pdb-tools 2.5.0__py3-none-any.whl → 2.5.1__py3-none-any.whl

tests/test_pdb_selseg.py

@@ -1,165 +0,0 @@
-#!/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_selseg`.
-"""
-
-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_selseg'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self):
-        """
-        Execs module.
-        """
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        return
-
-    def test_one_option(self):
-        """$ pdb_selseg -Z data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_selseg dummy.pdb
-        sys.argv = ['', '-Z', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 39)  # selected Z
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-    def test_multiple(self):
-        """
-        $ pdb_selseg -A,B data/dummy.pdb
-        """
-
-        sys.argv = ['', '-A,B', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 19)  # segments A & B (i.e. nothing)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_file_not_found(self):
-        """$ pdb_selseg not_existing.pdb"""
-
-        afile = os.path.join(data_dir, 'not_existing.pdb')
-        sys.argv = ['', afile]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)  # exit code is 1 (error)
-        self.assertEqual(len(self.stdout), 0)  # nothing written to stdout
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! File not found")  # proper error message
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_file_missing(self):
-        """$ pdb_selseg -A"""
-
-        sys.argv = ['', '-A']
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(self.stderr[0],
-                         "ERROR!! No data to process!")
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_helptext(self):
-        """$ pdb_selseg"""
-
-        sys.argv = ['']
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)  # ensure the program exited gracefully.
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
-
-    def test_invalid_option(self):
-        """$ pdb_selseg data/dummy.pdb"""
-
-        sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:47],
-                         "ERROR!! You must provide at least one segment i")
-
-    def test_invalid_option_2(self):
-        """$ pdb_selseg -ABCDE data/dummy.pdb"""
-
-        sys.argv = ['', '-ABCDE', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:40],
-                         "ERROR!! Segment identifier name is inval")
-
-    def test_not_an_option(self):
-        """$ pdb_selseg 20 data/dummy.pdb"""
-
-        sys.argv = ['', '20', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0],
-                         "ERROR! First argument is not an option: '20'")
-
-
-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()

tests/test_pdb_shiftres.py

@@ -1,241 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Copyright 1118 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_shiftres`.
-"""
-
-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_shiftres'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self):
-        """
-        Execs module.
-        """
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        return
-
-    def test_default(self):
-        """$ pdb_shiftres data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_shiftres dummy.pdb
-        sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 204)  # no lines deleted
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        records = (('ATOM', 'HETATM'))
-        resid_list = [int(l[22:26]) for l in self.stdout
-                      if l.startswith(records)]
-
-        expected = [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
-                    4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
-                    6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1,
-                    1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
-                    3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
-                    5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, -1, -1, -1, -1, -1, -1, -1, -1, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-                    301, 302, 303, 301, 301, 302, 303, 304, 305]
-
-        self.assertEqual(resid_list, expected)
-
-    def test_single_option_1(self):
-        """$ pdb_shiftres -10 data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_shiftres dummy.pdb
-        sys.argv = ['', '-10', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 204)  # no lines deleted
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        records = (('ATOM', 'HETATM'))
-        resid_list = [int(l[22:26]) for l in self.stdout
-                      if l.startswith(records)]
-
-        expected = [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
-                    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16, 16, 16,
-                    16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17,
-                    17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11,
-                    11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12,
-                    12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
-                    12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
-                    13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-                    15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12,
-                    12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9,
-                    9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
-                    12, 12, 12, 12, 12, 12, 12, 12, 12, 311, 312, 313, 311, 311,
-                    312, 313, 314, 315]
-
-        self.assertEqual(resid_list, expected)
-
-    def test_single_option_2(self):
-        """$ pdb_shiftres --10 data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_shiftres dummy.pdb
-        sys.argv = ['', '--10', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 204)  # no lines deleted
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        records = (('ATOM', 'HETATM'))
-        resid_list = [int(l[22:26]) for l in self.stdout
-                      if l.startswith(records)]
-
-        expected = [-6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6,
-                    -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -4, -4, -4, -4,
-                    -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -3, -3, -3, -3,
-                    -3, -3, -3, -3, -3, -3, -9, -9, -9, -9, -9, -9, -9, -9, -9,
-                    -9, -9, -9, -9, -9, -9, -9, -9, -8, -8, -8, -8, -8, -8, -8,
-                    -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
-                    -8, -8, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7,
-                    -7, -7, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,
-                    -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -8, -8,
-                    -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -11,
-                    -11, -11, -11, -11, -11, -11, -11, -8, -8, -8, -8, -8, -8,
-                    -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 291,
-                    292, 293, 291, 291, 292, 293, 294, 295]
-
-        self.assertEqual(resid_list, expected)
-
-    def test_too_many_residues(self):
-        """$ pdb_shiftres -9998 data/dummy.pdb"""
-
-        sys.argv = ['', '-9998', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(len(self.stderr), 1)
-
-        self.assertEqual(self.stderr[0][:22],
-                         "Cannot set residue num")  # proper error message
-
-    def test_file_not_found(self):
-        """$ pdb_shiftres -10 not_existing.pdb"""
-
-        afile = os.path.join(data_dir, 'not_existing.pdb')
-        sys.argv = ['', '-10', afile]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)  # exit code is 1 (error)
-        self.assertEqual(len(self.stdout), 0)  # nothing written to stdout
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! File not found")  # proper error message
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_file_missing(self):
-        """$ pdb_shiftres -10"""
-
-        sys.argv = ['', '-10']
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(self.stderr[0],
-                         "ERROR!! No data to process!")
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_helptext(self):
-        """$ pdb_shiftres"""
-
-        sys.argv = ['']
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)  # ensure the program exited gracefully.
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(self.stderr, self.module.__doc__.split("\n")[:-1])
-
-    def test_invalid_option(self):
-        """$ pdb_shiftres -A data/dummy.pdb"""
-
-        sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:36],
-                         "ERROR!! You provided an invalid numb")
-
-    def test_not_an_option(self):
-        """$ pdb_shiftres 11 data/dummy.pdb"""
-
-        sys.argv = ['', '11', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0],
-                         "ERROR! First argument is not an option: '11'")
-
-
-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()

