From 7c8b391dddd65ff58417df80dfc79cadddf4f4e6 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Sun, 8 Dec 2019 21:54:19 -0700
Subject: First commit

---
 read_db_edata.py | 76 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100644 read_db_edata.py

(limited to 'read_db_edata.py')

diff --git a/read_db_edata.py b/read_db_edata.py
new file mode 100644
index 000000000..bf006ded2
--- /dev/null
+++ b/read_db_edata.py
@@ -0,0 +1,76 @@
+import os
+import numpy as np
+import random
+
+
+# 'hof_qm7.txt.txt' retrieved from
+# https://github.com/qmlcode/tutorial
+def read_db_edata(zi_data,
+                  data_path,
+                  r_seed=111):
+    """
+    Reads molecule database and extracts
+    its contents as usable variables.
+    zi_data: dictionary containing nuclear charge data.
+    data_path: path to the data directory.
+    r_seed: random seed.
+    """
+    os.chdir(data_path)
+
+    fname = 'hof_qm7.txt'
+    with open(fname, 'r') as infile:
+        lines = infile.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)
+
+        energy_temp[xyz_name] = np.array([hof, hof - dftb])
+
+    # Use a random seed.
+    random.seed(r_seed)
+
+    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 = []
+    # 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))
+        for j, line in enumerate(lines[2:len_lines]):
+            line_list = line.split()
+
+            mol_nc_temp_data[j] = float(zi_data[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)
+
+    # 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()])
+
+    return molecules, nuclear_charge, energy_pbe0, energy_delta
-- 
cgit v1.2.3-54-g00ecf