diff options
| -rw-r--r-- | ml_exp/__init__.py | 2 | ||||
| -rw-r--r-- | ml_exp/compound.py | 3 | ||||
| -rw-r--r-- | ml_exp/qm7db.py | 68 |
3 files changed, 16 insertions, 57 deletions
diff --git a/ml_exp/__init__.py b/ml_exp/__init__.py index e9dd83eae..d685e7ccc 100644 --- a/ml_exp/__init__.py +++ b/ml_exp/__init__.py @@ -25,8 +25,6 @@ from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\ first_neighbor_matrix, adjacency_matrix, check_bond, bag_of_stuff from ml_exp.math import cholesky_solve -# If somebody does "from package import *", this is what they will -# be able to access: __all__ = ['Compound', 'coulomb_matrix', 'lennard_jones_matrix', diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 8b6af0ae9..0a8b89610 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -33,7 +33,7 @@ class Compound: Initialization of the Compound. xyz: (path to) the xyz file. """ - # empty_array = np.asarray([], dtype=float) + self.name = None self.n = None self.atoms = None @@ -137,6 +137,7 @@ class Compound: with open(filename, 'r') as f: lines = f.readlines() + self.name = filename.split('/')[-1] self.n = int(lines[0]) self.atoms = [] self.atoms_nc = np.empty(self.n, dtype=int) diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py index 1f1115ba0..f9950c317 100644 --- a/ml_exp/qm7db.py +++ b/ml_exp/qm7db.py @@ -20,6 +20,7 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ +from ml_exp.compound import Compound import numpy as np import random @@ -28,72 +29,31 @@ import random # https://github.com/qmlcode/tutorial def qm7db(nc, db_path='data', + is_shuffled=True, r_seed=111): """ Creates a list of compounds with the qm7 database. nc: dictionary containing nuclear charge data. db_path: path to the database directory. + is_shuffled: if the resulting list of compounds should be shuffled. r_seed: random seed to use for the shuffling. """ - fname = f'{db_path}/hof_qm7.txt' with open(fname, 'r') as f: lines = f.readlines() - # Temporary energy dictionary. - energy_temp = dict() - - for line in lines: - xyz_data = line.split() - - xyz_name = xyz_data[0] - hof = float(xyz_data[1]) - dftb = float(xyz_data[2]) - # print(xyz_name, hof, dftb) + compounds = [] + for i, line in enumerate(lines): + line = line.split() + compounds.append(Compound(f'{db_path}/{line[0]}')) + compounds[i].pbe0 = float(line[1]) + compounds[i].delta = float(line[1]) - float(line[2]) - energy_temp[xyz_name] = np.array([hof, hof - dftb]) - - # Use a random seed. + # Shuffle the compounds list random.seed(r_seed) + random.shuffle(compounds) - et_keys = list(energy_temp.keys()) - random.shuffle(et_keys) - - # Temporary energy dictionary, shuffled. - energy_temp_shuffled = dict() - for key in et_keys: - energy_temp_shuffled.update({key: energy_temp[key]}) - - mol_data = [] - mol_nc_data = [] - atoms = [] - # Actual reading of the xyz files. - for i, k in enumerate(energy_temp_shuffled.keys()): - with open(k, 'r') as xyz_file: - lines = xyz_file.readlines() - - len_lines = len(lines) - mol_temp_data = [] - mol_nc_temp_data = np.array(np.zeros(len_lines-2)) - atoms_temp = [] - for j, line in enumerate(lines[2:len_lines]): - line_list = line.split() - - atoms_temp.append(line_list[0]) - mol_nc_temp_data[j] = float(nc[line_list[0]]) - line_data = np.array(np.asarray(line_list[1:4], dtype=float)) - mol_temp_data.append(line_data) - - mol_data.append(mol_temp_data) - mol_nc_data.append(mol_nc_temp_data) - atoms.append(atoms_temp) - - # Convert everything to a numpy array. - molecules = np.array([np.array(mol) for mol in mol_data]) - nuclear_charge = np.array([nc_d for nc_d in mol_nc_data]) - energy_pbe0 = np.array([energy_temp_shuffled[k][0] - for k in energy_temp_shuffled.keys()]) - energy_delta = np.array([energy_temp_shuffled[k][1] - for k in energy_temp_shuffled.keys()]) + e_pbe0 = np.array([compound.pbe0 for compound in compounds], dtype=float) + e_delta = np.array([compound.delta for compound in compounds], dtype=float) - return molecules, nuclear_charge, energy_pbe0, energy_delta, atoms + return compounds, e_pbe0, e_delta |