diff --git a/phasecalculator/runners/similarityanalysisrunner.py b/phasecalculator/runners/similarityanalysisrunner.py
index f2ba03bf890f3712bb1895bca22fa218485ec777..de15917d8c2deacadda8d00a9e7c49778120deae 100755
--- a/phasecalculator/runners/similarityanalysisrunner.py
+++ b/phasecalculator/runners/similarityanalysisrunner.py
@@ -15,14 +15,155 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
-Created on Tue Jan 7 16:34:17 2020
+Script for running similarity analysis.
@author: Mark
"""
import logging
+import phasecalculator.runners.phasetransferrunner as phaserun
+import phasecalculator.analysis.similarityanalysis as simanalysis
+import phasecalculator.io.solventextractor as solvextract
+import phasecalculator.io.polynomialio as polyio
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
+def run_similarity_analysis(poly_filename_list, output_type, output_dir, output_filename="similaritymatrix.csv"):
+ """
+
+ Parameters
+ ----------
+ poly_filename_list : TYPE
+ DESCRIPTION.
+ output_type : TYPE
+ DESCRIPTION.
+ output_dir : TYPE
+ DESCRIPTION.
+ output_filename : TYPE, optional
+ DESCRIPTION. The default is "similaritymatrix.csv".
+
+ Returns
+ -------
+ None.
+
+ """
+ if output_type == "all":
+ simanalysis.compare_all_solvents(poly_filename_list, output_dir, output_filename)
+ elif output_type == "mixturecomparison":
+ simanalysis.compare_solvent_list(poly_filename_list, output_dir, output_filename)
+ elif output_type == "purecomparison":
+ simanalysis.compare_with_pure_solvents(poly_filename_list, output_dir)
+
+
+def extract_all_solvents_and_generate_polynomials(solv_energy_dict_list, directory_base):
+ """
+
+ Parameters
+ ----------
+ solv_energy_dict_list : TYPE
+ DESCRIPTION.
+ directory_base : TYPE
+ DESCRIPTION.
+
+ Returns
+ -------
+ combined_out_res : TYPE
+ DESCRIPTION.
+ combined_filename_list : TYPE
+ DESCRIPTION.
+
+ """
+ combined_out_res = []
+ combined_filename_list = []
+ for solv_energy_dict in solv_energy_dict_list:
+ directory = generate_directory(directory_base, solv_energy_dict["temperature"], solv_energy_dict["temperature_units"])
+ solvent_filename = solv_energy_dict["solvent_filename"]
+ energy_xml_filename = solv_energy_dict["energy_filename"]
+ out_res, filename_list = extract_solvents_and_generate_polynomials(solvent_filename, energy_xml_filename, directory)
+ combined_out_res.extend(out_res)
+ combined_filename_list.extend(filename_list)
+ return combined_out_res, combined_filename_list
+def generate_directory(directory_base, temperature, temperature_unit):
+ """Generate directory to put information based on temperature of simulation.
+
+ Contain in parent directory, specified by directory_base, so calculation
+ results are split up by temperature values.
+
+ Parameters
+ ----------
+ directory_base : str
+ base directory to put all information.
+ temperature : float
+ temperature of simulation.
+ temperature_unit : str
+ Unit for temperature. Either "KELVIN" or "CELSIUS".
+
+ Returns
+ -------
+ str
+ posix str for resulting directory created.
+
+
+ """
+ temperature_name = "{:.1f}{}".format(temperature, "K" if temperature_unit == "KELVIN" else "C").replace(".","_")
+ dir_path = pathlib.Path(directory_base) / temperature_name
+ dir_path.mkdir(parents=True,exist_ok=True)
+ return dir_path.as_posix()
+
+def extract_solvents_and_generate_polynomials(solvent_filename, energy_xml_filename, directory):
+ """Extract solvation free energies and calculate free energy polynomials per solvent.
+
+ Parameters
+ ----------
+ solvent_filename : str
+ filename for solvent XML.
+ energy_xml_filename : TYPE
+ DESCRIPTION.
+ directory : str
+ Directory to put files.
+
+ Returns
+ -------
+ out_res, filename_list : list, list of str
+ List of results for polynomial calculations,
+ list of polynomial filenames.
+
+ """
+ energy_xml_filenames = solvextract.extract_and_write_energy_values_from_files(solvent_filename, energy_xml_filename, "free", directory)
+ return polyio.generate_polynomial_data_free_energy_file_list(energy_xml_filenames)
+
+def run_free_energy_calculation(jar_path, output_filename, solvent_filename, **kwargs):
+ """Run solute solvation free energy calculation.
+
+ Parameters
+ ----------
+ jar_path : str
+ path to jar executable.
+ output_filename : str
+ Output filename for result output.
+ solvent_filename : str
+ filename for solvent XML.
+ memory_req : str, optional
+ Memory settings for jar executable. The default is None.
+ temperature : float, optional
+ Temperature value for calculation. The default is 298.0.
+ temperature_unit : str, optional
+ Specify temperature unit: either "KELVIN" or "CELSIUS" . The default is "KELVIN".
+ solute_filename : str, optional
+ Solute filename. The default is pureinf.SINGLE_SSIP_SOLUTE_FILE.
+
+
+ Raises
+ ------
+ FileNotFoundError
+ If jar file is not found.
+
+ Returns
+ -------
+ CompletedProcess
+ result of system call.
+
+ """
+ return phaserun.run_phasetransfer_free_energy(jar_path, output_filename, solvent_filename, **kwargs)
\ No newline at end of file
diff --git a/phasecalculator/test/runnerstest/similarityanalysisrunnertest.py b/phasecalculator/test/runnerstest/similarityanalysisrunnertest.py
new file mode 100755
index 0000000000000000000000000000000000000000..05a69cb23be00f44424f2901a9e7cdbbbe95383f
--- /dev/null
+++ b/phasecalculator/test/runnerstest/similarityanalysisrunnertest.py
@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+# phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+# Copyright (C) 2019 Mark D. Driver
+#
+# phasecalculator is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Script for similarity analysis runner tests.
+
+@author: Mark
+"""
+
+import logging
+import unittest
+import pandas
+import pathlib
+import numpy as np
+import phasecalculator.runners.similarityanalysisrunner as simrun
+
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SimilarityAnalysisRunnerTestCase(unittest.TestCase):
+ """Test case for similarity analysis."""
+ def setUp(self):
+ """Set up before tests.
+
+ Returns
+ -------
+ None.
+
+ """
+ def tearDown(self):
+ """Clean up after tests.
+
+ Returns
+ -------
+ None.
+
+ """
+ def test_run_similarity_analysis(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ self.fail("not implemented")
+ def test_extract_all_solvents_and_generate_polynomials(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ self.fail("not implemented")
+ def test_generate_directory(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ self.fail("not implemented")
+ def test_extract_solvents_and_generate_polynomials(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ self.fail("not implemented")
+ def test_run_free_energy_calculation(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ self.fail("not implemented")
\ No newline at end of file