From 2e2f758f9e2bd097bb33cc869026274b4786ede8 Mon Sep 17 00:00:00 2001
From: Logan Ward <ward.logan.t@gmail.com>
Date: Tue, 29 Jan 2019 16:42:36 -0600
Subject: [PATCH 1/2] Made Compound able to read file-like objects
I added a six dependency to make life easier
---
qml/data/compound.py | 15 +++++++++------
requirements.txt | 1 +
test/test_compound.py | 12 ++++++++++--
3 files changed, 20 insertions(+), 8 deletions(-)
diff --git a/qml/data/compound.py b/qml/data/compound.py
index 558ab6d84..263ebfa21 100644
--- a/qml/data/compound.py
+++ b/qml/data/compound.py
@@ -22,6 +22,7 @@
from __future__ import print_function
+from six import string_types
import numpy as np
import collections
@@ -341,13 +342,15 @@ def generate_acsf(self, elements = [1,6,7,8,16], nRs2 = 3, nRs3 = 3, nTs = 3, et
def read_xyz(self, filename):
"""(Re-)initializes the Compound-object with data from an xyz-file.
- :param filename: Input xyz-filename.
- :type filename: string
- """
+ :param filename: Input xyz-filename or file-like obejct
+ :type filename: string or file-like object
+ """
- f = open(filename, "r")
- lines = f.readlines()
- f.close()
+ if isinstance(filename, string_types):
+ with open(filename, "r") as f:
+ lines = f.readlines()
+ else:
+ lines = filename.readlines()
self.natoms = int(lines[0])
self.atomtypes = []
diff --git a/requirements.txt b/requirements.txt
index afdaacacd..bfcdf5a3d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,3 +2,4 @@ numpy>=1.13
scipy
scikit-learn
ase
+six
diff --git a/test/test_compound.py b/test/test_compound.py
index 0a902d699..0d7727994 100644
--- a/test/test_compound.py
+++ b/test/test_compound.py
@@ -50,8 +50,16 @@ def test_compound():
ref_atomtypes = ['C', 'Cl', 'Br', 'H', 'H']
ref_charges = [ 6, 17, 35, 1 , 1]
- assert compare_lists(ref_atomtypes, c.atomtypes), "Failed parsing atomtypes"
- assert compare_lists(ref_charges, c.nuclear_charges), "Failed parsing nuclear_charges"
+ assert compare_lists(ref_atomtypes, c2.atomtypes), "Failed parsing atomtypes"
+ assert compare_lists(ref_charges, c2.nuclear_charges), "Failed parsing nuclear_charges"
+
+ # Test extended xyz from a file pointer rather than a filename
+ with open(test_dir + "/data/compound_test.exyz") as fp:
+ c3 = Compound(xyz=fp)
+
+ assert compare_lists(ref_atomtypes, c3.atomtypes), "Failed parsing atomtypes"
+ assert compare_lists(ref_charges, c3.nuclear_charges), "Failed parsing nuclear_charges"
+
if __name__ == "__main__":
From db848a02d1fb3595d69672243d3a0b6bbed67a26 Mon Sep 17 00:00:00 2001
From: Logan Ward <ward.logan.t@gmail.com>
Date: Tue, 29 Jan 2019 16:54:38 -0600
Subject: [PATCH 2/2] Give Compound a name only if there is a filename
---
qml/data/compound.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/qml/data/compound.py b/qml/data/compound.py
index 263ebfa21..b2b7d9f5c 100644
--- a/qml/data/compound.py
+++ b/qml/data/compound.py
@@ -357,7 +357,8 @@ def read_xyz(self, filename):
self.nuclear_charges = np.empty(self.natoms, dtype=int)
self.coordinates = np.empty((self.natoms, 3), dtype=float)
- self.name = filename
+ # Give the Compound a name if it is a string
+ self.name = filename if isinstance(filename, string_types) else "Compound"
for i, line in enumerate(lines[2:self.natoms+2]):
tokens = line.split()