GetOnBits())
    (74, 114, 149, 155, 160)
    """
    global PubchemKeys
    if PubchemKeys is None:
        PubchemKeys = [(None, 0)] * len(smartsPatts.keys())
        InitKeys(PubchemKeys, smartsPatts)
    ctor = kwargs.get('ctor', DataStructs.SparseBitVect)
    res = ctor(len(PubchemKeys) + 1)
    for i, (patt, count) in enumerate(PubchemKeys):
        if patt is not None:
            if count == 0:
                res[i + 1] = mol.HasSubstructMatch(patt)
            else:
                matches = mol.GetSubstructMatches(patt)
                if len(matches) > count:
                    res[i + 1] = 1
    return res


def func_1(mol, bits):
    """ *Internal Use Only*
    Calculate PubChem Fingerprints （116-263)
    """
    ringSize = []
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    AllRingsAtom = mol.GetRingInfo().AtomRings()
    for ring in AllRingsAtom:
        ringSize.append(len(ring))
        for k, v in temp.items():
            if len(ring) == k:
                temp[k] += 1
    if temp[3] >= 2:
        bits[0] = 1
        bits[7] = 1
    elif temp[3] == 1:
        bits[0] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[14] = 1
        bits[21] = 1
    elif temp[4] == 1:
        bits[14] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[28] = 1
        bits[35] = 1
        bits[42] = 1
        bits[49] = 1
        bits[56] = 1
    elif temp[5] == 4:
        bits[28] = 1
        bits[35] = 1
        bits[42] = 1
        bits[49] = 1
    elif temp[5] == 3:
        bits[28] = 1
        bits[35] = 1
        bits[42] = 1
    elif temp[5] == 2:
        bits[28] = 1
        bits[35] = 1
    elif temp[5] == 1:
        bits[28] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[63] = 1
        bits[70] = 1
        bits[77] = 1
        bits[84] = 1
        bits[91] = 1
    elif temp[6] == 4:
        bits[63] = 1
        bits[70] = 1
        bits[77] = 1
        bits[84] = 1
    elif temp[6] == 3:
        bits[63] = 1
        bits[70] = 1
        bits[77] = 1
    elif temp[6] == 2:
        bits[63] = 1
        bits[70] = 1
    elif temp[6] == 1:
        bits[63] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[98] = 1
        bits[105] = 1
    elif temp[7] == 1:
        bits[98] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[112] = 1
        bits[119] = 1
    elif temp[8] == 1:
        bits[112] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[126] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[133] = 1
    else:
        pass

    return ringSize, bits


def func_2(mol, bits):
    """ *Internal Use Only*
    saturated or aromatic carbon-only ring
    """
    AllRingsBond = mol.GetRingInfo().BondRings()
    ringSize = []
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    for ring in AllRingsBond:
        ######### saturated
        nonsingle = False
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'SINGLE':
                nonsingle = True
                break
        if nonsingle == False:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
        ######## aromatic carbon-only     
        aromatic = True
        AllCarb = True
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'AROMATIC':
                aromatic = False
                break
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() != 6 or EndAtom.GetAtomicNum() != 6:
                AllCarb = False
                break
        if aromatic == True and AllCarb == True:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
    if temp[3] >= 2:
        bits[1] = 1
        bits[8] = 1
    elif temp[3] == 1:
        bits[1] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[15] = 1
        bits[22] = 1
    elif temp[4] == 1:
        bits[15] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[29] = 1
        bits[36] = 1
        bits[43] = 1
        bits[50] = 1
        bits[57] = 1
    elif temp[5] == 4:
        bits[29] = 1
        bits[36] = 1
        bits[43] = 1
        bits[50] = 1
    elif temp[5] == 3:
        bits[29] = 1
        bits[36] = 1
        bits[43] = 1
    elif temp[5] == 2:
        bits[29] = 1
        bits[36] = 1
    elif temp[5] == 1:
        bits[29] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[64] = 1
        bits[71] = 1
        bits[78] = 1
        bits[85] = 1
        bits[92] = 1
    elif temp[6] == 4:
        bits[64] = 1
        bits[71] = 1
        bits[78] = 1
        bits[85] = 1
    elif temp[6] == 3:
        bits[64] = 1
        bits[71] = 1
        bits[78] = 1
    elif temp[6] == 2:
        bits[64] = 1
        bits[71] = 1
    elif temp[6] == 1:
        bits[64] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[99] = 1
        bits[106] = 1
    elif temp[7] == 1:
        bits[99] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[113] = 1
        bits[120] = 1
    elif temp[8] == 1:
        bits[113] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[127] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[134] = 1
    else:
        pass
    return ringSize, bits