tests/test_pdb_sort.py

@@ -1,254 +0,0 @@
-#!/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_sort`.
-"""
-
-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_sort'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self):
-        """
-        Execs module.
-        """
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        return
-
-    def test_default(self):
-        """$ pdb_sort 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.
-        self.assertEqual(len(self.stdout), 200)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        # Check order of chains
-        records = ('ATOM', 'HETATM')
-        chain_ids = [l[21] for l in self.stdout if l.startswith(records)]
-
-        expected = ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
-                    'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'A', 'A', 'A', 'B',
-                    'C', 'C', 'C', 'C', 'C']
-
-        self.assertEqual(chain_ids, expected)
-
-        # Check order of residue numbers
-        resids = [int(l[22:26]) for l in self.stdout if l.startswith(records)]
-
-        expected = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-                    2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4,
-                    4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
-                    4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7,
-                    7, 7, 7, 7, 7, 7, 7, -1, -1, -1, -1, -1, -1, -1, -1, 2, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5,
-                    5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-                    301, 302, 303, 301, 301, 302, 303, 304, 305]
-
-        self.assertEqual(resids, expected)
-
-        # Check order of altlocs
-        altlocs = [l[16] for l in self.stdout if l.startswith(records)]
-
-        expected = [' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', 'A', 'B', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ']
-
-        self.assertEqual(altlocs, expected)
-
-    def test_sort_chains(self):
-        """$ pdb_sort -C data/dummy.pdb"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', '-C', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 200)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        # Check order of chains
-        records = ('ATOM', 'HETATM')
-        chain_ids = [l[21] for l in self.stdout if l.startswith(records)]
-
-        expected = ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
-                    'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
-                    'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
-                    'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
-                    'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'A', 'A', 'A', 'B',
-                    'C', 'C', 'C', 'C', 'C']
-
-        self.assertEqual(chain_ids, expected)
-
-        # Check order of residue numbers did NOT change
-        resids = [int(l[22:26]) for l in self.stdout if l.startswith(records)]
-
-        expected = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3,
-                    3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4,
-                    4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
-                    4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7,
-                    7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
-                    5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, -1, -1, -1, -1, -1, -1, -1, -1, 2,
-                    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-                    301, 302, 303, 301, 301, 302, 303, 304, 305]
-
-        self.assertEqual(resids, expected)
-
-        # Check order of altlocs
-        altlocs = [l[16] for l in self.stdout if l.startswith(records)]
-
-        expected = [' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', 'A', 'B', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                    ' ', ' ', ' ', ' ', ' ']
-
-        self.assertEqual(altlocs, expected)
-
-    def test_file_not_found(self):
-        """$ pdb_sort 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_sort"""
-
-        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_sort -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!! Sorting key is not valid: 'A")
-
-
-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()