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#!/usr/bin/env python
import contextlib
import io
import os
import sys
import unittest
try:
import numpy
except ImportError:
numpy = None
TOP_DIR = os.path.join(os.path.dirname(__file__), "..")
PDB_FILE = os.path.join(TOP_DIR, "tests", "1orc.pdb")
CIF_FILE = os.path.join(TOP_DIR, "tests", "5i55.cif")
JSON_FILE = os.path.join(TOP_DIR, "tests", "1pfe.json")
MAP_FILE = os.path.join(TOP_DIR, "tests", "5i55_tiny.ccp4")
PDB_1PFE_FILE = os.path.join(TOP_DIR, "tests", "1pfe.cif.gz")
MASK_1PFE_FILE = os.path.join(TOP_DIR, "tests", "1pfe_asu.msk.gz")
EXAMPLE_DIR = os.path.join(TOP_DIR, "examples")
sys.path.insert(0, EXAMPLE_DIR)
class TestExamples(unittest.TestCase):
def setUp(self):
sys.argv = ['example', CIF_FILE]
sys.stdout = open(os.devnull, 'w')
def tearDown(self):
sys.stdout.close()
sys.stdout = sys.__stdout__
def test_aafreq(self):
import aafreq # noqa: F401 - imported but unused
def test_col_order(self):
import col_order # noqa: F401
def test_hello(self):
import hello # noqa: F401
def test_matthews(self):
import matthews # noqa: F401
def test_monomers(self):
import monomers # noqa: F401
def test_simple_search(self):
import simple_search # noqa: F401
def test_weight(self):
import weight
weight.main()
def test_long_geom(self):
import long_geom
self.assertEqual(long_geom.run(PDB_FILE), 0)
self.assertEqual(long_geom.run(CIF_FILE), 1)
class TestExamples2(unittest.TestCase):
def test_from_json(self):
sys.argv = ['from_json.py', JSON_FILE, os.devnull]
import from_json # noqa: F401
def test_map2mtz(self):
sys.argv = ['map2mtz.py', MAP_FILE, os.devnull]
import map2mtz # noqa: F401
@unittest.skipIf(sys.version_info[0] == 2, 'this example is Py3 only')
def test_multiproc(self):
sys.stdout = open(os.devnull, 'w')
import multiproc # noqa: F401
multiproc.main(PDB_FILE)
# In this example we use file produced with two commands:
# $ cctbx.python -m mmtbx.command_line.mask 1pfe.pdb
# $ mapmask mapin mask.ccp4 mskout 1pfe_asu.msk << eof
# XYZLIM ASU
# MASK CUT 0.5
# AXIS X Z Y
# MODE mapin
# eof
@unittest.skipIf(numpy is None or sys.version_info[0] == 2,
'this example is Py3 only, requires NumPy')
def test_maskcheck(self):
import maskcheck
with io.StringIO() as buf, contextlib.redirect_stdout(buf):
maskcheck.maskcheck(MASK_1PFE_FILE, PDB_1PFE_FILE)
output = buf.getvalue()
expected_output = '''\
Generating CCTBX-compatible mask ...
Size: 72 x 72 x 150, total 777600 points
File-Gemmi Count Fraction
0-0 509676 65.54%
1-1 265788 34.18%
0-1 1452 0.19%
1-0 684 0.09%
'''
self.assertEqual(output.splitlines(), expected_output.splitlines())
if __name__ == '__main__':
unittest.main()
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