diff --git a/common/lib/capa/capa/chem/chemtools.py b/common/lib/capa/capa/chem/chemtools.py index d9559cce1e..2c7088cac9 100644 --- a/common/lib/capa/capa/chem/chemtools.py +++ b/common/lib/capa/capa/chem/chemtools.py @@ -1,20 +1,94 @@ +"""This module originally includes functions for grading Vsepr problems. + +Also, may be this module is the place for other chemistry-related grade functions. TODO: discuss it. +""" + import json import unittest import itertools + def vsepr_parse_user_answer(user_input): + """ + user_input is json generated by vsepr.js from dictionary. + There are must be only two keys in original user_input dictionary: "geometry" and "atoms". + Format: u'{"geometry": "AX3E0","atoms":{"c0": "B","p0": "F","p1": "B","p2": "F"}}' + Order of elements inside "atoms" subdict does not matters. + Return dict from parsed json. + + "Atoms" subdict stores positions of atoms in molecule. + General types of positions: + c0 - central atom + p0..pN - peripheral atoms + a0..aN - axial atoms + e0..eN - equatorial atoms + + Each position is dictionary key, i.e. user_input["atoms"]["c0"] is central atom, user_input["atoms"]["a0"] is one of axial atoms. + + Special position only for AX6 (Octahedral) geometry: + e10, e12 - atom pairs opposite the central atom, + e20, e22 - atom pairs opposite the central atom, + e1 and e2 pairs lying crosswise in equatorial plane. + + In user_input["atoms"] may be only 3 set of keys: + (c0,p0..pN), + (c0, a0..aN, e0..eN), + (c0, a0, a1, e10,e11,e20,e21) - if geometry is AX6. + """ return json.loads(user_input) def vsepr_build_correct_answer(geometry, atoms): + """ + geometry is string. + atoms is dict of atoms with proper positions. + Example: + + correct_answer = vsepr_build_correct_answer(geometry="AX4E0", atoms={"c0": "N", "p0": "H", "p1": "(ep)", "p2": "H", "p3": "H"}) + + returns a dictionary composed from input values: + {'geometry': geometry, 'atoms': atoms} + """ return {'geometry': geometry, 'atoms': atoms} -def vsepr_grade(user_input, correct_answer, convert_to_perepherial=False): +def vsepr_grade(user_input, correct_answer, convert_to_peripheral=False): """ - Allowed cases: - c0, a, e - c0, p + This function does comparison between user_input and correct_answer. + + Comparison is successful if all steps are successful: + + 1) geometries are equal + 2) central atoms (index in dictionary 'c0') are equal + 3): + In next steps there is comparing of corresponding subsets of atom positions: equatorial (e0..eN), axial (a0..aN) or peripheral (p0..pN) + + If convert_to_peripheral is True, then axial and equatorial positions are converted to peripheral. + This means that user_input from: + "atoms":{"c0": "Br","a0": "test","a1": "(ep)","e10": "H","e11": "(ep)","e20": "H","e21": "(ep)"}}' after parsing to json + is converted to: + {"c0": "Br", "p0": "(ep)", "p1": "test", "p2": "H", "p3": "H", "p4": "(ep)", "p6": "(ep)"} + i.e. aX and eX -> pX + + So if converted, p subsets are compared, + if not a and e subsets are compared + If all subsets are equal, grade succeeds. + + There is also one special case for AX6 geometry. + In this case user_input["atoms"] contains special 3 symbol keys: e10, e12, e20, and e21. + Correct answer for this geometry can be of 3 types: + 1) c0 and peripheral + 2) c0 and axial and equatorial + 3) c0 and axial and equatorial-subset-1 (e1X) and equatorial-subset-2 (e2X) + + If correct answer is type 1 or 2, then user_input is converted from type 3 to type 2 (or to type 1 if convert_to_peripheral is True) + + If correct_answer is type 3, then we done special case comparison. We have 3 sets of atoms positions both in user_input and correct_answer: axial, eq-1 and eq-2. + Answer will be correct if these sets are equals for one of permutations. For example, if : + user_axial = correct_eq-1 + user_eq-1 = correct-axial + user_eq-2 = correct-eq-2 + """ # import ipdb; ipdb.set_trace() # print user_input, type(user_input) @@ -25,7 +99,7 @@ def vsepr_grade(user_input, correct_answer, convert_to_perepherial=False): if user_input['atoms']['c0'] != correct_answer['atoms']['c0']: return False - if convert_to_perepherial: + if convert_to_peripheral: # convert user_input from (a,e,e1,e2) to (p) # correct_answer must be set in (p) using this flag c0 = user_input['atoms'].pop('c0') @@ -46,7 +120,7 @@ def vsepr_grade(user_input, correct_answer, convert_to_perepherial=False): return True return False - else: # no need to checl e1x,e2x symmetry - convert them to ex + else: # no need to check e1x,e2x symmetry - convert them to ex if 'e10' in user_input['atoms']: # e1x exists, it is AX6.. case e_index = 0 for k, v in user_input['atoms'].items(): @@ -74,52 +148,52 @@ class Test_Grade(unittest.TestCase): def test_incorrect_geometry(self): correct_answer = vsepr_build_correct_answer(geometry="AX4E0", atoms={"c0": "N", "p0": "H", "p1": "(ep)", "p2": "H", "p3": "H"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX3E0","atoms":{"c0":"B","p0":"F","p1":"B","p2":"F"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX3E0","atoms":{"c0": "B","p0": "F","p1": "B","p2": "F"}}') self.assertFalse(vsepr_grade(user_answer, correct_answer)) def test_correct_answer_p(self): correct_answer = vsepr_build_correct_answer(geometry="AX4E0", atoms={"c0": "N", "p0": "H", "p1": "(ep)", "p2": "H", "p3": "H"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX4E0","atoms":{"c0":"N","p0":"H","p1":"(ep)","p2":"H", "p3":"H"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX4E0","atoms":{"c0": "N","p0": "H","p1": "(ep)","p2": "H", "p3": "H"}}') self.assertTrue(vsepr_grade(user_answer, correct_answer)) def test_correct_answer_ae(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "test", "a1": "(ep)", "e0": "H", "e1": "H", "e2": "(ep)", "e3": "(ep)"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"test","a1":"(ep)","e10":"H","e11":"H","e20":"(ep)","e21":"(ep)"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "test","a1": "(ep)","e10": "H","e11": "H","e20": "(ep)","e21": "(ep)"}}') self.assertTrue(vsepr_grade(user_answer, correct_answer)) def test_correct_answer_ae_convert_to_p_but_input_not_in_p(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "(ep)", "a1": "test", "e0": "H", "e1": "H", "e2": "(ep)", "e3": "(ep)"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"test","a1":"(ep)","e10":"H","e11":"(ep)","e20":"H","e21":"(ep)"}}') - self.assertFalse(vsepr_grade(user_answer, correct_answer, convert_to_perepherial=True)) + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "test","a1": "(ep)","e10": "H","e11": "(ep)","e20": "H","e21": "(ep)"}}') + self.assertFalse(vsepr_grade(user_answer, correct_answer, convert_to_peripheral=True)) def test_correct_answer_ae_convert_to_p(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "p0": "(ep)", "p1": "test", "p2": "H", "p3": "H", "p4": "(ep)", "p6": "(ep)"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"test","a1":"(ep)","e10":"H","e11":"(ep)","e20":"H","e21":"(ep)"}}') - self.assertTrue(vsepr_grade(user_answer, correct_answer, convert_to_perepherial=True)) + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "test","a1": "(ep)","e10": "H","e11": "(ep)","e20": "H","e21": "(ep)"}}') + self.assertTrue(vsepr_grade(user_answer, correct_answer, convert_to_peripheral=True)) def test_correct_answer_e1e2_in_a(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "(ep)", "a1": "(ep)", "e10": "H", "e11": "H", "e20": "H", "e21": "H"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"(ep)","a1":"(ep)","e10":"H","e11":"H","e20":"H","e21":"H"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "(ep)","a1": "(ep)","e10": "H","e11": "H","e20": "H","e21": "H"}}') self.assertTrue(vsepr_grade(user_answer, correct_answer)) def test_correct_answer_e1e2_in_e1(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "(ep)", "a1": "(ep)", "e10": "H", "e11": "H", "e20": "H", "e21": "H"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"H","a1":"H","e10":"(ep)","e11":"(ep)","e20":"H","e21":"H"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "H","a1": "H","e10": "(ep)","e11": "(ep)","e20": "H","e21": "H"}}') self.assertTrue(vsepr_grade(user_answer, correct_answer)) def test_correct_answer_e1e2_in_e2(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "(ep)", "a1": "(ep)", "e10": "H", "e11": "H", "e20": "H", "e21": "H"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"H","a1":"H","e10":"H","e11":"H","e20":"(ep)","e21":"(ep)"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "H","a1": "H","e10": "H","e11": "H","e20": "(ep)","e21": "(ep)"}}') self.assertTrue(vsepr_grade(user_answer, correct_answer)) def test_incorrect_answer_e1e2(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "(ep)", "a1": "(ep)", "e10": "H", "e11": "H", "e20": "H", "e21": "H"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"Br","a0":"H","a1":"H","e10":"(ep)","e11":"H","e20":"H","e21":"(ep)"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "Br","a0": "H","a1": "H","e10": "(ep)","e11": "H","e20": "H","e21": "(ep)"}}') self.assertFalse(vsepr_grade(user_answer, correct_answer)) def test_incorrect_c0(self): correct_answer = vsepr_build_correct_answer(geometry="AX6E0", atoms={"c0": "Br", "a0": "(ep)", "a1": "test", "e0": "H", "e1": "H", "e2": "H", "e3": "(ep)"}) - user_answer = vsepr_parse_user_answer(u'{"geometry":"AX6E0","atoms":{"c0":"H","a0":"test","a1":"(ep)","e0":"H","e1":"H","e2":"(ep)","e3":"H"}}') + user_answer = vsepr_parse_user_answer(u'{"geometry": "AX6E0","atoms":{"c0": "H","a0": "test","a1": "(ep)","e0": "H","e1": "H","e2": "(ep)","e3": "H"}}') self.assertFalse(vsepr_grade(user_answer, correct_answer))