scaffold3D_data.py

import logging
import os
import re
import shutil
import tarfile
import tempfile
from urllib import request as request
from urllib.error import HTTPError, URLError

import numpy as np
import torch
from ase.db import connect
from ase_io_extxyz import read_xyz
#from ase.units import Debye, Bohr, Hartree, eV

from schnetpack import Properties
from schnetpack.datasets import DownloadableAtomsData
from utility_classes import ConnectivityCompressor
from scaffold3D_preprocess_dataset import preprocess_dataset


class scaffold3Dgen(DownloadableAtomsData):
    """ scaffold3D benchmark dataset for organic molecules with up to nine non-hydrogen atoms
        from {C, O, N, F}.

        This class adds convenience functions to download scaffold3D from figshare,
        pre-process the data such that it can be used for moleculec generation with the
        G-SchNet model, and load the data into pytorch.

        Args:
            path (str): path to directory containing scaffold3D database
            subset (list, optional): indices of subset, set to None for entire dataset
                (default: None).

            precompute_distances (bool, optional): if True and the pre-processed
                database does not yet exist, the pairwise distances of atoms in the
                dataset's molecules will be computed during pre-processing and stored in
                the database (increases storage demand of the dataset but decreases
                computational cost during training as otherwise the distances will be
                computed once in every epoch, default: True)
            remove_invalid (bool, optional): if True scaffold3D molecules that do not pass the
                valence check will be removed from the training data (note 1: the
                validity is per default inferred from a pre-computed list in our
                repository but will be assessed locally if the download fails,
                note2: only works if the pre-processed database does not yet exist,
                default: True)


    """

    # general settings for the dataset
    available_atom_types = [1, 6, 7, 8, 9, 16, 17]  # all atom types found in the dataset
    atom_types_valence = [1, 6, 7, 8, 9, 16, 17]  # valence constraints of the atom types
    radial_limits = [0.9, 1.7]  # minimum and maximum distance between neighboring atoms

    # properties
    A = 'rotational_constant_A'
    B = 'rotational_constant_B'
    C = 'rotational_constant_C'
    mu = 'dipole_moment'
    alpha = 'isotropic_polarizability'
    homo = 'homo'
    lumo = 'lumo'
    gap = 'gap'
    r2 = 'electronic_spatial_extent'
    zpve = 'zpve'
    U0 = 'energy_U0'
    U = 'energy_U'
    H = 'enthalpy_H'
    G = 'free_energy'
    Cv = 'heat_capacity'

    properties = [
        A, B, C, mu, alpha,
        homo, lumo, gap, r2, zpve,
        U0, U, H, G, Cv
    ]

    units = [1., 1., 1., 1., 1.,
             1., 1., 1.,
             1., 1.,
             1., 1., 1.,
             1., 1.,
            ]

    units_dict = dict(zip(properties, units))

    connectivity_compressor = ConnectivityCompressor()

    def __init__(self, path, subset=None, download=True, precompute_distances=True,
                 remove_invalid=True):
        self.path = path
        self.dbpath = os.path.join(self.path,'scaffold3Dgen.db')#
        self.precompute_distances = precompute_distances
        self.remove_invalid = remove_invalid
    
        super().__init__(self.dbpath, subset=subset,
                         available_properties=self.properties,
                         units=self.units, download=download)

    def create_subset(self, idx):
        """
        Returns a new dataset that only consists of provided indices.

        Args:
            idx (numpy.ndarray): subset indices

        Returns:
            schnetpack.data.AtomsData: dataset with subset of original data
        """ 
        idx = np.array(idx)
       
        subidx = idx if self.subset is None or len(idx) == 0 \
            else np.array(self.subset)[idx]
        return type(self)(self.path, subidx, download=False)

    def get_properties(self, idx):
        #logging.info("indixes.....",str(idx))
        _idx = self._subset_index(idx)
        with connect(self.dbpath) as conn:
            row = conn.get(_idx+1)
        at = row.toatoms()
        properties = {}
        properties[Properties.Z] = torch.LongTensor(at.numbers.astype(np.int))
        positions = at.positions.astype(np.float32)
        properties[Properties.R] = torch.FloatTensor(positions)
        properties[Properties.cell] = torch.FloatTensor(at.cell.astype(np.float32))

        # recover connectivity matrix from compressed format
        con_mat = self.connectivity_compressor.decompress(row.data['con_mat'])
        # save in dictionary
        properties['_con_mat'] = torch.FloatTensor(con_mat.astype(np.float32))