def func_3(mol, bits):
    """ *Internal Use Only*
    saturated or aromatic nitrogen-containing
    """
    AllRingsBond = mol.GetRingInfo().BondRings()
    ringSize = []
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    for ring in AllRingsBond:
        ######### saturated
        nonsingle = False
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'SINGLE':
                nonsingle = True
                break
        if nonsingle == False:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
        ######## aromatic nitrogen-containing    
        aromatic = True
        ContainNitro = False
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'AROMATIC':
                aromatic = False
                break
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() == 7 or EndAtom.GetAtomicNum() == 7:
                ContainNitro = True
                break
        if aromatic == True and ContainNitro == True:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
    if temp[3] >= 2:
        bits[2] = 1
        bits[9] = 1
    elif temp[3] == 1:
        bits[2] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[16] = 1
        bits[23] = 1
    elif temp[4] == 1:
        bits[16] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[30] = 1
        bits[37] = 1
        bits[44] = 1
        bits[51] = 1
        bits[58] = 1
    elif temp[5] == 4:
        bits[30] = 1
        bits[37] = 1
        bits[44] = 1
        bits[51] = 1
    elif temp[5] == 3:
        bits[30] = 1
        bits[37] = 1
        bits[44] = 1
    elif temp[5] == 2:
        bits[30] = 1
        bits[37] = 1
    elif temp[5] == 1:
        bits[30] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[65] = 1
        bits[72] = 1
        bits[79] = 1
        bits[86] = 1
        bits[93] = 1
    elif temp[6] == 4:
        bits[65] = 1
        bits[72] = 1
        bits[79] = 1
        bits[86] = 1
    elif temp[6] == 3:
        bits[65] = 1
        bits[72] = 1
        bits[79] = 1
    elif temp[6] == 2:
        bits[65] = 1
        bits[72] = 1
    elif temp[6] == 1:
        bits[65] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[100] = 1
        bits[107] = 1
    elif temp[7] == 1:
        bits[100] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[114] = 1
        bits[121] = 1
    elif temp[8] == 1:
        bits[114] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[128] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[135] = 1
    else:
        pass
    return ringSize, bits


def func_4(mol, bits):
    """ *Internal Use Only*
    saturated or aromatic heteroatom-containing
    """
    AllRingsBond = mol.GetRingInfo().BondRings()
    ringSize = []
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    for ring in AllRingsBond:
        ######### saturated
        nonsingle = False
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'SINGLE':
                nonsingle = True
                break
        if nonsingle == False:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
        ######## aromatic heteroatom-containing
        aromatic = True
        heteroatom = False
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'AROMATIC':
                aromatic = False
                break
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() not in [1, 6] or EndAtom.GetAtomicNum() not in [1, 6]:
                heteroatom = True
                break
        if aromatic == True and heteroatom == True:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
    if temp[3] >= 2:
        bits[3] = 1
        bits[10] = 1
    elif temp[3] == 1:
        bits[3] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[17] = 1
        bits[24] = 1
    elif temp[4] == 1:
        bits[17] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[31] = 1
        bits[38] = 1
        bits[45] = 1
        bits[52] = 1
        bits[59] = 1
    elif temp[5] == 4:
        bits[31] = 1
        bits[38] = 1
        bits[45] = 1
        bits[52] = 1
    elif temp[5] == 3:
        bits[31] = 1
        bits[38] = 1
        bits[45] = 1
    elif temp[5] == 2:
        bits[31] = 1
        bits[38] = 1
    elif temp[5] == 1:
        bits[31] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[66] = 1
        bits[73] = 1
        bits[80] = 1
        bits[87] = 1
        bits[94] = 1
    elif temp[6] == 4:
        bits[66] = 1
        bits[73] = 1
        bits[80] = 1
        bits[87] = 1
    elif temp[6] == 3:
        bits[66] = 1
        bits[73] = 1
        bits[80] = 1
    elif temp[6] == 2:
        bits[66] = 1
        bits[73] = 1
    elif temp[6] == 1:
        bits[66] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[101] = 1
        bits[108] = 1
    elif temp[7] == 1:
        bits[101] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[115] = 1
        bits[122] = 1
    elif temp[8] == 1:
        bits[115] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[129] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[136] = 1
    else:
        pass
    return ringSize, bits


