From fcbee42bc272ecb68143b176a9a3f36a4dcb3ad7 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Sun, 13 Aug 2017 23:20:41 +0100
Subject: [PATCH] added writer for solvation matrix.
---
solventmapcreator/io/solvationmapwriter.py | 41 +++++++++++++
.../test/iotest/solvationmapwritertest.py | 59 +++++++++++++++++++
.../test/resources/similmatrix.csv | 4 ++
.../test/solvationmapcreatortests.py | 3 +-
4 files changed, 106 insertions(+), 1 deletion(-)
create mode 100644 solventmapcreator/io/solvationmapwriter.py
create mode 100644 solventmapcreator/test/iotest/solvationmapwritertest.py
create mode 100644 solventmapcreator/test/resources/similmatrix.csv
diff --git a/solventmapcreator/io/solvationmapwriter.py b/solventmapcreator/io/solvationmapwriter.py
new file mode 100644
index 0000000..f5130a7
--- /dev/null
+++ b/solventmapcreator/io/solvationmapwriter.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for writing out the solvation values generated for a solvent map.
+
+Format is
+
+ Y1 Y2 ...
+X1 S(X1,Y1) S(X1,Y2) ...
+X2 S(X2,Y1) S(X2,Y2) ...
+. .
+. .
+. .
+XN S(XN,Y1) S(XN,Y2) ...
+
+@author: mark
+"""
+
+import logging
+import csv
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def write_matrix_to_file(filename, x_values, y_values, solvation_matrix):
+ """This writes the matrix to file.
+ """
+ with open(filename, 'w') as outfile:
+ csv_writer = csv.writer(outfile, delimiter='\t',
+ quoting=csv.QUOTE_NONE)
+ csv_writer.writerow(["", *y_values])
+ for i in range(len(x_values)):
+ csv_writer.writerow(write_matrix_line(x_values[i], solvation_matrix[i]))
+ return 0
+
+
+def write_matrix_line(x_value, solvation_matrix_row):
+ """This creates the list of entries ready for writing.
+ """
+ return ["{:.3f}".format(x_value), *["{:.7f}".format(val) for val in solvation_matrix_row]]
diff --git a/solventmapcreator/test/iotest/solvationmapwritertest.py b/solventmapcreator/test/iotest/solvationmapwritertest.py
new file mode 100644
index 0000000..93232b2
--- /dev/null
+++ b/solventmapcreator/test/iotest/solvationmapwritertest.py
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Sun Aug 13 22:42:58 2017
+
+@author: mark
+"""
+
+import logging
+import numpy as np
+import os
+import unittest
+import solventmapcreator.io.solvationmapwriter as solvmapwriter
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SolvationMapWriterTestCase(unittest.TestCase):
+ """Test case for the solvation
+ """
+ def setUp(self):
+ """Set up for tests.
+ """
+ self.x_list = np.array([float(x) for x in range(3)])
+ self.y_list = np.array([float(x) for x in range(2)])
+ self.similarity_matrix = np.array([[-4.332289, -5.403718],
+ [-5.403718, -5.757629],
+ [-6.475146, -6.167992]])
+ def tearDown(self):
+ """Clean up after tests
+ """
+ del self.x_list
+ del self.y_list
+ del self.similarity_matrix
+ if os.path.isfile("actualsimilmatrix.csv"):
+ os.remove("actualsimilmatrix.csv")
+ def test_write_similarity_matrix_file(self):
+ """Test to see if expected file is written out.
+ """
+ expected_file_name = "resources/similmatrix.csv"
+ actual_file_name = "actualsimilmatrix.csv"
+ simil_out_file = solvmapwriter.write_matrix_to_file(actual_file_name,
+ self.x_list,
+ self.y_list,
+ self.similarity_matrix)
+ self.assertEqual(0, simil_out_file)
+ with open(expected_file_name, 'r') as exp_file:
+ exp_file_lines = exp_file.readlines()
+ with open(actual_file_name, 'r') as act_file:
+ act_file_lines = act_file.readlines()
+ self.assertListEqual(act_file_lines, exp_file_lines)
+ def test_create_file_line(self):
+ """Test to see if expected list is returned.
+ """
+ expected_list = ['0.000', '-4.3322890', '-5.4037180']
+ actual_list = solvmapwriter.write_matrix_line(self.x_list[0], self.similarity_matrix[0])
+ self.assertListEqual(expected_list, actual_list)
+
\ No newline at end of file
diff --git a/solventmapcreator/test/resources/similmatrix.csv b/solventmapcreator/test/resources/similmatrix.csv
new file mode 100644
index 0000000..d4471c7
--- /dev/null
+++ b/solventmapcreator/test/resources/similmatrix.csv
@@ -0,0 +1,4 @@
+ 0.0 1.0
+0.000 -4.3322890 -5.4037180
+1.000 -5.4037180 -5.7576290
+2.000 -6.4751460 -6.1679920
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
index 0eec45c..1b714e1 100644
--- a/solventmapcreator/test/solvationmapcreatortests.py
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -15,6 +15,7 @@ from solventmapcreator.test.iotest.polynomialdatareadertest import PolynomialDat
from solventmapcreator.test.iotest.similaritymatrixwritertest import SimilarityMatrixWriterTestCase
from solventmapcreator.test.iotest.similaritymatrixreadertest import SimilarityMatrixReaderTestCase
from solventmapcreator.test.iotest.linkagewritertest import LinkageWriterTestCase
+from solventmapcreator.test.iotest.solvationmapwritertest import SolvationMapWriterTestCase
from solventmapcreator.test.solvationcalculationtest.solvationcalculatortest import SolvationCalculatorTestCase
from solventmapcreator.test.solvationcalculationtest.solvationmapgeneratortest import SolvationMapGeneratorTestCase
from solventmapcreator.test.solvationcalculationtest.solvationplotinformationtest import SolvationPlotInformationTestCase
@@ -34,7 +35,7 @@ LOGGER.setLevel(logging.WARN)
IO_TEST_CASES = [SolvationEnergyReaderTestCase, SolventXMLReaderTestCase,
PolynomialDataWriterTestCase, PolynomialDataReaderTestCase,
SimilarityMatrixReaderTestCase, SimilarityMatrixWriterTestCase,
- LinkageWriterTestCase]
+ LinkageWriterTestCase, SolvationMapWriterTestCase]
SOLVATION_CALCULATION_TEST_CASES = [SolvationCalculatorTestCase,
SolvationMapGeneratorTestCase,
--
GitLab