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Commit cec1d8f8 authored by Mark Driver's avatar Mark Driver
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update to add methods to gnerate input phase and solvent XML.

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phasecalculator/io/phasetransferxmlcreator.py 0 → 100755
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− 0
View file @ cec1d8f8
# -*- 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/>.
"""
Module for creating Solvent and Phase XML for phase transfer calculations.
@author: Mark
"""
import logging
import phasexmlcreator.multicomponentassembler as multiassem
import phasexmlcreator.phasexmlmaker as phasemake
import phasexmlcreator.solventxmlmaker as solvmake
import puresolventinformation.information as pureinfo
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
def create_phase_and_solvent_files(mole_fraction_dict_list, temperature_info, solvent_filename, phase_filename, **kwargs):
"""Create phase XML and solvent XML files for given composiiton and
temperature information.
Parameters
----------
mole_fraction_dict_list : list of dicts
List of dictionaries of name: mole fraction pairs per phase/solvent to
create.
temperature_info : list of dicts
Temperature information with dictionaries containing value and unit.
solvent_filename : str
Solvent XML output filename.
phase_filename : str
Phase XML output filename.
solvent_filename : str, optional
Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
ssip_filename_list : list of str, optional
Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns
-------
None.
"""
solvent_info_list = generate_solv_info_list(mole_fraction_dict_list, **kwargs)
write_solvent_file(solvent_info_list, solvent_filename)
write_phase_file(solvent_info_list, temperature_info, phase_filename)
def create_solvent_file(mole_fraction_dict_list, solvent_filename, **kwargs):
"""Create solvent XML file for given compositions.
Parameters
----------
mole_fraction_dict_list : list of dicts
List of dictionaries of name: mole fraction pairs per solvent to
create.
solvent_filename : str
Solvent XML output filename.
solvent_filename : str, optional
Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
ssip_filename_list : list of str, optional
Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns
-------
None.
"""
solvent_info_list = generate_solv_info_list(mole_fraction_dict_list, **kwargs)
write_solvent_file(solvent_info_list, solvent_filename)
def create_phase_file(mole_fraction_dict_list, temperature_info, phase_filename, **kwargs):
"""Create phase XML file for given compositions and temperatures.
Parameters
----------
mole_fraction_dict_list : list of dicts
List of dictionaries of name: mole fraction pairs per phase to
create.
temperature_info : list of dicts
Temperature information with dictionaries containing value and unit.
phase_filename : str
Phase XML output filename.
solvent_filename : str, optional
Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
ssip_filename_list : list of str, optional
Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns
-------
None.
"""
phase_info_list = generate_solv_info_list(mole_fraction_dict_list, **kwargs)
write_phase_file(phase_info_list, temperature_info, phase_filename)
def write_solvent_file(solvent_info_list, solvent_filename):
"""Write solvent XML file for given compositions.
Parameters
----------
solvent_info_list : list of dicts
List of dictionaries of information to create XML for given solvent
compositions.
solvent_filename : str
Output filename.
Returns
-------
None.
"""
solvmake.write_solvent_information_to_file(solvent_info_list, solvent_filename)
def write_phase_file(phase_info_list, temperature_info, phase_filename):
"""Write phase XML file for given compositions and temperatures.
Parameters
----------
phase_info_list : list of dicts
List of dictionaries of information to create XML for given phase
compositions.
temperature_info : list of dicts
Temperature information with dictionaries containing value and unit.
phase_filename : str
Output filename.
Returns
-------
None.
"""
phasemake.write_phase_information_to_file(phase_info_list, temperature_info, phase_filename)
def generate_solv_info_list(mole_fraction_dict_list, **kwargs):
"""Generate solvent info from read in SSIP files and solvent information.
Parameters
----------
mole_fraction_dict_list : list of dicts
List of dictionaries of name: mole fraction pairs per phase/solvent to
create.
solvent_filename : str, optional
Filename for file containing solvent information. Defaults to file in
phasexmlcreator module.
ssip_filename_list : list of str, optional
Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
module.
name_inchikey_map : dict, optional
inchikey: name pairs. Defaults to names of solvents in pureinformation
module.
Returns
-------
solv_info_list : list of dicts
List of dictionaries of information to create XML for given solvent
compositions.
