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Merge pull request #1005 from MITx/fix-alex-vsepr-2-mitx

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Fix alex vsepr 2 mitx
This commit is contained in:
Victor Shnayder
2012-11-01 17:52:16 -07:00
parent 482800064b 3ed4b77d8c
commit d05f6c8a06
1 changed files with 151 additions and 81 deletions
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232
common/lib/capa/capa/chem/chemtools.py
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@@ -1,63 +1,143 @@
from collections import OrderedDict
"""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):
d = OrderedDict(json.loads(user_input))
d['atoms'] = OrderedDict(sorted(d['atoms'].items()))
return d
"""
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):
correct_answer = OrderedDict()
correct_answer['geometry'] = geometry
correct_answer['atoms'] = OrderedDict(sorted(atoms.items()))
return correct_answer
def vsepr_grade(user_input, correct_answer, ignore_p_order=False, ignore_a_order=False, ignore_e_order=False):
""" Flags ignore_(a,p,e)_order are for checking order in axial, perepherial or equatorial positions.
Allowed cases:
c0, a, e
c0, p
Not implemented and not tested cases when p with a or e (no need for now)
"""
# print user_input, type(user_input)
# print correct_answer, type(correct_answer)
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_peripheral=False):
"""
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
"""
if user_input['geometry'] != correct_answer['geometry']:
return False
if user_input['atoms']['c0'] != correct_answer['atoms']['c0']:
return False
# not order-aware comparisons
for ignore in [(ignore_p_order, 'p'), (ignore_e_order, 'e'), (ignore_a_order, 'a')]:
if ignore[0]:
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')
user_input['atoms'] = {'p' + str(i): v for i, v in enumerate(user_input['atoms'].values())}
user_input['atoms']['c0'] = c0
# special case for AX6
if 'e10' in correct_answer['atoms']: # need check e1x, e2x symmetry for AX6..
a_user = {}
a_correct = {}
for ea_position in ['a', 'e1', 'e2']: # collecting positions:
a_user[ea_position] = [v for k, v in user_input['atoms'].items() if k.startswith(ea_position)]
a_correct[ea_position] = [v for k, v in correct_answer['atoms'].items() if k.startswith(ea_position)]
correct = [sorted(a_correct['a'])] + [sorted(a_correct['e1'])] + [sorted(a_correct['e2'])]
for permutation in itertools.permutations(['a', 'e1', 'e2']):
if correct == [sorted(a_user[permutation[0]])] + [sorted(a_user[permutation[1]])] + [sorted(a_user[permutation[2]])]:
return True
return False
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():
if len(k) == 3: # e1x
del user_input['atoms'][k]
user_input['atoms']['e' + str(e_index)] = v
e_index += 1
# common case
for ea_position in ['p', 'a', 'e']:
# collecting atoms:
a_user = [v for k, v in user_input['atoms'].items() if k.startswith(ignore[1])]
a_correct = [v for k, v in correct_answer['atoms'].items() if k.startswith(ignore[1])]
# print ignore[0], ignore[1], a_user, a_correct
a_user = [v for k, v in user_input['atoms'].items() if k.startswith(ea_position)]
a_correct = [v for k, v in correct_answer['atoms'].items() if k.startswith(ea_position)]
# print a_user, a_correct
if len(a_user) != len(a_correct):
return False
if sorted(a_user) != sorted(a_correct):
return False
# order-aware comparisons
for ignore in [(ignore_p_order, 'p'), (ignore_e_order, 'e'), (ignore_a_order, 'a')]:
if not ignore[0]:
# collecting atoms:
a_user = [v for k, v in user_input['atoms'].items() if k.startswith(ignore[1])]
a_correct = [v for k, v in correct_answer['atoms'].items() if k.startswith(ignore[1])]
# print '2nd', ignore[0], ignore[1], a_user, a_correct
if len(a_user) != len(a_correct):
return False
if len(a_correct) == 0:
continue
if a_user != a_correct:
return False
return True
return True
class Test_Grade(unittest.TestCase):
@@ -65,63 +145,53 @@ 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_incorrect_positions(self):
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":"B","p0":"F","p1":"B","p2":"F"}}')
self.assertFalse(vsepr_grade(user_answer, correct_answer))
def test_correct_answer(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_incorrect_position_order_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":"H","p2":"(ep)", "p3":"H"}}')
self.assertFalse(vsepr_grade(user_answer, correct_answer))
def test_correct_position_order_with_ignore_p_order(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":"H","p2":"(ep)", "p3":"H"}}')
self.assertTrue(vsepr_grade(user_answer, correct_answer, ignore_p_order=True))
def test_incorrect_position_order_ae(self):
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)","e0":"H","e1":"(ep)","e2":"(ep)","e3":"(ep)"}}')
self.assertFalse(vsepr_grade(user_answer, correct_answer))
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_position_order_with_ignore_a_order_not_e(self):
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)","e0":"H","e1":"H","e2":"(ep)","e3":"(ep)"}}')
self.assertTrue(vsepr_grade(user_answer, correct_answer, ignore_a_order=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_incorrect_position_order_with_ignore_a_order_not_e(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":"Br","a0":"test","a1":"(ep)","e0":"H","e1":"H","e2":"(ep)","e3":"H"}}')
self.assertFalse(vsepr_grade(user_answer, correct_answer, ignore_a_order=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_peripheral=True))
def test_correct_position_order_with_ignore_e_order_not_a(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":"Br","a0":"(ep)","a1":"test","e0":"H","e1":"H","e2":"(ep)","e3":"H"}}')
self.assertTrue(vsepr_grade(user_answer, correct_answer, ignore_e_order=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"}}')
self.assertTrue(vsepr_grade(user_answer, correct_answer))
def test_incorrect_position_order_with_ignore_e_order__not_a(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":"Br","a0":"test","a1":"(ep)","e0":"H","e1":"H","e2":"(ep)","e3":"H"}}')
self.assertFalse(vsepr_grade(user_answer, correct_answer, ignore_e_order=True))
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"}}')
self.assertTrue(vsepr_grade(user_answer, correct_answer))
def test_correct_position_order_with_ignore_ae_order(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":"Br","a0":"test","a1":"(ep)","e0":"H","e1":"H","e2":"(ep)","e3":"H"}}')
self.assertTrue(vsepr_grade(user_answer, correct_answer, ignore_e_order=True, ignore_a_order=True))
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)"}}')
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)"}}')
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"}}')
self.assertFalse(vsepr_grade(user_answer, correct_answer, ignore_e_order=True, ignore_a_order=True))
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))
def suite():