From a0245756b5359e6523da2b95a26bc2e147feb950 Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 10 Mar 2020 15:12:35 -0700
Subject: Add qm9 entries to read_xyz)
---
ml_exp/compound.py | 15 +++++++++++++++
1 file changed, 15 insertions(+)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index 6d9790c3b..f41710588 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -35,6 +35,8 @@ class Compound:
xyz: (path to) the xyz file.
db: which db is the xyz file based on.
"""
+ self.dbtype = None
+
# xyz and nc data.
self.name = None
self.n = None
@@ -176,6 +178,8 @@ class Compound:
with open(filename, 'r') as f:
lines = f.readlines()
+ self.dbtype = db
+
self.name = filename.split('/')[-1]
self.n = np.int32(lines[0])
self.comment = lines[1]
@@ -183,9 +187,20 @@ class Compound:
self.nc = np.empty(self.n, dtype=np.int64)
self.coordinates = np.empty((self.n, 3), dtype=np.float64)
+ if db == 'qm9':
+ self.qm9prop = np.asarray(self.comment.split()[2:],
+ dtype=np.float64)
+ self.qm9frec = np.asarray(lines[self.n + 2].split(),
+ dtype=np.float64)
+ self.qm9SMILES = lines[self.n + 3].split()
+ self.qm9InChI = lines[self.n + 4].split()
+ self.qm9Mulliken = np.empty(self.n, dtype=np.float64)
+
for i, atom in enumerate(lines[2:self.n + 2]):
atom_d = atom.split()
self.atoms.append(atom_d[0])
self.nc[i] = NUCLEAR_CHARGE[atom_d[0]]
self.coordinates[i] = np.asarray(atom_d[1:4], dtype=np.float64)
+ if db == 'qm9':
+ self.qm9Mulliken[i] = atom_d[4]
--
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