"""
solvent_filename = kwargs.get("solvent_filename", multiassem.solvconcreader.DEFAULT_SOLVENT_INFORMATION_FILE)
ssip_filename_list = kwargs.get("ssip_filename_list",pureinfo.get_ssip_file_dict().values())
name_inchikey_map = kwargs.get("name_inchikey_map", pureinfo.get_name_inchikey_mapping())
return multiassem.generate_solv_info_from_files(mole_fraction_dict_list, solvent_filename, ssip_filename_list, name_inchikey_map)
phasecalculator/test/iotest/phasetransferxmlcreatortest.py 0 → 100755
+ 282
− 0
View file @ cec1d8f8
# -*- 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/>.
"""
Test case for phasetransferxmlcreator module.
@author: mark
"""
import logging
import unittest
import pathlib
import os
from lxml import etree
import phasecalculator.io.phasetransferxmlcreator as phasexmlmaker
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
class PhasetransferXMLCreatorTestCase(unittest.TestCase):
def setUp(self):
"""Set up for tests.
Returns
-------
None.
"""
self.maxDiff = None
parent_directory = pathlib.Path(__file__).parents[1]
self.expected_water_xml = """<ssip:SSIPMolecule xmlns:cml="http://www.xml-cml.org/schema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ssip:ssipSoftwareVersion="6.0.0" ssip:parameterVersion="1.0.0" xsi:schemaLocation="http://www.xml-cml.org/schema http://www-hunter.ch.cam.ac.uk/schema/cmlschema.xsd http://www-hunter.ch.cam.ac.uk/SSIP http://www-hunter.ch.cam.ac.uk/schema/SSIP.xsd">
<cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
<cml:atomArray>
<cml:atom cml:elementType="O" cml:id="a1" cml:formalCharge="0" cml:x3="-0.197781963496" cml:y3="-7.5088692891E-35" cml:z3="0.34665983175"/>
<cml:atom cml:elementType="H" cml:id="a2" cml:formalCharge="0" cml:x3="0.760536914227" cml:y3="-9.28739754019E-37" cml:z3="0.204548524786"/>
<cml:atom cml:elementType="H" cml:id="a3" cml:formalCharge="0" cml:x3="-0.56175495073" cml:y3="5.1742035555E-35" cml:z3="-0.551208356536"/>
</cml:atomArray>
<cml:bondArray>
<cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
</cml:bondArray>
</cml:molecule>
<ssip:SurfaceInformation>
<ssip:Surfaces>
<ssip:Surface>
<ssip:TotalSurfaceArea ssip:unit="Å^2">37.46449353147367</ssip:TotalSurfaceArea>
<ssip:NegativeSurfaceArea ssip:unit="Å^2">18.417074471275452</ssip:NegativeSurfaceArea>
<ssip:PositiveSurfaceArea ssip:unit="Å^2">19.047419060197754</ssip:PositiveSurfaceArea>
<ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
<ssip:NumberOFMEPSPoints>2267</ssip:NumberOFMEPSPoints>
<ssip:VdWVolume ssip:unit="Å^3">21.118225673870302</ssip:VdWVolume>
<ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">222.31155482388002</ssip:ElectrostaticPotentialMax>
<ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-185.78297861082</ssip:ElectrostaticPotentialMin>
</ssip:Surface>
</ssip:Surfaces>
</ssip:SurfaceInformation>
<ssip:SSIPs>
<ssip:SSIP ssip:value="2.8" ssip:nearestAtomID="a2" cml:x3="1.7703677783019898" cml:y3="-0.037716579245226" cml:z3="-0.12404973071057998"/>
<ssip:SSIP ssip:value="2.8" ssip:nearestAtomID="a3" cml:x3="-0.78007076629588" cml:y3="-0.131868324564555" cml:z3="-1.585252051411308"/>
<ssip:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.78007076629588" cml:y3="-1.185660785500926" cml:z3="1.34163366293468"/>
<ssip:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.9035034763341259" cml:y3="0.8351649972210169" cml:z3="1.5735514132586688"/>
</ssip:SSIPs>
</ssip:SSIPMolecule>"""
self.expected_butanol_xml = """<ssip:SSIPMolecule xmlns:cml="http://www.xml-cml.org/schema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ssip:ssipSoftwareVersion="6.0.0" ssip:parameterVersion="1.0.0" xsi:schemaLocation="http://www.xml-cml.org/schema http://www-hunter.ch.cam.ac.uk/schema/cmlschema.xsd http://www-hunter.ch.cam.ac.uk/SSIP http://www-hunter.ch.cam.ac.uk/schema/SSIP.xsd">