def func_5(mol, bits):
    """ *Internal Use Only*
    unsaturated non-aromatic carbon-only
    """
    ringSize = []
    AllRingsBond = mol.GetRingInfo().BondRings()
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    for ring in AllRingsBond:
        unsaturated = False
        nonaromatic = True
        Allcarb = True
        ######### unsaturated
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'SINGLE':
                unsaturated = True
                break
        ######## non-aromatic
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name == 'AROMATIC':
                nonaromatic = False
                break
        ######## allcarb
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() != 6 or EndAtom.GetAtomicNum() != 6:
                Allcarb = False
                break
        if unsaturated == True and nonaromatic == True and Allcarb == True:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
    if temp[3] >= 2:
        bits[4] = 1
        bits[11] = 1
    elif temp[3] == 1:
        bits[4] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[18] = 1
        bits[25] = 1
    elif temp[4] == 1:
        bits[18] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[32] = 1
        bits[39] = 1
        bits[46] = 1
        bits[53] = 1
        bits[60] = 1
    elif temp[5] == 4:
        bits[32] = 1
        bits[39] = 1
        bits[46] = 1
        bits[53] = 1
    elif temp[5] == 3:
        bits[32] = 1
        bits[39] = 1
        bits[46] = 1
    elif temp[5] == 2:
        bits[32] = 1
        bits[39] = 1
    elif temp[5] == 1:
        bits[32] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[67] = 1
        bits[74] = 1
        bits[81] = 1
        bits[88] = 1
        bits[95] = 1
    elif temp[6] == 4:
        bits[67] = 1
        bits[74] = 1
        bits[81] = 1
        bits[88] = 1
    elif temp[6] == 3:
        bits[67] = 1
        bits[74] = 1
        bits[81] = 1
    elif temp[6] == 2:
        bits[67] = 1
        bits[74] = 1
    elif temp[6] == 1:
        bits[67] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[102] = 1
        bits[109] = 1
    elif temp[7] == 1:
        bits[102] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[116] = 1
        bits[123] = 1
    elif temp[8] == 1:
        bits[116] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[130] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[137] = 1
    else:
        pass
    return ringSize, bits


