1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
import os
import sys
from pymol import cmd, testing, stored
@testing.requires_version('2.3')
class TestSeqalign(testing.PyMOLTestCase):
def testLoadAlnMatchingIds(self):
cmd.fab('ACDEFGHIKLMNPQRS', 'seq1')
cmd.fab('ACDIKLMNP', 'seq2')
cmd.fab('GHIKPQRS', 'seq3')
cmd.load(self.datafile('alignment.aln'), 'aln')
self.assertEqual(cmd.count_atoms('guide & aln & seq1'), 11)
self.assertEqual(cmd.count_atoms('guide & aln & seq2'), 7)
self.assertEqual(cmd.count_atoms('guide & aln & seq3'), 6)
def testLoadAlnMappingStr(self):
cmd.fab('ACDEFGHIKLMNPQRS', 'm1')
cmd.fab('ACDIKLMNP', 'm2')
from pymol.seqalign import load_aln_multi
load_aln_multi(self.datafile('alignment.aln'), 'aln', mapping=
'seq1 m1 '
'seq2 m2 '
)
self.assertEqual(cmd.count_atoms('guide & aln & m1'), 7)
self.assertEqual(cmd.count_atoms('guide & aln & m2'), 7)
def testLoadAlnMappingDict(self):
cmd.fab('ACDIKLMNP', 'm2')
cmd.fab('GHIKPQRS', 'm3')
from pymol.seqalign import load_aln_multi
load_aln_multi(self.datafile('alignment.aln'), 'aln', mapping={
'seq2': 'm2',
'seq3': 'm3',
})
self.assertEqual(cmd.count_atoms('guide & aln & m2'), 2)
self.assertEqual(cmd.count_atoms('guide & aln & m3'), 2)
|