<cml:molecule ssip:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" cml:id="LRHPLDYGYMQRHN-UHFFFAOYSA-N">
<cml:atomArray>
<cml:atom cml:elementType="C" cml:id="a1" cml:formalCharge="0" cml:x3="0.453161473082" cml:y3="-1.03446801266" cml:z3="-0.0905306598548"/>
<cml:atom cml:elementType="H" cml:id="a10" cml:formalCharge="0" cml:x3="-0.711314642651" cml:y3="-1.77936986861" cml:z3="1.57182493824"/>
<cml:atom cml:elementType="H" cml:id="a11" cml:formalCharge="0" cml:x3="-2.35918900768" cml:y3="-0.976902587046" cml:z3="-0.14772459368"/>
<cml:atom cml:elementType="H" cml:id="a12" cml:formalCharge="0" cml:x3="-1.77474726333" cml:y3="-2.19616982792" cml:z3="-1.27745306344"/>
<cml:atom cml:elementType="H" cml:id="a13" cml:formalCharge="0" cml:x3="-2.519145554" cml:y3="-4.00559237167" cml:z3="0.302707946329"/>
<cml:atom cml:elementType="H" cml:id="a14" cml:formalCharge="0" cml:x3="-3.10209800172" cml:y3="-2.77368664521" cml:z3="1.42866821719"/>
<cml:atom cml:elementType="H" cml:id="a15" cml:formalCharge="0" cml:x3="-4.0901443513" cml:y3="-3.10664597908" cml:z3="-1.18904146578"/>
<cml:atom cml:elementType="C" cml:id="a2" cml:formalCharge="0" cml:x3="-0.564202390594" cml:y3="-2.0116665412" cml:z3="0.507612692817"/>
<cml:atom cml:elementType="C" cml:id="a3" cml:formalCharge="0" cml:x3="-1.92163762747" cml:y3="-1.98241261328" cml:z3="-0.206572876019"/>
<cml:atom cml:elementType="C" cml:id="a4" cml:formalCharge="0" cml:x3="-2.92693672032" cml:y3="-2.98225012861" cml:z3="0.367318952425"/>
<cml:atom cml:elementType="O" cml:id="a5" cml:formalCharge="0" cml:x3="-4.208010389" cml:y3="-2.9017666367" cml:z3="-0.248445606999"/>
<cml:atom cml:elementType="H" cml:id="a6" cml:formalCharge="0" cml:x3="0.655827908609" cml:y3="-1.26752859656" cml:z3="-1.14312376632"/>
<cml:atom cml:elementType="H" cml:id="a7" cml:formalCharge="0" cml:x3="0.0848553777946" cml:y3="-0.00239243828223" cml:z3="-0.0456709489122"/>
<cml:atom cml:elementType="H" cml:id="a8" cml:formalCharge="0" cml:x3="1.40666917559" cml:y3="-1.07214682201" cml:z3="0.448356319391"/>
<cml:atom cml:elementType="H" cml:id="a9" cml:formalCharge="0" cml:x3="-0.154987987004" cml:y3="-3.03150093117" cml:z3="0.472873914607"/>
</cml:atomArray>
<cml:bondArray>
<cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a6" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a7" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a8" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a10" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a3" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a9" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a11" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a12" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a4" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a13" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a14" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a5" cml:order="1"/>
<cml:bond cml:atomRefs2="a5 a15" cml:order="1"/>
</cml:bondArray>
</cml:molecule>
<ssip:SurfaceInformation>
<ssip:Surfaces>
<ssip:Surface>
<ssip:TotalSurfaceArea ssip:unit="Å^2">122.2095781704891</ssip:TotalSurfaceArea>
<ssip:NegativeSurfaceArea ssip:unit="Å^2">20.900319182402814</ssip:NegativeSurfaceArea>
<ssip:PositiveSurfaceArea ssip:unit="Å^2">101.30925898808572</ssip:PositiveSurfaceArea>
<ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
<ssip:NumberOFMEPSPoints>9580</ssip:NumberOFMEPSPoints>
<ssip:VdWVolume ssip:unit="Å^3">99.3920085615431</ssip:VdWVolume>
<ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">213.86532254634</ssip:ElectrostaticPotentialMax>
<ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-172.51370353134</ssip:ElectrostaticPotentialMin>
</ssip:Surface>
</ssip:Surfaces>
</ssip:SurfaceInformation>
<ssip:SSIPs>
<ssip:SSIP ssip:value="2.784040024744081" ssip:nearestAtomID="a15" cml:x3="-3.8161781356582187" cml:y3="-3.342557618498982" cml:z3="-2.192649106294994"/>
<ssip:SSIP ssip:value="0.773639545237379" ssip:nearestAtomID="a12" cml:x3="-2.239105576984704" cml:y3="-3.099174713898159" cml:z3="-2.0252301249653697"/>
<ssip:SSIP ssip:value="0.5071846345423165" ssip:nearestAtomID="a13" cml:x3="-2.8499750929763277" cml:y3="-4.524230524251444" cml:z3="-0.8462517897648159"/>
<ssip:SSIP ssip:value="0.4784372492163057" ssip:nearestAtomID="a6" cml:x3="0.9270005337214728" cml:y3="-1.649107340870889" cml:z3="-2.251805301783455"/>
<ssip:SSIP ssip:value="0.46383776537503163" ssip:nearestAtomID="a9" cml:x3="0.136470579099108" cml:y3="-4.205322913496092" cml:z3="0.352187567944962"/>
<ssip:SSIP ssip:value="0.4557099985213939" ssip:nearestAtomID="a8" cml:x3="2.420223369759191" cml:y3="-1.188501408973558" cml:z3="1.0796321860050409"/>
<ssip:SSIP ssip:value="0.4355872186992693" ssip:nearestAtomID="a7" cml:x3="-0.30271267022695597" cml:y3="1.1313523827905538" cml:z3="0.031343697635518995"/>
<ssip:SSIP ssip:value="0.43429343831228867" ssip:nearestAtomID="a14" cml:x3="-2.937811637006091" cml:y3="-2.45801773806002" cml:z3="2.5781764284587028"/>
<ssip:SSIP ssip:value="0.33435822085360595" ssip:nearestAtomID="a11" cml:x3="-2.5158938537831497" cml:y3="0.207568717565752" cml:z3="0.059691722864448994"/>
<ssip:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337"/>
<ssip:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337"/>
<ssip:SSIP ssip:value="-5.3386085001748205" ssip:nearestAtomID="a5" cml:x3="-5.4850745889327115" cml:y3="-3.640825199834338" cml:z3="0.48092898414517593"/>
<ssip:SSIP ssip:value="-5.365217010700665" ssip:nearestAtomID="a5" cml:x3="-5.353424285394745" cml:y3="-1.7849561367024218" cml:z3="0.11271581239149799"/>
</ssip:SSIPs>
</ssip:SSIPMolecule>"""
self.mol_info_list = [{"concentration_value":10.8702104695089,
"inchikey":"LRHPLDYGYMQRHN-UHFFFAOYSA-N",
"mole_fraction":0.16452830188679246,
"ssip_molecule":self.expected_butanol_xml},
{"concentration_value":55.3496115427303,
"inchikey":"XLYOFNOQVPJJNP-UHFFFAOYSA-N",
"mole_fraction":0.8354716981132075,
"ssip_molecule":self.expected_water_xml,},
]
self.mole_fraction_dict_list = [{"water":0.8354716981132075,
"1-butanol":0.16452830188679246}]
self.solvent_info_list = phasexmlmaker.generate_solv_info_list(self.mole_fraction_dict_list)
self.expected_phase_file = (parent_directory /"resources" / "expected_phase.xml").absolute().as_posix()
self.expected_solvent_file = (parent_directory /"resources" / "expected_solvent.xml").absolute().as_posix()
self.temperature_info = [{"temperature_value": 298.0, "temperature_units": "KELVIN"}]
self.phase_filename = "actual_phase.xml"
self.solvent_filename = "actual_solvent.xml"
def tearDown(self):
"""Clean up after tests.
Returns
-------
None.
"""
if os.path.isfile(self.phase_filename):
os.remove(self.phase_filename)
if os.path.isfile(self.solvent_filename):
os.remove(self.solvent_filename)
def test_create_phase_and_solvent_files(self):
"""Test
Returns
-------
None.
"""
phasexmlmaker.create_phase_and_solvent_files(self.mole_fraction_dict_list, self.temperature_info, self.solvent_filename, self.phase_filename)
with open(self.phase_filename, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_phase_file, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
with open(self.solvent_filename, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_solvent_file, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
def test_create_solvent_file(self):
"""Test
Returns
-------
None.
