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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2018 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Unit Tests for `pdb_tidy`.
"""
try:
from StringIO import StringIO # python 2.7
except ImportError:
from io import StringIO # python 3.x
import os
import sys
import unittest
from .config import data_dir
from .utils import OutputCapture
class TestTool(unittest.TestCase):
"""
Generic class for testing tools.
"""
def setUp(self):
# Dynamically import the module
name = 'pdbtools.pdb_tidy'
self.module = __import__(name, fromlist=[''])
def exec_module(self, stdin=None):
"""
Execs module.
"""
if stdin is not None:
sys.stdin = StringIO(stdin)
with OutputCapture() as output:
try:
self.module.main()
except SystemExit as e:
self.retcode = e.code
self.stdout = output.stdout
self.stderr = output.stderr
sys.stdin = sys.__stdin__ # restore
return
def test_default(self):
"""$ pdb_tidy data/dummy.pdb"""
fpath = os.path.join(data_dir, 'dummy.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 205 lines
self.assertEqual(len(self.stdout), 205)
self.assertEqual(len(self.stderr), 0) # no errors
# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 5)
# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
self.assertEqual(c_conect, 0)
# Check if we added END statements correctly
self.assertTrue(self.stdout[-1].startswith('END'))
def test_default_in_lib(self):
"""
Test command-line versus lib.
$ pdb_tidy data/dummy.pdb
>>> original_lines = open('dummy.pdb').readlines()
>>> lines = list(pdb_tidy.run(original_lines))
`lines` and the result from the command-line must be the same.
"""
fpath = os.path.join(data_dir, 'dummy.pdb')
sys.argv = ['', fpath]
# Execute the script
self.exec_module()
fin = open(os.path.join(data_dir, 'dummy.pdb'))
original_lines = fin.readlines()
fin.close()
lines = list(self.module.run(original_lines))
self.assertEqual(len(lines), 205)
# Check if we added TER statements correctly
n_ter = len([r for r in lines if r.startswith('TER')])
self.assertEqual(n_ter, 5)
# Check no CONECT in output
c_conect = sum(1 for i in lines if i.startswith('CONECT'))
self.assertEqual(c_conect, 0)
# Check if we added END statements correctly
self.assertTrue(lines[-1].startswith('END'))
self.assertTrue(lines, self.stdout)
def test_tidy_removes_master(self):
"""Test pdb_tidy removes MASTER lines as well."""
sys.argv = ['']
self.exec_module(
'MASTER 378 0 9 5 3 '
'0 29 6 847 1 76 7'
)
# Check no MASTER in output
m_master = sum(1 for i in self.stdout if i.startswith('MASTER'))
self.assertEqual(m_master, 0)
def test_default_stdin(self):
"""$ cat data/dummy.pdb | pdb_tidy"""
fpath = os.path.join(data_dir, 'dummy.pdb')
sys.argv = ['']
# Execute the script with file as stdin
with open(fpath) as fp:
self.exec_module(fp.read())
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 205 lines
self.assertEqual(len(self.stdout), 205)
self.assertEqual(len(self.stderr), 0) # no errors
# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 5)
# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
self.assertEqual(c_conect, 0)
# Check if we added END statements correctly
self.assertTrue(self.stdout[-1].startswith('END'))
def test_default_strict(self):
"""$ pdb_tidy -strict data/dummy.pdb"""
fpath = os.path.join(data_dir, 'dummy.pdb')
sys.argv = ['', '-strict', fpath]
# Execute the script
self.exec_module()
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 204 lines
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stderr), 0) # no errors
# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 4)
# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
self.assertEqual(c_conect, 0)
# Check if we added END statements correctly
self.assertTrue(self.stdout[-1].startswith('END'))
def test_default_strict_stdin(self):
"""$ cat data/dummy.pdb | pdb_tidy -strict"""
fpath = os.path.join(data_dir, 'dummy.pdb')
sys.argv = ['', '-strict']
# Execute the script
with open(fpath) as fp:
self.exec_module(fp.read())
# Validate results
self.assertEqual(self.retcode, 0) # ensure the program exited OK.
