EPT/data/format.py

#!/usr/bin/python
# -*- coding:utf-8 -*-
from copy import copy
from typing import List

class MoleculeVocab:

    def __init__(self):

        self.backbone_atoms = ['N', 'CA', 'C', 'O']
        self.PAD, self.MASK, self.UNK, self.GLB = '#', '*', '?', '&' # pad / mask / unk / global node
        specials = [# special added
                (self.PAD, 'PAD'), (self.MASK, 'MASK'), (self.UNK, 'UNK'), # pad / mask / unk
                (self.GLB, '<G>')  # global node
            ]
        aas = [  # amino acids (1-letter symbol, 3-letter abbreviation)
                ('G', 'GLY'), ('A', 'ALA'), ('V', 'VAL'), ('L', 'LEU'),
                ('I', 'ILE'), ('F', 'PHE'), ('W', 'TRP'), ('Y', 'TYR'),
                ('D', 'ASP'), ('H', 'HIS'), ('N', 'ASN'), ('E', 'GLU'),
                ('K', 'LYS'), ('Q', 'GLN'), ('M', 'MET'), ('R', 'ARG'),
                ('S', 'SER'), ('T', 'THR'), ('C', 'CYS'), ('P', 'PRO') # 20 aa
                # ('U', 'SEC') # 21 aa for eukaryote
            ]
        
        chemical_symbols = [ # Periodic Table
            # 1
            'H', 'He',
            # 2
            'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
            # 3
            'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
            # 4
            'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn',
            'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',
            # 5
            'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd',
            'In', 'Sn', 'Sb', 'Te', 'I', 'Xe',
            # 6
            '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',
            # 7
            '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']

        # previous
        # sms = [  # small molecules (symbol, abbreviation - upper case)
        #         ('c', 'C'), ('n', 'N'), ('o', 'O'), ('s', 'S'),
        #         ('p', 'P'), ('b', 'B'), ('cl', 'CL'), ('f', 'F'),
        #         ('br', 'BR'), ('i', 'I')
        #     ]

        sms = [(e.lower(), e.upper()) for e in chemical_symbols]

        bases = [ # bases for RNA/DNA
                ('DA', 'DA'), ('DG', 'DG'), ('DC', 'DC'), ('DT', 'DT'), # DNA
                ('R-A', 'R-A'), ('R-G', 'R-G'), ('R-C', 'R-C'), ('R-U', 'R-U')      # RNA
        ]

        self.atom_pad, self.atom_mask, self.atom_global = 'pad', 'msk', 'glb' # Avoid conflict with atom P
        self.atom_pos_pad, self.atom_pos_mask, self.atom_pos_global = 'pad', 'msk', 'glb'
        self.atom_pos_sm = 'sml'  # small molecule

        # block level vocab
        self.idx2block = specials + aas + sms + bases
        self.symbol2idx, self.abrv2idx = {}, {}
        for i, (symbol, abrv) in enumerate(self.idx2block):
            self.symbol2idx[symbol] = i
            self.abrv2idx[abrv] = i
        self.special_mask = [1 for _ in specials] + [0 for _ in aas] + [0 for _ in sms] + [0 for _ in bases]


        # atom level vocab
        self.idx2atom = [self.atom_pad, self.atom_mask, self.atom_global] + [e.upper() for e in chemical_symbols]
        self.idx2atom_pos = [self.atom_pos_pad, self.atom_pos_mask, self.atom_pos_global, '', 'A', 'B', 'G', 'D', 'E', 'Z', 'H', 'XT', 'P', self.atom_pos_sm] # SM is for atoms in small molecule, 'P' for O1P, O2P, O3P
        self.atom2idx, self.atom_pos2idx = {}, {}
        for i, atom in enumerate(self.idx2atom):
            self.atom2idx[atom] = i
        for i, atom_pos in enumerate(self.idx2atom_pos):
            self.atom_pos2idx[atom_pos] = i
    