"""
phasexmlmaker.create_solvent_file(self.mole_fraction_dict_list, self.solvent_filename)
with open(self.solvent_filename, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_solvent_file, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
def test_create_phase_file(self):
"""Test
Returns
-------
None.
"""
phasexmlmaker.create_phase_file(self.mole_fraction_dict_list, self.temperature_info, self.phase_filename)
with open(self.phase_filename, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_phase_file, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
def test_write_solvent_file(self):
"""Test
Returns
-------
None.
"""
phasexmlmaker.write_solvent_file(self.solvent_info_list, self.solvent_filename)
with open(self.solvent_filename, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_solvent_file, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
def test_write_phase_file(self):
"""Test
Returns
-------
None.
"""
phasexmlmaker.write_phase_file(self.solvent_info_list, self.temperature_info, self.phase_filename)
with open(self.phase_filename, "r") as act_file:
actual_contents = act_file.read()
with open(self.expected_phase_file, "r") as exp_file:
expected_contents = exp_file.read()
self.assertMultiLineEqual(expected_contents, actual_contents)
def test_generate_solv_info_list(self):
"""Test
Returns
-------
None.
"""
expected_list = self.mol_info_list
expected_keys = [
"concentration_value",
"inchikey",
"mole_fraction",
"ssip_molecule",
]
actual_info_list = self.solvent_info_list
self.assertEqual(1, len(actual_info_list))
actual_information = actual_info_list[0]
self.assertEqual("1-butanol0.165water0.835", actual_information["solvent_name"])
self.assertEqual("1-butanol0.165water0.835", actual_information["solvent_id"])
actual_list = actual_information["ssip_info_list"]
for entry, information_dict in enumerate(actual_list):
with self.subTest(entry=entry):
expected_dict = expected_list[entry]
self.assertListEqual(expected_keys, sorted(information_dict.keys()))
self.assertEqual(
expected_dict["inchikey"], information_dict["inchikey"]
)
self.assertAlmostEqual(expected_dict["concentration_value"], information_dict["concentration_value"])
self.assertAlmostEqual(expected_dict["mole_fraction"], information_dict["mole_fraction"])
self.assertMultiLineEqual(
expected_dict["ssip_molecule"],
etree.tounicode(information_dict["ssip_molecule"]),
)
\ No newline at end of file
phasecalculator/test/phasecalculatortests.py
+ 2
− 1
View file @ cec1d8f8
......@@ -23,12 +23,13 @@ Created on Tue Jan 7 16:34:17 2020
import logging
import unittest
import sys
from phasecalculator.test.iotest.phasetransferxmlcreatortest import PhasetransferXMLCreatorTestCase
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
IO_TEST_CASES = []
IO_TEST_CASES = [PhasetransferXMLCreatorTestCase,]
RUNNERS_TEST_CASES = []
......
phasecalculator/test/resources/expected_phase.xml 0 → 100644
+ 90
− 0
View file @ cec1d8f8
<?xml version='1.0' encoding='UTF-8'?>
<phase:MixtureCollection xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:cml="http://www.xml-cml.org/schema">
<phase:Mixtures>
<phase:Mixture phase:soluteID="298.000KELVIN">
<phase:Phases>
<phase:Phase phase:solventID="1-butanol0.165water0.835298.000KELVIN" phase:units="MOLAR">
<phase:Molecules>
<phase:Molecule phase:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleFraction="0.1645"><cml:molecule ssip:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" cml:id="LRHPLDYGYMQRHN-UHFFFAOYSA-N">
<cml:atomArray>
<cml:atom cml:elementType="C" cml:id="a1" cml:formalCharge="0" cml:x3="0.453161473082" cml:y3="-1.03446801266" cml:z3="-0.0905306598548"/>
<cml:atom cml:elementType="H" cml:id="a10" cml:formalCharge="0" cml:x3="-0.711314642651" cml:y3="-1.77936986861" cml:z3="1.57182493824"/>
<cml:atom cml:elementType="H" cml:id="a11" cml:formalCharge="0" cml:x3="-2.35918900768" cml:y3="-0.976902587046" cml:z3="-0.14772459368"/>
