molscribe/constants.py

from typing import List
import re

ORGANIC_SET = {'B', 'C', 'N', 'O', 'P', 'S', 'F', 'Cl', 'Br', 'I'}

RGROUP_SYMBOLS = ['R', 'R1', 'R2', 'R3', 'R4', 'R5', 'R6', 'R7', 'R8', 'R9', 'R10', 'R11', 'R12', "R'",
                  'Ra', 'Rb', 'Rc', 'Rd', 'X', 'Y', 'Z', 'Q', 'A', 'E', 'Ar']

PLACEHOLDER_ATOMS = ["Lv", "Lu", "Nd", "Yb", "At", "Fm", "Er"]


class Substitution(object):
    '''Define common substitutions for chemical shorthand'''
    def __init__(self, abbrvs, smarts, smiles, probability):
        assert type(abbrvs) is list
        self.abbrvs = abbrvs
        self.smarts = smarts
        self.smiles = smiles
        self.probability = probability


SUBSTITUTIONS: List[Substitution] = [
    Substitution(['NO2', 'O2N'], '[N+](=O)[O-]', "[N+](=O)[O-]", 0.5),
    Substitution(['OCOCH3'], '[#8]-[#6](=[#8])-[#6]', "[O]C(=O)C]", 0.5),
    Substitution(['CHO', 'OHC'], '[CH1](=O)', "[CH1](=O)", 0.5),
    Substitution(['CO2Et', 'COOEt', 'EtO2C'], 'C(=O)[OH0;D2][CH2;D2][CH3]', "[C](=O)OCC", 0.5),

    Substitution(['OAc'], '[OH0;X2]C(=O)[CH3]', "[O]C(=O)C", 0.7),
    Substitution(['NHAc'], '[NH1;D2]C(=O)[CH3]', "[NH]C(=O)C", 0.7),
    Substitution(['Ac'], 'C(=O)[CH3]', "[C](=O)C", 0.1),

    Substitution(['OBz'], '[OH0;D2]C(=O)[cH0]1[cH][cH][cH][cH][cH]1', "[O]C(=O)c1ccccc1", 0.7),  # Benzoyl
    Substitution(['Bz'], 'C(=O)[cH0]1[cH][cH][cH][cH][cH]1', "[C](=O)c1ccccc1", 0.2),  # Benzoyl

    Substitution(['OBn'], '[OH0;D2][CH2;D2][cH0]1[cH][cH][cH][cH][cH]1', "[O]Cc1ccccc1", 0.7),  # Benzyl
    Substitution(['Bn'], '[CH2;D2][cH0]1[cH][cH][cH][cH][cH]1', "[CH2]c1ccccc1", 0.2),  # Benzyl

    Substitution(['NHBoc'], '[NH1;D2]C(=O)OC([CH3])([CH3])[CH3]', "[NH1]C(=O)OC(C)(C)C", 0.6),
    Substitution(['NBoc'], '[NH0;D3]C(=O)OC([CH3])([CH3])[CH3]', "[NH1]C(=O)OC(C)(C)C", 0.6),
    Substitution(['Boc'], 'C(=O)OC([CH3])([CH3])[CH3]', "[C](=O)OC(C)(C)C", 0.2),

    Substitution(['Cbm'], 'C(=O)[NH2;D1]', "[C](=O)N", 0.2),
    Substitution(['Cbz'], 'C(=O)OC[cH]1[cH][cH][cH1][cH][cH]1', "[C](=O)OCc1ccccc1", 0.4),
    Substitution(['Cy'], '[CH1;X3]1[CH2][CH2][CH2][CH2][CH2]1', "[CH1]1CCCCC1", 0.3),
    Substitution(['Fmoc'], 'C(=O)O[CH2][CH1]1c([cH1][cH1][cH1][cH1]2)c2c3c1[cH1][cH1][cH1][cH1]3',
                 "[C](=O)OCC1c(cccc2)c2c3c1cccc3", 0.6),
    Substitution(['Mes'], '[cH0]1c([CH3])cc([CH3])cc([CH3])1', "[c]1c(C)cc(C)cc(C)1", 0.5),
    Substitution(['OMs'], '[OH0;D2]S(=O)(=O)[CH3]', "[O]S(=O)(=O)C", 0.7),
    Substitution(['Ms'], 'S(=O)(=O)[CH3]', "[S](=O)(=O)C", 0.2),
    Substitution(['Ph'], '[cH0]1[cH][cH][cH1][cH][cH]1', "[c]1ccccc1", 0.5),
    Substitution(['PMB'], '[CH2;D2][cH0]1[cH1][cH1][cH0](O[CH3])[cH1][cH1]1', "[CH2]c1ccc(OC)cc1", 0.2),
    Substitution(['Py'], '[cH0]1[n;+0][cH1][cH1][cH1][cH1]1', "[c]1ncccc1", 0.1),
    Substitution(['SEM'], '[CH2;D2][CH2][Si]([CH3])([CH3])[CH3]', "[CH2]CSi(C)(C)C", 0.2),
    Substitution(['Suc'], 'C(=O)[CH2][CH2]C(=O)[OH]', "[C](=O)CCC(=O)O", 0.2),
    Substitution(['TBS'], '[Si]([CH3])([CH3])C([CH3])([CH3])[CH3]', "[Si](C)(C)C(C)(C)C", 0.5),
    Substitution(['TBZ'], 'C(=S)[cH]1[cH][cH][cH1][cH][cH]1', "[C](=S)c1ccccc1", 0.2),
    Substitution(['OTf'], '[OH0;D2]S(=O)(=O)C(F)(F)F', "[O]S(=O)(=O)C(F)(F)F", 0.7),
    Substitution(['Tf'], 'S(=O)(=O)C(F)(F)F', "[S](=O)(=O)C(F)(F)F", 0.2),
    Substitution(['TFA'], 'C(=O)C(F)(F)F', "[C](=O)C(F)(F)F", 0.3),
    Substitution(['TMS'], '[Si]([CH3])([CH3])[CH3]', "[Si](C)(C)C", 0.5),
    Substitution(['Ts'], 'S(=O)(=O)c1[cH1][cH1][cH0]([CH3])[cH1][cH1]1', "[S](=O)(=O)c1ccc(C)cc1", 0.6),  # Tos

