add phases class.

phasecalculator/classes/phases.py

+# -*- 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 Phases class.
+
+@author: Mark
+"""
+
+import logging
+from lxml import etree
+from phasecalculator.classes.phase import Phase
+from phasecalculator.classes.xmlnamespacing import PHASE_CALCULATOR, PHASE_CALC_NAMESPACE_DICT
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class Phases(object):
+    """Phases class."""
+
+    def __init__(self, phase_list):
+        self.phase_list = phase_list
+        
+    def __eq__(self, other):
+        """Overload equality comparison operator.
+
+        Parameters
+        ----------
+        other : object
+            object to compare.
+
+        Returns
+        -------
+        boolean
+            is equal.
+
+        """
+        if other is None:
+            return False
+        if isinstance(other, type(self)):
+            if len(self.phase_list) != len(other.phase_list):
+                return False
+            phase_comps = all([self.phase_list[i] == other.phase_list[i] for i in range(len(self.phase_list))])
+            return phase_comps
+        else:
+            return False
+    
+    @classmethod
+    def parse_xml(cls, phases_xml):
+        """Parse XML representation to new instance.
+
+        Parameters
+        ----------
+        phases_xml : lxml.etree.ElementTree
+            Element tree representation of phases XML.
+
+        Returns
+        -------
+        Phases
+            New instance.
+
+        """
+        phase_xpath = "phasecalc:Phase"
+        phase_xml_list = phases_xml.xpath(phase_xpath, namespaces=PHASE_CALC_NAMESPACE_DICT)
+        phase_list = [Phase.parse_xml(phase_xml) for phase_xml in phase_xml_list]
+        return Phases(phase_list)
+    def write_to_xml(self):
+        """Write phases to XML.
+
+        Returns
+        -------
+        phases_element : lxml.etree.Element
+            XML representation of Phases.
+
+        """
+        phases_element = etree.Element(PHASE_CALCULATOR + "Phases", nsmap=PHASE_CALC_NAMESPACE_DICT)
+        for phase in self.phase_list:
+            phases_element.append(phase.write_to_xml())
+        return phases_element
+    def get_phase_compositions_by_temperature(self):
+        """Get phases split up by temperature. This is for solvent XML generation.
+
+        Returns
+        -------
+        phase_dict : dict 
+            Temperature: list of Phase objects pairs.
+
+        """
+        phase_dict = {}
+        for phase in self.phase_list:
+            if phase.temperature in phase_dict.keys():
+                phase_dict[phase.temperature].append(phase)
+            else:
+                phase_dict[phase.temperature] = [phase]
+        return phase_dict
+
+    def get_ssip_file_locations(self):
+        """Gets the SSIP file locations for all molecules in a contained phase.
+
+        Returns
+        -------
+        set of str
+            Set of unique SSIP file locations.
+
+        """
+        ssip_file_locations = []
+        for phase in self.phase_list:
+            ssip_file_locations.extend(phase.get_ssip_file_locations())
+        return set(ssip_file_locations)
+        
+    
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phasecalculator/test/classestest/phasestest.py

+# -*- 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 phases class tests.
+
+@author: Mark
+"""
+
+import logging
+from lxml import etree
+import unittest
+from phasecalculator.classes.temperature import Temperature
+from phasecalculator.classes.molecule import Molecule
+from phasecalculator.classes.phase import Phase
+from phasecalculator.classes.phases import Phases
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class PhasesTestCase(unittest.TestCase):
+    """Test case for Phases class."""
+    def setUp(self):
+        """Set up before tests.
+
+        Returns
+        -------
+        None.
+
+        """
+        self.temperature = Temperature(298.0, "KELVIN")
+        self.molecule = Molecule("water", "XLYOFNOQVPJJNP-UHFFFAOYSA-N", "XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml", 1.0)
+        self.phase = Phase([self.molecule], self.temperature)
+        self.phases = Phases([self.phase])
+    def tearDown(self):
+        """Clean up after tests.
+
+        Returns
+        -------
+        None.
+
+        """
+        del self.phase
+        del self.molecule
+        del self.temperature
+        del self.phases
+    def test_parse_xml(self):
+        """Test expected phases object is created.
+
+        Returns
+        -------
+        None.
+
+        """
+        actual_phases = Phases.parse_xml(self.phases.write_to_xml())
+        self.assertEqual(self.phases, actual_phases)
+    def test_write_to_xml(self):
+        """Test expected XML is produced.
+
+        Returns
+        -------
+        None.
+
+        """
+        expected_xml = """<phasecalc:Phases xmlns:phasecalc="http://www-hunter.ch.cam.ac.uk/schema/PhaseCalculatorSchema.xsd">
+  <phasecalc:Phase>
+    <phasecalc:Molecule phasecalc:name="water" phasecalc:inChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phasecalc:ssipFileLocation="XLYOFNOQVPJJNP-UHFFFAOYSA-N_ssip.xml" phasecalc:molefraction="1.0000"/>
+    <phasecalc:Temperature phasecalc:value="298.0" phasecalc:unit="KELVIN"/>
+  </phasecalc:Phase>
+</phasecalc:Phases>
+"""
+        actual_xml = self.phases.write_to_xml()
+        self.assertMultiLineEqual(expected_xml, etree.tounicode(actual_xml, pretty_print=True))
+    def test_get_phase_compositions_by_temperature(self):
+        """Test expected dictionary produced.
+
+        Returns
+        -------
+        None.
+
+        """
+        expected_dict = {self.temperature: [self.phase]}
+        actual_dict = self.phases.get_phase_compositions_by_temperature()
+        self.assertDictEqual(expected_dict, actual_dict)
+    def test_get_ssip_file_locations(self):
+        """Test expected set of file locations is returned.
+
+        Returns
+        -------
+        None.
+
+        """
+        expected_set = {self.molecule.ssip_file_loc}
+        actual_set = self.phases.get_ssip_file_locations()
+        self.assertSetEqual(expected_set, actual_set)
\ No newline at end of file