From 5a85580b5f99484b957b65326ec5a19ab627d801 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Wed, 26 Feb 2020 05:26:21 -0700
Subject: Optimize qm7db reading for the rewrite
---
ml_exp/__init__.py | 2 --
ml_exp/compound.py | 3 ++-
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
--
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