<cml:atom cml:elementType="H" cml:id="a12" cml:formalCharge="0" cml:x3="-1.77474726333" cml:y3="-2.19616982792" cml:z3="-1.27745306344"/>
<cml:atom cml:elementType="H" cml:id="a13" cml:formalCharge="0" cml:x3="-2.519145554" cml:y3="-4.00559237167" cml:z3="0.302707946329"/>
<cml:atom cml:elementType="H" cml:id="a14" cml:formalCharge="0" cml:x3="-3.10209800172" cml:y3="-2.77368664521" cml:z3="1.42866821719"/>
<cml:atom cml:elementType="H" cml:id="a15" cml:formalCharge="0" cml:x3="-4.0901443513" cml:y3="-3.10664597908" cml:z3="-1.18904146578"/>
<cml:atom cml:elementType="C" cml:id="a2" cml:formalCharge="0" cml:x3="-0.564202390594" cml:y3="-2.0116665412" cml:z3="0.507612692817"/>
<cml:atom cml:elementType="C" cml:id="a3" cml:formalCharge="0" cml:x3="-1.92163762747" cml:y3="-1.98241261328" cml:z3="-0.206572876019"/>
<cml:atom cml:elementType="C" cml:id="a4" cml:formalCharge="0" cml:x3="-2.92693672032" cml:y3="-2.98225012861" cml:z3="0.367318952425"/>
<cml:atom cml:elementType="O" cml:id="a5" cml:formalCharge="0" cml:x3="-4.208010389" cml:y3="-2.9017666367" cml:z3="-0.248445606999"/>
<cml:atom cml:elementType="H" cml:id="a6" cml:formalCharge="0" cml:x3="0.655827908609" cml:y3="-1.26752859656" cml:z3="-1.14312376632"/>
<cml:atom cml:elementType="H" cml:id="a7" cml:formalCharge="0" cml:x3="0.0848553777946" cml:y3="-0.00239243828223" cml:z3="-0.0456709489122"/>
<cml:atom cml:elementType="H" cml:id="a8" cml:formalCharge="0" cml:x3="1.40666917559" cml:y3="-1.07214682201" cml:z3="0.448356319391"/>
<cml:atom cml:elementType="H" cml:id="a9" cml:formalCharge="0" cml:x3="-0.154987987004" cml:y3="-3.03150093117" cml:z3="0.472873914607"/>
</cml:atomArray>
<cml:bondArray>
<cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a6" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a7" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a8" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a10" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a3" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a9" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a11" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a12" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a4" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a13" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a14" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a5" cml:order="1"/>
<cml:bond cml:atomRefs2="a5 a15" cml:order="1"/>
</cml:bondArray>
</cml:molecule>
<ssip:SurfaceInformation>
<ssip:Surfaces>
<ssip:Surface>
<ssip:TotalSurfaceArea ssip:unit="Å^2">122.2095781704891</ssip:TotalSurfaceArea>
<ssip:NegativeSurfaceArea ssip:unit="Å^2">20.900319182402814</ssip:NegativeSurfaceArea>
<ssip:PositiveSurfaceArea ssip:unit="Å^2">101.30925898808572</ssip:PositiveSurfaceArea>
<ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
<ssip:NumberOFMEPSPoints>9580</ssip:NumberOFMEPSPoints>
<ssip:VdWVolume ssip:unit="Å^3">99.3920085615431</ssip:VdWVolume>
<ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">213.86532254634</ssip:ElectrostaticPotentialMax>
<ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-172.51370353134</ssip:ElectrostaticPotentialMin>
</ssip:Surface>
</ssip:Surfaces>
</ssip:SurfaceInformation>
<phase:SSIPs phase:units="MOLAR"><phase:SSIP ssip:value="2.784040024744081" ssip:nearestAtomID="a15" cml:x3="-3.8161781356582187" cml:y3="-3.342557618498982" cml:z3="-2.192649106294994" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.773639545237379" ssip:nearestAtomID="a12" cml:x3="-2.239105576984704" cml:y3="-3.099174713898159" cml:z3="-2.0252301249653697" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.5071846345423165" ssip:nearestAtomID="a13" cml:x3="-2.8499750929763277" cml:y3="-4.524230524251444" cml:z3="-0.8462517897648159" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.4784372492163057" ssip:nearestAtomID="a6" cml:x3="0.9270005337214728" cml:y3="-1.649107340