test_dummy.py at fcab626 ⋅ slochower/pAPRika

5

38

import os

7

38

import parmed as pmd

9

38

import paprika.dummy as dummy

10

38

from paprika.align import zalign

13

38

def test_extract_dummy():

14

38

    cb6 = pmd.load_file(

17

38

    aligned_cb6 = zalign(cb6, ":CB6", ":BUT")

18

38

    aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM1", z=-6.0)

19

38

    aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM2", z=-9.0)

20

38

    aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM3", z=-11.2, y=2.2)

22

38

    dm_index = []

23

38

    for atom in aligned_cb6.topology.atoms():

24

38

        if atom.residue.name in ["DM1", "DM2", "DM3"]:

25

38

            dm_index.append(atom.index)

27

38

    assert len(dm_index) != 0

29

38

    dummy_dict = dummy.extract_dummy_atoms(aligned_cb6, serial=False)

31

38

    assert all(dummy_dict["DM1"]["pos"] == [0.0, 0.0, -6.0])

32

38

    assert all(dummy_dict["DM2"]["pos"] == [0.0, 0.0, -9.0])

33

38

    assert all(dummy_dict["DM3"]["pos"] == [0.0, 2.2, -11.2])

35

38

    assert dummy_dict["DM1"]["mass"] == 208.0

36

38

    assert dummy_dict["DM2"]["mass"] == 208.0

37

38

    assert dummy_dict["DM3"]["mass"] == 208.0

39

38

    assert dummy_dict["DM1"]["idx"] == dm_index[0]

40

38

    assert dummy_dict["DM2"]["idx"] == dm_index[1]

41

38

    assert dummy_dict["DM3"]["idx"] == dm_index[2]

Navigation	Overlay
`t` Navigate files	`h` Toggle hits
`y` Change url to tip of branch	`m` Toggle misses
`b / v` Jump to prev/next hit line	`p` Toggle partial
`z / x` Jump to prev/next missed or partial line	`1..9` Toggle flags
`shift + o` Open current page in GitHub	`a` Toggle all on
`/ or ?` Show keyboard shortcuts dialog	`c` Toggle context lines or commits

1		"""
2		Tests the dummy atoms utilities.
3		"""
4
5	38	import os
6
7	38	import parmed as pmd
8
9	38	import paprika.dummy as dummy
10	38	from paprika.align import zalign
11
12
13	38	def test_extract_dummy():
14	38	cb6 = pmd.load_file(
15		os.path.join(os.path.dirname(__file__), "../data/cb6-but/vac.pdb")
16		)
17	38	aligned_cb6 = zalign(cb6, ":CB6", ":BUT")
18	38	aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM1", z=-6.0)
19	38	aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM2", z=-9.0)
20	38	aligned_cb6 = dummy.add_dummy(aligned_cb6, residue_name="DM3", z=-11.2, y=2.2)
21
22	38	dm_index = []
23	38	for atom in aligned_cb6.topology.atoms():
24	38	if atom.residue.name in ["DM1", "DM2", "DM3"]:
25	38	dm_index.append(atom.index)
26
27	38	assert len(dm_index) != 0
28
29	38	dummy_dict = dummy.extract_dummy_atoms(aligned_cb6, serial=False)
30
31	38	assert all(dummy_dict["DM1"]["pos"] == [0.0, 0.0, -6.0])
32	38	assert all(dummy_dict["DM2"]["pos"] == [0.0, 0.0, -9.0])
33	38	assert all(dummy_dict["DM3"]["pos"] == [0.0, 2.2, -11.2])
34
35	38	assert dummy_dict["DM1"]["mass"] == 208.0
36	38	assert dummy_dict["DM2"]["mass"] == 208.0
37	38	assert dummy_dict["DM3"]["mass"] == 208.0
38
39	38	assert dummy_dict["DM1"]["idx"] == dm_index[0]
40	38	assert dummy_dict["DM2"]["idx"] == dm_index[1]
41	38	assert dummy_dict["DM3"]["idx"] == dm_index[2]