    # block level APIs

    def abrv_to_symbol(self, abrv):
        idx = self.abrv_to_idx(abrv)
        return None if idx is None else self.idx2block[idx][0]

    def symbol_to_abrv(self, symbol):
        idx = self.symbol_to_idx(symbol)
        return None if idx is None else self.idx2block[idx][1]

    def abrv_to_idx(self, abrv):
        # abrv = abrv.upper()
        return self.abrv2idx.get(abrv, self.abrv2idx['UNK'])

    def symbol_to_idx(self, symbol):
        # symbol = symbol.upper()
        return self.symbol2idx.get(symbol, self.abrv2idx['UNK'])
    
    def idx_to_symbol(self, idx):
        return self.idx2block[idx][0]

    def idx_to_abrv(self, idx):
        return self.idx2block[idx][1]

    def get_pad_idx(self):
        return self.symbol_to_idx(self.PAD)

    def get_mask_idx(self):
        return self.symbol_to_idx(self.MASK)
    
    def get_special_mask(self):
        return copy(self.special_mask)
    
    # atom level APIs 

    def get_atom_pad_idx(self):
        return self.atom2idx[self.atom_pad]
    
    def get_atom_mask_idx(self):
        return self.atom2idx[self.atom_mask]
    
    def get_atom_global_idx(self):
        return self.atom2idx[self.atom_global]
    
    def get_atom_pos_pad_idx(self):
        return self.atom_pos2idx[self.atom_pos_pad]

    def get_atom_pos_mask_idx(self):
        return self.atom_pos2idx[self.atom_pos_mask]
    
    def get_atom_pos_global_idx(self):
        return self.atom_pos2idx[self.atom_pos_global]
    
    def idx_to_atom(self, idx):
        return self.idx2atom[idx]

    def atom_to_idx(self, atom):
        atom = atom.upper()
        return self.atom2idx.get(atom, self.atom2idx[self.atom_mask])

    def idx_to_atom_pos(self, idx):
        return self.idx2atom_pos[idx]
    
    def atom_pos_to_idx(self, atom_pos):
        return self.atom_pos2idx.get(atom_pos, self.atom_pos2idx[self.atom_pos_mask])

    # sizes

    def get_num_atom_type(self):
        return len(self.idx2atom)
    
    def get_num_atom_pos(self):
        return len(self.idx2atom_pos)

    def get_num_block_type(self):
        return len(self.special_mask) - sum(self.special_mask)

    def is_nuclear_acid(self, idx):
        return len(self.symbol2idx) - idx <= 8

    def __len__(self):
        return len(self.symbol2idx)


VOCAB = MoleculeVocab()


class Atom:
    def __init__(self, atom_name: str, coordinate: List, element: str, pos_code: str=None):
        self.name = atom_name
        self.coordinate = coordinate
        self.element = element
        if pos_code is None:
            pos_code = atom_name.lstrip(element)
            pos_code = ''.join((c for c in pos_code if not c.isdigit()))
            self.pos_code = pos_code
        else:
            self.pos_code = pos_code

    def get_element(self):
        return self.element
    
    def get_coord(self):
        return copy(self.coordinate)
    
    def get_pos_code(self):
        return self.pos_code
    
    def __str__(self) -> str:
        return self.name

    def __repr__(self) -> str:
        return f"Atom ({self.name}): {self.element}({self.pos_code}) [{','.join(['{:.4f}'.format(num) for num in self.coordinate])}]"


class Block:
    def __init__(self, symbol: str, units: List[Atom], ) -> None:
        self.symbol = symbol
        self.units = units

    def __len__(self):
        return len(self.units)
    
    def __iter__(self):
        return iter(self.units)

    def to_data(self):
        b = VOCAB.symbol_to_idx(self.symbol)
        x, a, positions = [], [], []
        for atom in self.units:
            a.append(VOCAB.atom_to_idx(atom.get_element()))
            x.append(atom.get_coord())
            positions.append(VOCAB.atom_pos_to_idx(atom.get_pos_code()))
        block_len = len(self)
        return b, a, x, positions, block_len

    
    def __repr__(self) -> str:
        return f"Block ({self.symbol}):\n\t" + '\n\t'.join([repr(at) for at in self.units]) + '\n'