870889" cml:z3="-2.251805301783455" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.46383776537503163" ssip:nearestAtomID="a9" cml:x3="0.136470579099108" cml:y3="-4.205322913496092" cml:z3="0.352187567944962" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.4557099985213939" ssip:nearestAtomID="a8" cml:x3="2.420223369759191" cml:y3="-1.188501408973558" cml:z3="1.0796321860050409" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.4355872186992693" ssip:nearestAtomID="a7" cml:x3="-0.30271267022695597" cml:y3="1.1313523827905538" cml:z3="0.031343697635518995" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.43429343831228867" ssip:nearestAtomID="a14" cml:x3="-2.937811637006091" cml:y3="-2.45801773806002" cml:z3="2.5781764284587028" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.33435822085360595" ssip:nearestAtomID="a11" cml:x3="-2.5158938537831497" cml:y3="0.207568717565752" cml:z3="0.059691722864448994" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-5.3386085001748205" ssip:nearestAtomID="a5" cml:x3="-5.4850745889327115" cml:y3="-3.640825199834338" cml:z3="0.48092898414517593" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-5.365217010700665" ssip:nearestAtomID="a5" cml:x3="-5.353424285394745" cml:y3="-1.7849561367024218" cml:z3="0.11271581239149799" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP></phase:SSIPs></phase:Molecule>
<phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:moleFraction="0.8355"><cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
<cml:atomArray>
<cml:atom cml:elementType="O" cml:id="a1" cml:formalCharge="0" cml:x3="-0.197781963496" cml:y3="-7.5088692891E-35" cml:z3="0.34665983175"/>
<cml:atom cml:elementType="H" cml:id="a2" cml:formalCharge="0" cml:x3="0.760536914227" cml:y3="-9.28739754019E-37" cml:z3="0.204548524786"/>
<cml:atom cml:elementType="H" cml:id="a3" cml:formalCharge="0" cml:x3="-0.56175495073" cml:y3="5.1742035555E-35" cml:z3="-0.551208356536"/>
</cml:atomArray>
<cml:bondArray>
<cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
</cml:bondArray>
</cml:molecule>
<ssip:SurfaceInformation>
<ssip:Surfaces>
<ssip:Surface>
<ssip:TotalSurfaceArea ssip:unit="Å^2">37.46449353147367</ssip:TotalSurfaceArea>
<ssip:NegativeSurfaceArea ssip:unit="Å^2">18.417074471275452</ssip:NegativeSurfaceArea>
<ssip:PositiveSurfaceArea ssip:unit="Å^2">19.047419060197754</ssip:PositiveSurfaceArea>
<ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
<ssip:NumberOFMEPSPoints>2267</ssip:NumberOFMEPSPoints>
<ssip:VdWVolume ssip:unit="Å^3">21.118225673870302</ssip:VdWVolume>
<ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">222.31155482388002</ssip:ElectrostaticPotentialMax>
<ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-185.78297861082</ssip:ElectrostaticPotentialMin>
</ssip:Surface>
</ssip:Surfaces>
</ssip:SurfaceInformation>
<phase:SSIPs phase:units="MOLAR"><phase:SSIP ssip:value="2.8" ssip:nearestAtomID="a2" cml:x3="1.7703677783019898" cml:y3="-0.037716579245226" cml:z3="-0.12404973071057998" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="2.8" ssip:nearestAtomID="a3" cml:x3="-0.78007076629588" cml:y3="-0.131868324564555" cml:z3="-1.585252051411308" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.78007076629588" cml:y3="-1.185660785500926" cml:z3="1.34163366293468" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.9035034763341259" cml:y3="0.8351649972210169" cml:z3="1.5735514132586688" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP></phase:SSIPs></phase:Molecule>
</phase:Molecules>
<phase:Temperature phase:units="KELVIN">298.000</phase:Temperature>
</phase:Phase>
</phase:Phases>
</phase:Mixture>
</phase:Mixtures>
</phase:MixtureCollection>
phasecalculator/test/resources/expected_solvent.xml 0 → 100644
+ 85
− 0
View file @ cec1d8f8
<?xml version='1.0' encoding='UTF-8'?>
<phase:SolventList xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:cml="http://www.xml-cml.org/schema">
