def test_empty_frames(self):
"""
Tests that the multithreading doesnt discard a fragment when no contacts are found in the first frame
(see issue #38).
"""
outfile = "tests/5xnd_contacts.tsv"
argv = [
"--topology", "tests/5xnd_topology.pdb", "--trajectory",
"tests/5xnd_trajectory.dcd", "--itypes", "sb", "--sele",
"resname ASP LYS", "--output", outfile
]
get_dynamic_contacts.main(argv=argv)
self.assertTrue(os.path.exists(outfile))
with open(outfile) as f:
lines = f.readlines()
self.assertEqual(len(lines), 22)
# Check that first two lines are comments
self.assertEqual(lines[0][0], "#")
self.assertEqual(lines[1][0], "#")
self.assertEqual(lines[2][0], "1")
# Check that 12 frames total are generated
frames = set([int(l.split()[0]) for l in lines[2:]])
self.assertEqual(frames,
set([1, 2, 3, 4, 5, 8, 12, 13, 15, 16, 18, 19]))
os.remove(outfile)
def test_5xnd_nolabel(self):
"""
Take the 5xnd trajectory, compute contacts and then use TICC to extract two sets of frequencies
"""
top_file = "tests/5xnd_topology.pdb"
trj_file = "tests/5xnd_trajectory.dcd"
contact_file = "tests/5xnd_contacts.tsv"
args = "--topology %s --trajectory %s --output %s --itypes all" % (
top_file, trj_file, contact_file)
get_dynamic_contacts.main(argv=args.split(" "))
self.assertTrue(os.path.exists(contact_file))
ticc_output = ("tests/5xnd_segments.txt", "tests/5xnd_ticc")
args = "--input_contacts %s --clusters 2 --tab_output %s --frequency_output %s" % \
((contact_file,) + ticc_output)
get_contact_ticc.main(argv=args.split(" "))
ticc_output = (ticc_output[0],
"tests/5xnd_ticc_resfreq_cluster000.tsv",
"tests/5xnd_ticc_resfreq_cluster001.tsv")
for output_file in ticc_output:
self.assertTrue(os.path.exists(output_file))
for output_file in ticc_output:
os.remove(output_file)
os.remove(contact_file)
def test_5xnd_nolabel(self):
contact_file = "tests/5xnd_contacts.tsv"
argv = ("--topology tests/5xnd_topology.pdb "
"--trajectory tests/5xnd_trajectory.dcd "
"--output " + contact_file + " "
"--itypes all").split(" ")
get_dynamic_contacts.main(argv=argv)
self.assertTrue(os.path.exists(contact_file))
flare_file = "tests/5xnd_timeflare.json"
argv = ("--input " + contact_file + " "
"--output " + flare_file).split(" ")
get_contact_flare.main(argv=argv)
self.assertTrue(os.path.exists(flare_file))
# TODO: test contents of flare_file
os.remove(contact_file)
os.remove(flare_file)
def test_5xnd(self):
outfile = "tests/5xnd_contacts.tsv"
argv = ("--topology tests/5xnd_topology.pdb "
"--trajectory tests/5xnd_trajectory.dcd "
"--output " + outfile + " "
"--itypes all").split(" ")
get_dynamic_contacts.main(argv=argv)
self.assertTrue(os.path.exists(outfile))
with open(outfile) as f:
lines = f.readlines()
self.assertEqual(len(lines), 20283)
# Check that first two lines are comments
self.assertEqual(lines[0][0], "#")
self.assertEqual(lines[1][0], "#")
self.assertEqual(lines[2][0], "0")
# Check that 20 frames total are generated
frames = set([int(l.split()[0]) for l in lines[2:]])
self.assertEqual(frames, set(range(20)))
# Check that there are no duplicate interactions, even if atom pairs are swapped
contact_hashes = set()
for line in lines[2:]:
tokens = line.strip().split("\t")
a1 = tokens[2]
a2 = tokens[3]
if a2 < a1:
a1, a2 = a2, a1
chash = "\t".join(tokens[0:2] + [a1, a2])
if chash in contact_hashes:
print(chash)
self.assertFalse(chash in contact_hashes)
contact_hashes.add(chash)
os.remove(outfile)
#!/usr/bin/env python3
import get_dynamic_contacts
import os
if __name__ == "__main__":
get_dynamic_contacts.main(traj_required=False)
# Suppress stdout from vmd as program terminates
devnull = open('/dev/null', "w")
os.dup2(devnull.fileno(), 1)