def func_6(mol, bits):
    """ *Internal Use Only*
    unsaturated non-aromatic nitrogen-containing
    """
    ringSize = []
    AllRingsBond = mol.GetRingInfo().BondRings()
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    for ring in AllRingsBond:
        unsaturated = False
        nonaromatic = True
        ContainNitro = False
        ######### unsaturated
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'SINGLE':
                unsaturated = True
                break
        ######## non-aromatic
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name == 'AROMATIC':
                nonaromatic = False
                break
        ######## nitrogen-containing
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() == 7 or EndAtom.GetAtomicNum() == 7:
                ContainNitro = True
                break
        if unsaturated == True and nonaromatic == True and ContainNitro == True:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
    if temp[3] >= 2:
        bits[5] = 1
        bits[12] = 1
    elif temp[3] == 1:
        bits[5] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[19] = 1
        bits[26] = 1
    elif temp[4] == 1:
        bits[19] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[33] = 1
        bits[40] = 1
        bits[47] = 1
        bits[54] = 1
        bits[61] = 1
    elif temp[5] == 4:
        bits[33] = 1
        bits[40] = 1
        bits[47] = 1
        bits[54] = 1
    elif temp[5] == 3:
        bits[33] = 1
        bits[40] = 1
        bits[47] = 1
    elif temp[5] == 2:
        bits[33] = 1
        bits[40] = 1
    elif temp[5] == 1:
        bits[33] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[68] = 1
        bits[75] = 1
        bits[82] = 1
        bits[89] = 1
        bits[96] = 1
    elif temp[6] == 4:
        bits[68] = 1
        bits[75] = 1
        bits[82] = 1
        bits[89] = 1
    elif temp[6] == 3:
        bits[68] = 1
        bits[75] = 1
        bits[82] = 1
    elif temp[6] == 2:
        bits[68] = 1
        bits[75] = 1
    elif temp[6] == 1:
        bits[68] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[103] = 1
        bits[110] = 1
    elif temp[7] == 1:
        bits[103] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[117] = 1
        bits[124] = 1
    elif temp[8] == 1:
        bits[117] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[131] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[138] = 1
    else:
        pass
    return ringSize, bits


def func_7(mol, bits):
    """ *Internal Use Only*
    unsaturated non-aromatic heteroatom-containing
    """
    ringSize = []
    AllRingsBond = mol.GetRingInfo().BondRings()
    temp = {3: 0, 4: 0, 5: 0, 6: 0, 7: 0, 8: 0, 9: 0, 10: 0}
    for ring in AllRingsBond:
        unsaturated = False
        nonaromatic = True
        heteroatom = False
        ######### unsaturated
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'SINGLE':
                unsaturated = True
                break
        ######## non-aromatic
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name == 'AROMATIC':
                nonaromatic = False
                break
        ######## heteroatom-containing
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() not in [1, 6] or EndAtom.GetAtomicNum() not in [1, 6]:
                heteroatom = True
                break
        if unsaturated == True and nonaromatic == True and heteroatom == True:
            ringSize.append(len(ring))
            for k, v in temp.items():
                if len(ring) == k:
                    temp[k] += 1
    if temp[3] >= 2:
        bits[6] = 1
        bits[13] = 1
    elif temp[3] == 1:
        bits[6] = 1
    else:
        pass
    if temp[4] >= 2:
        bits[20] = 1
        bits[27] = 1
    elif temp[4] == 1:
        bits[20] = 1
    else:
        pass
    if temp[5] >= 5:
        bits[34] = 1
        bits[41] = 1
        bits[48] = 1
        bits[55] = 1
        bits[62] = 1
    elif temp[5] == 4:
        bits[34] = 1
        bits[41] = 1
        bits[48] = 1
        bits[55] = 1
    elif temp[5] == 3:
        bits[34] = 1
        bits[41] = 1
        bits[48] = 1
    elif temp[5] == 2:
        bits[34] = 1
        bits[41] = 1
    elif temp[5] == 1:
        bits[34] = 1
    else:
        pass
    if temp[6] >= 5:
        bits[69] = 1
        bits[76] = 1
        bits[83] = 1
        bits[90] = 1
        bits[97] = 1
    elif temp[6] == 4:
        bits[69] = 1
        bits[76] = 1
        bits[83] = 1
        bits[90] = 1
    elif temp[6] == 3:
        bits[69] = 1
        bits[76] = 1
        bits[83] = 1
    elif temp[6] == 2:
        bits[69] = 1
        bits[76] = 1
    elif temp[6] == 1:
        bits[69] = 1
    else:
        pass
    if temp[7] >= 2:
        bits[104] = 1
        bits[111] = 1
    elif temp[7] == 1:
        bits[104] = 1
    else:
        pass
    if temp[8] >= 2:
        bits[118] = 1
        bits[125] = 1
    elif temp[8] == 1:
        bits[118] = 1
    else:
        pass
    if temp[9] >= 1:
        bits[132] = 1
    else:
        pass
    if temp[10] >= 1:
        bits[139] = 1
    else:
        pass
    return ringSize, bits


