From 16e18f8df2f60e3ff3dd6ccdbb8527bf08ae4d91 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Sun, 25 Mar 2018 22:54:13 +0100
Subject: [PATCH] created methods for solvation energy extraction, and set up
test case, but tests need to be implemented.
---
.../io/solvationenergyextraction.py | 128 ++++++++++++++++++
.../iotest/solvationenergyextractiontest.py | 95 +++++++++++++
2 files changed, 223 insertions(+)
create mode 100644 solventmapcreator/io/solvationenergyextraction.py
create mode 100644 solventmapcreator/test/iotest/solvationenergyextractiontest.py
diff --git a/solventmapcreator/io/solvationenergyextraction.py b/solventmapcreator/io/solvationenergyextraction.py
new file mode 100644
index 0000000..1ee7f8a
--- /dev/null
+++ b/solventmapcreator/io/solvationenergyextraction.py
@@ -0,0 +1,128 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for extracting and splitting up solvation energies based on solvent.
+This is to produce more manageable files from the full information dump from
+the phasetransfer code.
+
+@author: mark
+"""
+
+import logging
+import copy
+from lxml import etree
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.INFO)
+
+PHASE_NAMESPACE_DICT = {"phase":"http://www-hunter.ch.cam.ac.uk/PhaseSchema"}
+
+PHASE = "{{{}}}".format(PHASE_NAMESPACE_DICT["phase"])
+
+def read_in_solvent_id_list(solvent_filename):
+ """This reads in the solvent XML, and extracts the solvent IDs.
+ """
+ solvent_list_element_tree = read_xml_file(solvent_filename)
+ return get_solvent_id_list(solvent_list_element_tree)
+
+def get_solvent_id_list(solvent_list_element_tree):
+ """This gets the solventIDs from the solvent list.
+ """
+ xpath_expression = "phase:SolventList/phase:Solvents/phase:Solvent/@phase:solventID"
+ solvent_ids = solvent_list_element_tree.xpath(xpath_expression,
+ namespaces=PHASE_NAMESPACE_DICT)
+ LOGGER.info("Solvent IDs found %i", len(solvent_ids))
+ return solvent_ids
+
+def create_output_filename(to_solvent_id, energy_type):
+ """This creates an output filename based on the solvent id and energy type.
+ """
+ filename_stem = to_solvent_id.replace(",", "_")
+ filename_stem += energy_type
+ return filename_stem +".xml"
+
+def write_element_tree_to_file(element_tree, filename):
+ """Writes element tree to file.
+ """
+ element_tree.write(filename, encoding="UTF-8", xml_declaration=True,
+ pretty_print=True)
+
+def create_element_tree(element):
+ """This creates an element tree, ready for writing to file.
+ """
+ return etree.ElementTree(element)
+
+def generate_energy_values_element(energy_elements, energy_type):
+ """This generates an EnergyValues element, containing the information given
+ in the energy elements within a Collection element of the appropriate type.
+ """
+ energy_values = create_energy_values_element()
+ if energy_type == "binding":
+ energy_collection = generate_binding_energy_collection(energy_elements)
+ energy_values.append(energy_collection)
+ return energy_values
+ elif energy_type == "free":
+ energy_collection = generate_free_energy_collection(energy_elements)
+ energy_values.append(energy_collection)
+ return energy_values
+
+def generate_free_energy_collection(free_energy_elements):
+ """This generates a FreeEnergyCollection element, with the given BindingEnergy
+ elements.
+ """
+ free_energy_collection = create_free_energy_collection_element()
+ append_energies_to_collection(free_energy_collection, free_energy_elements)
+ return free_energy_collection
+
+def generate_binding_energy_collection(binding_energy_elements):
+ """This generates a BindingEnergyCollection element, with the given BindingEnergy
+ elements.
+ """
+ binding_energy_collection = create_binding_energy_collection_element()
+ append_energies_to_collection(binding_energy_collection, binding_energy_elements)
+ return binding_energy_collection
+
+def append_energies_to_collection(energy_collection_element, energy_elements):
+ """This appends the energies to the collection element.
+ """
+ for energy_element in energy_elements:
+ energy_collection_element.append(copy.deepcopy(energy_element))
+
+def create_energy_values_element():
+ """This creates a new EnergyValues Element.
+ """
+ return etree.Element(PHASE + "EnergyValues", nsmap=PHASE_NAMESPACE_DICT)
+
+def create_free_energy_collection_element():
+ """This creates a FreeEnergyCollection element.
+ """
+ return etree.Element(PHASE + "FreeEnergyCollection", nsmap=PHASE_NAMESPACE_DICT)
+
+def create_binding_energy_collection_element():
+ """This creates a BindingEnergyCollection element.
+ """
+ return etree.Element(PHASE + "BindingEnergyCollection", nsmap=PHASE_NAMESPACE_DICT)
+
+def get_energy_elements(element_tree, xpath_expression):
+ """This gets Energy elements that match the given XPath expression.
+ """
+ return element_tree.xpath(xpath_expression, namespaces=PHASE_NAMESPACE_DICT)
+
+def generate_free_energy_xpath_expression(to_solvent_id):
+ """This generates the XPath expression needed to get values for free energies.
+ """
+ return "/phase:EnergyValues/phase:FreeEnergyCollection/phase:FreeEnergy[@phase:fromSolventID=''][@phase:toSolventID='{:s}']".format(to_solvent_id)
+
+def generate_binding_energy_xpath_expression(to_solvent_id):
+ """This generates the XPath expression needed to get values for binding energies.
+ """
+ return "/phase:EnergyValues/phase:BindingEnergyCollection/phase:BindingEnergy[@phase:fromSolventID=''][@phase:toSolventID='{:s}']".format(to_solvent_id)
+
+def read_xml_file(filename):
+ """This reads in an xml file and returns ElementTree. Note that this is
+ used to handle the large file size.
+ """
+ parser = etree.XMLParser(huge_tree=True)
+ return etree.parse(filename, parser=parser)
+
diff --git a/solventmapcreator/test/iotest/solvationenergyextractiontest.py b/solventmapcreator/test/iotest/solvationenergyextractiontest.py
new file mode 100644
index 0000000..80e7c6a
--- /dev/null
+++ b/solventmapcreator/test/iotest/solvationenergyextractiontest.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for testing the solvation energy extraction methods.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import os
+from lxml import etree
+import solventmapcreator.io.solvationenergyextraction as solvationenergyextraction
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.DEBUG)
+
+class SolvationEnergyExtractionTestCase(unittest.TestCase):
+ """Test case for solvationenergyextraction.
+ """
+ def setUp(self):
+ """Set up for tests
+ """
+ def tearDown(self):
+ """clean up after tests.
+ """
+ def test_(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_read_in_solvent_id_list(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_get_solvent_id_list(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_create_output_filename(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_write_element_tree_to_file(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_create_element_tree(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_generate_energy_values_element(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_generate_free_energy_collection(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_generate_binding_energy_collection(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_append_energies_to_collection(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_create_energy_values_element(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_create_free_energy_collection_element(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_create_binding_energy_collection_element(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_get_energy_elements(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_generate_free_energy_xpath_expression(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_generate_binding_energy_xpath_expression(self):
+ """
+ """
+ self.fail("not implemented")
+ def test_read_xml_file(self):
+ """
+ """
+ self.fail("not implemented")
\ No newline at end of file
--
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