From f0ea2db1bfc21f35aa37de1ec0b0da497f5e30eb Mon Sep 17 00:00:00 2001
From: David Luevano Alvarado <55825613+luevano@users.noreply.github.com>
Date: Tue, 10 Mar 2020 14:50:26 -0700
Subject: Prepare for qm9 db
---
ml_exp/compound.py | 31 ++++++++++++++++++++++---------
ml_exp/qm7db.py | 10 +++++-----
2 files changed, 27 insertions(+), 14 deletions(-)
diff --git a/ml_exp/compound.py b/ml_exp/compound.py
index eae280d38..6d9790c3b 100644
--- a/ml_exp/compound.py
+++ b/ml_exp/compound.py
@@ -28,20 +28,31 @@ from ml_exp.representations import coulomb_matrix, lennard_jones_matrix,\
class Compound:
def __init__(self,
- xyz=None):
+ xyz=None,
+ db='qm7'):
"""
Initialization of the Compound.
xyz: (path to) the xyz file.
+ db: which db is the xyz file based on.
"""
- # General compound data.
+ # xyz and nc data.
self.name = None
self.n = None
- self.extra = None
+ self.comment = None
+ self.coordinates = None
self.atoms = None
self.nc = None
- self.coordinates = None
- self.pbe0 = None
- self.delta = None
+
+ # qm7 data.
+ self.qm7pbe0 = None
+ self.qm7delta = None
+
+ # qm9 data.
+ self.qm9prop = None
+ self.qm9Mulliken = None
+ self.qm9frec = None
+ self.qm9SMILES = None
+ self.qm9InChI = None
# Computed data.
self.cm = None
@@ -61,7 +72,7 @@ class Compound:
self.bonds_f = None
if xyz is not None:
- self.read_xyz(xyz)
+ self.read_xyz(xyz, db=db)
def gen_cm(self,
size=23,
@@ -155,17 +166,19 @@ class Compound:
size=size)
def read_xyz(self,
- filename):
+ filename,
+ db='qm7'):
"""
Reads an xyz file and adds the corresponding data to the Compound.
filename: (path to) the xyz file.
+ db: which db is the xyz file based on.
"""
with open(filename, 'r') as f:
lines = f.readlines()
self.name = filename.split('/')[-1]
self.n = np.int32(lines[0])
- self.extra = lines[1]
+ self.comment = lines[1]
self.atoms = []
self.nc = np.empty(self.n, dtype=np.int64)
self.coordinates = np.empty((self.n, 3), dtype=np.float64)
diff --git a/ml_exp/qm7db.py b/ml_exp/qm7db.py
index d4734f4ee..1e78b8d56 100644
--- a/ml_exp/qm7db.py
+++ b/ml_exp/qm7db.py
@@ -53,16 +53,16 @@ def qm7db(db_path='data',
compounds = []
for i, line in enumerate(lines):
line = line.split()
- compounds.append(Compound(f'{db_path}/{line[0]}'))
- compounds[i].pbe0 = np.float64(line[1])
- compounds[i].delta = np.float64(line[1]) - np.float64(line[2])
+ compounds.append(Compound(f'{db_path}/{line[0]}', db='qm7'))
+ compounds[i].qm7pbe0 = np.float64(line[1])
+ compounds[i].qm7delta = np.float64(line[1]) - np.float64(line[2])
if is_shuffled:
random.seed(r_seed)
random.shuffle(compounds)
- e_pbe0 = np.array([comp.pbe0 for comp in compounds], dtype=np.float64)
- e_delta = np.array([comp.delta for comp in compounds], dtype=np.float64)
+ e_pbe0 = np.array([comp.qm7pbe0 for comp in compounds], dtype=np.float64)
+ e_delta = np.array([comp.qm7delta for comp in compounds], dtype=np.float64)
if use_tf:
# Check if there's a gpu available and use the first one.
--
cgit v1.2.3-70-g09d2