    # Alkyl chains
    Substitution(['OMe', 'MeO'], '[OH0;D2][CH3;D1]', "[O]C", 0.3),
    Substitution(['SMe', 'MeS'], '[SH0;D2][CH3;D1]', "[S]C", 0.3),
    Substitution(['NMe', 'MeN'], '[N;X3][CH3;D1]', "[NH]C", 0.3),
    Substitution(['Me'], '[CH3;D1]', "[CH3]", 0.1),
    Substitution(['OEt', 'EtO'], '[OH0;D2][CH2;D2][CH3]', "[O]CC", 0.5),
    Substitution(['Et', 'C2H5'], '[CH2;D2][CH3]', "[CH2]C", 0.3),
    Substitution(['Pr', 'nPr', 'n-Pr'], '[CH2;D2][CH2;D2][CH3]', "[CH2]CC", 0.3),
    Substitution(['Bu', 'nBu', 'n-Bu'], '[CH2;D2][CH2;D2][CH2;D2][CH3]', "[CH2]CCC", 0.3),

    # Branched
    Substitution(['iPr', 'i-Pr'], '[CH1;D3]([CH3])[CH3]', "[CH1](C)C", 0.2),
    Substitution(['iBu', 'i-Bu'], '[CH2;D2][CH1;D3]([CH3])[CH3]', "[CH2]C(C)C", 0.2),
    Substitution(['OiBu'], '[OH0;D2][CH2;D2][CH1;D3]([CH3])[CH3]', "[O]CC(C)C", 0.2),
    Substitution(['OtBu'], '[OH0;D2][CH0]([CH3])([CH3])[CH3]', "[O]C(C)(C)C", 0.6),
    Substitution(['tBu', 't-Bu'], '[CH0]([CH3])([CH3])[CH3]', "[C](C)(C)C", 0.3),

    # Other shorthands (MIGHT NOT WANT ALL OF THESE)
    Substitution(['CF3', 'F3C'], '[CH0;D4](F)(F)F', "[C](F)(F)F", 0.5),
    Substitution(['NCF3', 'F3CN'], '[N;X3][CH0;D4](F)(F)F', "[NH]C(F)(F)F", 0.5),
    Substitution(['OCF3', 'F3CO'], '[OH0;X2][CH0;D4](F)(F)F', "[O]C(F)(F)F", 0.5),
    Substitution(['CCl3'], '[CH0;D4](Cl)(Cl)Cl', "[C](Cl)(Cl)Cl", 0.5),
    Substitution(['CO2H', 'HO2C', 'COOH'], 'C(=O)[OH]', "[C](=O)O", 0.5),  # COOH
    Substitution(['CN', 'NC'], 'C#[ND1]', "[C]#N", 0.5),
    Substitution(['OCH3', 'H3CO'], '[OH0;D2][CH3]', "[O]C", 0.4),
    Substitution(['SO3H'], 'S(=O)(=O)[OH]', "[S](=O)(=O)O", 0.4),
    Substitution(['CH3O'], '[OH0;D2][CH3]', "[O]C", 0),
    Substitution(['PhCH2CH2'], '[OH0;D2][CH3]', "C1=CC=CC=C1CC", 0),
    Substitution(['SO2ToI','SO2Tol'], '[OH0;D2][CH3]', "CS(=O)(=O)C1=CC=CC=C1", 0),






]

ABBREVIATIONS = {abbrv: sub for sub in SUBSTITUTIONS for abbrv in sub.abbrvs}

VALENCES = {
    "H": [1], "Li": [1], "Be": [2], "B": [3], "C": [4], "N": [3, 5], "O": [2], "F": [1],
    "Na": [1], "Mg": [2], "Al": [3], "Si": [4], "P": [5, 3], "S": [6, 2, 4], "Cl": [1], "K": [1], "Ca": [2],
    "Br": [1], "I": [1]
}

ELEMENTS = [
    "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
    "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca",
    "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn",
    "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr",
    "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn",
    "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd",
    "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb",
    "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg",
    "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th",
    "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm",
    "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds",
    "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og"
]

COLORS = {
    u'c': '0.0,0.75,0.75', u'b': '0.0,0.0,1.0', u'g': '0.0,0.5,0.0', u'y': '0.75,0.75,0',
    u'k': '0.0,0.0,0.0', u'r': '1.0,0.0,0.0', u'm': '0.75,0,0.75'
}

# tokens of condensed formula
FORMULA_REGEX = re.compile(
    '(' + '|'.join(list(ABBREVIATIONS.keys())) + '|R[0-9]*|[A-Z][a-z]+|[A-Z]|[0-9]+|\(|\))')