# CONECTs are ignored by issue #72, expected only 204 lines
self.assertEqual(len(self.stdout), 204)
self.assertEqual(len(self.stderr), 0) # no errors
# Check if we added TER statements correctly
n_ter = len([r for r in self.stdout if r.startswith('TER')])
self.assertEqual(n_ter, 4)
# Check no CONECT in output
c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
self.assertEqual(c_conect, 0)
# Check if we added END statements correctly
self.assertTrue(self.stdout[-1].startswith('END'))
def test_corrects_model_format_and_numbers(self):
"""Correct MODEL lines."""
fpath = os.path.join(data_dir, 'ensemble_error_MODEL.pdb')
sys.argv = ['', fpath]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 16)
self.assertEqual(len(self.stderr), 0)
self.assertEqual(len(self.stdout[5].strip()), 14)
self.assertEqual(len(self.stdout[5]), 80)
self.assertEqual(len(self.stdout[10].strip()), 14)
self.assertEqual(len(self.stdout[10]), 80)
self.assertEqual(self.stdout[5].strip(), "MODEL 1")
self.assertEqual(self.stdout[10].strip(), "MODEL 2")
def test_corrects_model_ENDMDL(self):
"""Correct MODEL lines."""
fpath = os.path.join(data_dir, 'ensemble_error_4.pdb')
sys.argv = ['', fpath]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 14)
self.assertEqual(len(self.stderr), 0)
# MODEL lines
self.assertEqual(len(self.stdout[3].strip()), 14)
self.assertEqual(len(self.stdout[3]), 80)
self.assertEqual(len(self.stdout[3].strip()), 14)
self.assertEqual(len(self.stdout[8]), 80)
self.assertEqual(self.stdout[3].strip(), "MODEL 1")
self.assertEqual(self.stdout[8].strip(), "MODEL 2")
# ENDMDL LINES
self.assertEqual(len(self.stdout[7]), 80)
self.assertEqual(len(self.stdout[12]), 80)
self.assertEqual(self.stdout[7].strip(), "ENDMDL")
self.assertEqual(self.stdout[12].strip(), "ENDMDL")
# END LINES
self.assertEqual(self.stdout[-1].strip(), "END")
self.assertEqual(len(self.stdout[-1]), 80)
def test_corrects_model_ENDMDL_with_HETATM(self):
"""Correct MODEL lines."""
fpath = os.path.join(data_dir, 'hetatm_ensemble.pdb')
sys.argv = ['', fpath]
self.exec_module()
self.assertEqual(self.retcode, 0)
self.assertEqual(len(self.stdout), 45)
self.assertEqual(len(self.stderr), 0)
# MODEL lines
self.assertEqual(len(self.stdout[0]), 80)
self.assertEqual(len(self.stdout[0].strip()), 14)
self.assertEqual(len(self.stdout[22]), 80)
self.assertEqual(len(self.stdout[22].strip()), 14)
self.assertEqual(self.stdout[0].strip(), "MODEL 1")
self.assertEqual(self.stdout[22].strip(), "MODEL 2")
# ENDMDL LINES
self.assertEqual(len(self.stdout[21]), 80)
self.assertEqual(len(self.stdout[43]), 80)
self.assertEqual(self.stdout[21].strip(), "ENDMDL")
self.assertEqual(self.stdout[43].strip(), "ENDMDL")
# END LINES
self.assertEqual(self.stdout[-1].strip(), "END")
self.assertEqual(len(self.stdout[-1]), 80)
def test_file_not_found(self):
"""$ pdb_tidy not_existing.pdb"""
# Error (file not found)
afile = os.path.join(data_dir, 'not_existing.pdb')
sys.argv = ['', afile]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:22],
"ERROR!! File not found")
@unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
def test_helptext(self):
"""$ pdb_tidy"""
sys.argv = ['']
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
def test_invalid_option(self):
"""$ pdb_tidy -A data/dummy.pdb"""
sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
# Execute the script
self.exec_module()
self.assertEqual(self.retcode, 1)
self.assertEqual(len(self.stdout), 0)
self.assertEqual(self.stderr[0][:36],
"ERROR! First argument is not a valid")
if __name__ == '__main__':
from config import test_dir
mpath = os.path.abspath(os.path.join(test_dir, '..'))
sys.path.insert(0, mpath) # so we load dev files before any installation
unittest.main()
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