def func_8(mol, bits):
    """ *Internal Use Only*
    aromatic rings or hetero-aromatic rings
    """
    AllRingsBond = mol.GetRingInfo().BondRings()
    temp = {'aromatic': 0, 'heteroatom': 0}
    for ring in AllRingsBond:
        aromatic = True
        heteroatom = False
        for bondIdx in ring:
            if mol.GetBondWithIdx(bondIdx).GetBondType().name != 'AROMATIC':
                aromatic = False
                break
        if aromatic == True:
            temp['aromatic'] += 1
        for bondIdx in ring:
            BeginAtom = mol.GetBondWithIdx(bondIdx).GetBeginAtom()
            EndAtom = mol.GetBondWithIdx(bondIdx).GetEndAtom()
            if BeginAtom.GetAtomicNum() not in [1, 6] or EndAtom.GetAtomicNum() not in [1, 6]:
                heteroatom = True
                break
        if heteroatom == True:
            temp['heteroatom'] += 1
    if temp['aromatic'] >= 4:
        bits[140] = 1
        bits[142] = 1
        bits[144] = 1
        bits[146] = 1
    elif temp['aromatic'] == 3:
        bits[140] = 1
        bits[142] = 1
        bits[144] = 1
    elif temp['aromatic'] == 2:
        bits[140] = 1
        bits[142] = 1
    elif temp['aromatic'] == 1:
        bits[140] = 1
    else:
        pass
    if temp['aromatic'] >= 4 and temp['heteroatom'] >= 4:
        bits[141] = 1
        bits[143] = 1
        bits[145] = 1
        bits[147] = 1
    elif temp['aromatic'] == 3 and temp['heteroatom'] == 3:
        bits[141] = 1
        bits[143] = 1
        bits[145] = 1
    elif temp['aromatic'] == 2 and temp['heteroatom'] == 2:
        bits[141] = 1
        bits[143] = 1
    elif temp['aromatic'] == 1 and temp['heteroatom'] == 1:
        bits[141] = 1
    else:
        pass
    return bits


def calcPubChemFingerPart2(mol):  # 116-263
    """ *Internal Use Only*
    Calculate PubChem Fingerprints （116-263)
    """
    bits = [0] * 148
    bits = func_1(mol, bits)[1]
    bits = func_2(mol, bits)[1]
    bits = func_3(mol, bits)[1]
    bits = func_4(mol, bits)[1]
    bits = func_5(mol, bits)[1]
    bits = func_6(mol, bits)[1]
    bits = func_7(mol, bits)[1]
    bits = func_8(mol, bits)

    return bits


def GetPubChemFPs(mol):
    """*Internal Use Only*
    Calculate PubChem Fingerprints
    """
    mol = Chem.AddHs(mol)
    AllBits = [0] * 881
    res1 = list(calcPubChemFingerPart1(mol).ToBitString())
    for index, item in enumerate(res1[1:116]):
        if item == '1':
            AllBits[index] = 1
    for index2, item2 in enumerate(res1[116:734]):
        if item2 == '1':
            AllBits[index2 + 115 + 148] = 1
    res2 = calcPubChemFingerPart2(mol)
    for index3, item3 in enumerate(res2):
        if item3 == 1:
            AllBits[index3 + 115] = 1
    AllBits = np.array(AllBits, dtype=np.bool_)

    return AllBits


# ------------------------------------


file_path = os.path.dirname(__file__)


def GetPubChemFPInfos():
    return pd.read_excel(os.path.join(file_path, 'pubchemfp.xlsx'))


if __name__ == '__main__':
    print('-' * 10 + 'START' + '-' * 10)
    SMILES = 'C1=NC2NC3=CNCC3=CC2CC1'
    mol = Chem.MolFromSmiles(SMILES)
    mol2 = Chem.AddHs(mol)
    result = GetPubChemFPs(mol2)
    print('Molecule: %s' % SMILES)
    print('-' * 25)
    print('Results: %s' % result)
    print('-' * 10 + 'END' + '-' * 10)