<phase:Solvents>
<phase:Solvent phase:solventID="1-butanol0.165water0.835" phase:solventName="1-butanol0.165water0.835" phase:units="MOLAR">
<phase:Molecules>
<phase:Molecule phase:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleFraction="0.1645"><cml:molecule ssip:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" cml:id="LRHPLDYGYMQRHN-UHFFFAOYSA-N">
<cml:atomArray>
<cml:atom cml:elementType="C" cml:id="a1" cml:formalCharge="0" cml:x3="0.453161473082" cml:y3="-1.03446801266" cml:z3="-0.0905306598548"/>
<cml:atom cml:elementType="H" cml:id="a10" cml:formalCharge="0" cml:x3="-0.711314642651" cml:y3="-1.77936986861" cml:z3="1.57182493824"/>
<cml:atom cml:elementType="H" cml:id="a11" cml:formalCharge="0" cml:x3="-2.35918900768" cml:y3="-0.976902587046" cml:z3="-0.14772459368"/>
<cml:atom cml:elementType="H" cml:id="a12" cml:formalCharge="0" cml:x3="-1.77474726333" cml:y3="-2.19616982792" cml:z3="-1.27745306344"/>
<cml:atom cml:elementType="H" cml:id="a13" cml:formalCharge="0" cml:x3="-2.519145554" cml:y3="-4.00559237167" cml:z3="0.302707946329"/>
<cml:atom cml:elementType="H" cml:id="a14" cml:formalCharge="0" cml:x3="-3.10209800172" cml:y3="-2.77368664521" cml:z3="1.42866821719"/>
<cml:atom cml:elementType="H" cml:id="a15" cml:formalCharge="0" cml:x3="-4.0901443513" cml:y3="-3.10664597908" cml:z3="-1.18904146578"/>
<cml:atom cml:elementType="C" cml:id="a2" cml:formalCharge="0" cml:x3="-0.564202390594" cml:y3="-2.0116665412" cml:z3="0.507612692817"/>
<cml:atom cml:elementType="C" cml:id="a3" cml:formalCharge="0" cml:x3="-1.92163762747" cml:y3="-1.98241261328" cml:z3="-0.206572876019"/>
<cml:atom cml:elementType="C" cml:id="a4" cml:formalCharge="0" cml:x3="-2.92693672032" cml:y3="-2.98225012861" cml:z3="0.367318952425"/>
<cml:atom cml:elementType="O" cml:id="a5" cml:formalCharge="0" cml:x3="-4.208010389" cml:y3="-2.9017666367" cml:z3="-0.248445606999"/>
<cml:atom cml:elementType="H" cml:id="a6" cml:formalCharge="0" cml:x3="0.655827908609" cml:y3="-1.26752859656" cml:z3="-1.14312376632"/>
<cml:atom cml:elementType="H" cml:id="a7" cml:formalCharge="0" cml:x3="0.0848553777946" cml:y3="-0.00239243828223" cml:z3="-0.0456709489122"/>
<cml:atom cml:elementType="H" cml:id="a8" cml:formalCharge="0" cml:x3="1.40666917559" cml:y3="-1.07214682201" cml:z3="0.448356319391"/>
<cml:atom cml:elementType="H" cml:id="a9" cml:formalCharge="0" cml:x3="-0.154987987004" cml:y3="-3.03150093117" cml:z3="0.472873914607"/>
</cml:atomArray>
<cml:bondArray>
<cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a6" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a7" cml:order="1"/>
<cml:bond cml:atomRefs2="a1 a8" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a10" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a3" cml:order="1"/>
<cml:bond cml:atomRefs2="a2 a9" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a11" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a12" cml:order="1"/>
<cml:bond cml:atomRefs2="a3 a4" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a13" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a14" cml:order="1"/>
<cml:bond cml:atomRefs2="a4 a5" cml:order="1"/>
<cml:bond cml:atomRefs2="a5 a15" cml:order="1"/>
</cml:bondArray>
</cml:molecule>
<ssip:SurfaceInformation>
<ssip:Surfaces>
<ssip:Surface>
<ssip:TotalSurfaceArea ssip:unit="Å^2">122.2095781704891</ssip:TotalSurfaceArea>
<ssip:NegativeSurfaceArea ssip:unit="Å^2">20.900319182402814</ssip:NegativeSurfaceArea>
<ssip:PositiveSurfaceArea ssip:unit="Å^2">101.30925898808572</ssip:PositiveSurfaceArea>
<ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
<ssip:NumberOFMEPSPoints>9580</ssip:NumberOFMEPSPoints>
<ssip:VdWVolume ssip:unit="Å^3">99.3920085615431</ssip:VdWVolume>
<ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">213.86532254634</ssip:ElectrostaticPotentialMax>
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