        # extract pre-computed distances (if they exist)
        if 'dists' in row.data:
            properties['dists'] = row.data['dists']

        # get atom environment
        nbh_idx, offsets = self.environment_provider.get_environment(at)
           # store neighbors, cell, and index
        properties[Properties.neighbors] = torch.LongTensor(nbh_idx.astype(np.int))
        properties[Properties.cell_offset] = torch.FloatTensor(
            offsets.astype(np.float32))
        properties["_idx"] = torch.LongTensor(np.array([idx], dtype=np.int))

        return at, properties

    def _download(self):
        works = True
        if not os.path.exists(self.dbpath):
            scaffold3D_path = os.path.join(self.path, 'scaffold3D.db')
            if not os.path.exists(scaffold3D_path):
                works = works and self._load_data()
            works = works and self._preprocess_scaffold3D()
        return works

    def _load_data(self):
        logging.info('Downloading GDB-9 data...')
        tmpdir = tempfile.mkdtemp('gdb9')
        tar_path = os.path.join(tmpdir, 'gdb9.tar.gz')
        raw_path = os.path.join(tmpdir, 'gdb9_xyz')
        url = 'https://ndownloader.figshare.com/files/3195389'

        try:
            request.urlretrieve(url, tar_path)
            logging.info('Done.')
        except HTTPError as e:
            logging.error('HTTP Error:', e.code, url)
            return False
        except URLError as e:
            logging.error('URL Error:', e.reason, url)
            return False

        logging.info('Extracting data from tar file...')
        tar = tarfile.open(tar_path)
        tar.extractall(raw_path)
        tar.close()
        logging.info('Done.')
        logging.info("Raw path----------",raw_path)
        logging.info('Parsing xyz files...')
        with connect(os.path.join(self.path, 'scaffold3D.db')) as con:
            ordered_files = sorted(os.listdir(raw_path),
                                   key=lambda x: (int(re.sub('\D', '', x)), x))
            for i, xyzfile in enumerate(ordered_files):
                xyzfile = os.path.join(raw_path, xyzfile)

                if (i + 1) % 10000 == 0:
                    logging.info('Parsed: {:6d} / 133885'.format(i + 1))
                properties = {}
                tmp = os.path.join(tmpdir, 'tmp.xyz')

                with open(xyzfile, 'r') as f:
                    lines = f.readlines()
                    l = lines[1].split()[2:]
                    for pn, p in zip(self.properties, l):
                        properties[pn] = float(p) * self.units[pn]
                    with open(tmp, "wt") as fout:
                        for line in lines:
                            fout.write(line.replace('*^', 'e'))

                with open(tmp, 'r') as f:
                    ats = list(read_xyz(f, 0))[0]
                con.write(ats, data=properties)
        logging.info('Done.')

        shutil.rmtree(tmpdir)

        return True

    def _preprocess_scaffold3D(self):
        # try to download pre-computed list of invalid molecules
        logging.info('Downloading pre-computed list of invalid scaffold3D molecules...')
        raw_path = os.path.join(self.path, 'scaffold3D_invalid.txt')
        url = 'https://github.com/atomistic-machine-learning/G-SchNet/blob/master/' \
              'scaffold3D_invalid.txt?raw=true'

        try:
            request.urlretrieve(url, raw_path)
            logging.info('Done.')
            invalid_list = np.loadtxt(raw_path)
        except HTTPError as e:
            logging.error('HTTP Error:', e.code, url)
            logging.info('CAUTION: Could not download pre-computed list, will assess '
                         'validity during pre-processing.')
            invalid_list = None
        except URLError as e:
            logging.error('URL Error:', e.reason, url)
            logging.info('CAUTION: Could not download pre-computed list, will assess '
                         'validity during pre-processing.')
            invalid_list = None
        # check validity of molecules and store connectivity matrices and inter-atomic
        # distances in database as a pre-processing step
        scaffold3D_db = os.path.join(self.path, 'scaffold3D.db')
        valence_list = \
            np.array([self.available_atom_types, self.atom_types_valence]).flatten('F')
        preprocess_dataset(datapath=scaffold3D_db, valence_list=valence_list,
                           n_threads=8, n_mols_per_thread=125, logging_print=True,
                           new_db_path=self.dbpath,
                           precompute_distances=self.precompute_distances,
                           remove_invalid=False,
                           invalid_list=None)
        return True

    def get_available_properties(self, available_properties):
        # we don't use properties other than stored connectivity matrices (and
        # distances, if they were precomputed) so we skip this part
        return available_properties