Source code for conkit.io.tests.test_ncont
"""Testing facility for conkit.io.ncont"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 2016"
import os
import unittest
from conkit.io.ncont import NcontParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestNcontParser(ParserTestCase):
[docs] def test_read_1(self):
content = """
###############################################################
###############################################################
###############################################################
### CCP4 7.0.045: NCONT version 7.0.045 : ##
###############################################################
User: unknown Run date: 16/11/2017 Run time: 09:51:16
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
------------------------------------------------------------------------------
PDB file /home/felix/Dropbox/subprojects/ample-rio/tmppyndBZ.pdb has been read in.
------------------------------------------------------------------------------
Input cards
Data line--- source A//CA
Data line--- target B//CA
Data line--- mindist 0.0
Data line--- maxdist 1.5
Data line--- sort target inc
------------------------------------------------------------------------------
Selected 15 source atoms
Selected 8154 target atoms
------------------------------------------------------------------------------
12 contacts found:
SOURCE ATOMS TARGET ATOMS DISTANCE
/1/A/ 127(ALA). / CA [ C]: /1/B/ 129(GLY). / CA [ C]: 0.41
/1/A/ 128(GLN). / CA [ C]: /1/B/ 130(ALA). / CA [ C]: 0.37
/1/A/ 129(GLY). / CA [ C]: /1/B/ 131(MET). / CA [ C]: 0.19
/1/A/ 130(ALA). / CA [ C]: /1/B/ 132(ASN). / CA [ C]: 0.10
/1/A/ 131(MET). / CA [ C]: /1/B/ 133(LYS). / CA [ C]: 0.35
/1/A/ 132(ASN). / CA [ C]: /1/B/ 134(ALA). / CA [ C]: 0.20
/1/A/ 133(LYS). / CA [ C]: /1/B/ 135(LEU). / CA [ C]: 0.39
/1/A/ 134(ALA). / CA [ C]: /1/B/ 136(GLU). / CA [ C]: 0.34
/1/A/ 135(LEU). / CA [ C]: /1/B/ 137(LEU). / CA [ C]: 0.48
/1/A/ 136(GLU). / CA [ C]: /1/B/ 138(PHE). / CA [ C]: 0.46
/1/A/ 137(LEU). / CA [ C]: /1/B/ 139(ARG). / CA [ C]: 0.47
/1/A/ 138(PHE). / CA [ C]: /1/B/ 140(LYS). / CA [ C]: 0.89
Total 12 contacts
--------------------------------------------------------------------------
NCONT: Normal termination
Times: User: 0.1s System: 0.0s Elapsed: 0:00
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = NcontParser().read(f_in)
cmap = contact_file.top
self.assertEqual(cmap.ncontacts, 12)
self.assertEqual([c.res1_seq for c in cmap], list(range(127, 139)))
self.assertEqual([c.res2_seq for c in cmap], list(range(129, 141)))
self.assertEqual(set([c.res1_chain for c in cmap]), set(["A"]))
self.assertEqual(set([c.res2_chain for c in cmap]), set(["B"]))
[docs] def test_read_2(self):
content = """
###############################################################
###############################################################
###############################################################
### CCP4 7.0.045: NCONT version 7.0.045 : ##
###############################################################
User: unknown Run date: 16/11/2017 Run time: 10:04:06
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
------------------------------------------------------------------------------
PDB file /home/felix/Dropbox/subprojects/ample-rio/tmp5x3eJ1.pdb has been read in.
------------------------------------------------------------------------------
Input cards
Data line--- source A//CA
Data line--- target B//CA
Data line--- mindist 0.0
Data line--- maxdist 0.01
Data line--- sort target inc
------------------------------------------------------------------------------
Selected 15 source atoms
Selected 8154 target atoms
------------------------------------------------------------------------------
NO CONTACTS FOUND.
Total 0 contacts
--------------------------------------------------------------------------
NCONT: Normal termination
Times: User: 0.1s System: 0.0s Elapsed: 0:00
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = NcontParser().read(f_in)
cmap = contact_file.top
self.assertEqual(cmap.ncontacts, 0)
[docs] def test_read_3(self):
content = """
###############################################################
###############################################################
###############################################################
### CCP4 7.0.045: NCONT version 7.0.045 : ##
###############################################################
User: unknown Run date: 16/11/2017 Run time: 10:07:41
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
------------------------------------------------------------------------------
PDB file /home/felix/Dropbox/subprojects/ample-rio/tmpftYndd.pdb has been read in.
------------------------------------------------------------------------------
Input cards
Data line--- source A//*
Data line--- target B//*
Data line--- mindist 0.0
Data line--- maxdist 0.2
Data line--- sort target inc
------------------------------------------------------------------------------
Selected 74 source atoms
Selected 57888 target atoms
------------------------------------------------------------------------------
9 contacts found:
SOURCE ATOMS TARGET ATOMS DISTANCE
/1/A/ 129(GLY). / CA [ C]: /1/B/ 131(MET). / CA [ C]: 0.19
/1/A/ 129(GLY). / C [ C]: /1/B/ 131(MET). / C [ C]: 0.13
/1/A/ 129(GLY). / O [ O]: /1/B/ 131(MET). / O [ O]: 0.15
/1/A/ 130(ALA). / N [ N]: /1/B/ 132(ASN). / N [ N]: 0.10
/1/A/ 130(ALA). / CA [ C]: /1/B/ 132(ASN). / CA [ C]: 0.10
/1/A/ 130(ALA). / CB [ C]: /1/B/ 132(ASN). / CB [ C]: 0.14
/1/A/ 131(MET). / O [ O]: /1/B/ 133(LYS). / O [ O]: 0.19
/1/A/ 132(ASN). / C [ C]: /1/B/ 134(ALA). / C [ C]: 0.18
/1/A/ 135(LEU). / N [ N]: /1/B/ 137(LEU). / N [ N]: 0.20
Total 9 contacts
--------------------------------------------------------------------------
NCONT: Normal termination
Times: User: 0.1s System: 0.0s Elapsed: 0:00
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = NcontParser().read(f_in)
cmap = contact_file.top
self.assertEqual(cmap.ncontacts, 5)
self.assertEqual([c.res1_seq for c in cmap], [129, 130, 131, 132, 135])
self.assertEqual([c.res2_seq for c in cmap], [131, 132, 133, 134, 137])
self.assertEqual(set([c.res1_chain for c in cmap]), set(["A"]))
self.assertEqual(set([c.res2_chain for c in cmap]), set(["B"]))
if __name__ == "__main__":
unittest.main(verbosity=2)
