pdb-tools 2.5.0__py3-none-any.whl → 2.6.0__py3-none-any.whl

tests/test_pdb_reatom.py

@@ -1,243 +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_reatom`.
-"""
-
-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_reatom'
-        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_reatom data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_reatom 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'))
-        serial_list = [int(l[6:11]) for l in self.stdout
-                       if l.startswith(records)]
-
-        expected = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
-                    18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
-                    33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
-                    48, 49, 50, 51, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
-                    64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
-                    79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93,
-                    94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106,
-                    107, 108, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,
-                    120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,
-                    132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
-                    144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155,
-                    156, 157, 158, 160, 161, 162, 163, 164, 165, 166, 167, 168,
-                    169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180,
-                    181, 182, 183, 184, 185, 186, 187, 188]
-
-        self.assertEqual(serial_list, expected)
-
-    def test_two_options_pos(self):
-        """$ pdb_reatom -10 data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_reatom 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'))
-        serial_list = [int(l[6:11]) for l in self.stdout
-                       if l.startswith(records)]
-
-        expected = [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
-                    25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
-                    40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
-                    55, 56, 57, 58, 59, 60, 62, 63, 64, 65, 66, 67, 68, 69, 70,
-                    71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85,
-                    86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100,
-                    101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,
-                    113, 114, 115, 116, 117, 119, 120, 121, 122, 123, 124, 125,
-                    126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137,
-                    138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149,
-                    150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161,
-                    162, 163, 164, 165, 166, 167, 169, 170, 171, 172, 173, 174,
-                    175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,
-                    187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
-
-        self.assertEqual(serial_list, expected)
-
-    def test_two_options_neg(self):
-        """$ pdb_reatom --10 data/dummy.pdb"""
-
-        sys.argv = ['', '--10', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 204)
-        self.assertEqual(len(self.stderr), 0)
-
-        records = (('ATOM', 'HETATM'))
-        serial_list = [int(l[6:11]) for l in self.stdout
-                       if l.startswith(records)]
-
-        expected = [-10, -9, -8, -7, -6, -5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5,
-                    6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
-                    22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,
-                    37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
-                    53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
-                    68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,
-                    83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97,
-                    99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,
-                    111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,
-                    123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134,
-                    135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146,
-                    147, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
-                    160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171,
-                    172, 173, 174, 175, 176, 177]
-
-        self.assertEqual(serial_list, expected)
-
-    def test_too_many_atoms(self):
-        """$ pdb_reatom -99998 data/dummy.pdb"""
-
-        sys.argv = ['', '-99998', 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 atom serial")  # proper error message
-
-    def test_file_not_found(self):
-        """$ pdb_reatom -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_reatom -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_reatom"""
-
-        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_reatom -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][:47],
-                         "ERROR!! You provided an invalid atom serial num")
-
-    def test_not_an_option(self):
-        """$ pdb_reatom 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_reres.py

@@ -1,281 +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_reres`.
-"""
-
-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_reres'
-        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_reres data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_reres 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 = [1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
-                    5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7,
-                    7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8,
-                    8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10,
-                    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
-                    10, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
-
-        self.assertEqual(resid_list, expected)
-
-    def test_two_options_pos(self):
-        """$ pdb_reres -10 data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_reres 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 = [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
-                    10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 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, 13, 13, 13, 13, 13, 13, 13, 13, 13,
-                    13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14,
-                    14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
-                    14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
-                    15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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, 17, 17, 17, 17, 17, 18, 18,
-                    18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19,
-                    19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 21, 22, 23,
-                    24, 25, 26, 27, 28]
-
-        self.assertEqual(resid_list, expected)
-
-    def test_two_options_neg(self):
-        """$ pdb_reres --10 data/dummy.pdb"""
-
-        sys.argv = ['', '--10', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 204)
-        self.assertEqual(len(self.stderr), 0)
-
-        records = (('ATOM', 'HETATM'))
-        resid_list = [int(l[22:26]) for l in self.stdout
-                      if l.startswith(records)]
-
-        expected = [-10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,
-                    -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10,
-                    -10, -10, -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, -7, -7,
-                    -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7, -7,
-                    -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6, -6,
-                    -6, -6, -6, -6, -6, -6, -6, -6, -6, -5, -5, -5, -5, -5, -5,
-                    -5, -5, -5, -5, -5, -5, -5, -5, -5, -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, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3,
-                    -3, -3, -3, -3, -3, -2, -2, -2, -2, -2, -2, -2, -2, -1, -1,
-                    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-                    -1, -1, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8]
-
-        self.assertEqual(resid_list, expected)
-
-    def test_three_with_single_res_models(self):
-        """$ pdb_reres -4 data/ensemble.OK.pdb"""
-        sys.argv = ['', '-4', os.path.join(data_dir, 'ensemble_OK.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 11)
-        self.assertEqual(len(self.stderr), 0)
-
-        records = ('ATOM', 'HETATM')
-        resid_list = [int(l[22:26]) for l in self.stdout
-                      if l.startswith(records)]
-
-        expected = [4, 4, 4, 4]
-        self.assertEqual(resid_list, expected)
-
-        models = ('MODEL',)
-        models_int = [int(l[5:]) for l in self.stdout if l.startswith(models)]
-        models_expected = [1, 2]
-        self.assertEqual(models_int, models_expected)
-
-    def test_three_with_models(self):
-        """$ pdb_reres -4 data/ensemble.OK.pdb"""
-        sys.argv = ['', '-4', os.path.join(data_dir, 'ensemble_more_OK.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 13)
-        self.assertEqual(len(self.stderr), 0)
-
-        records = ('ATOM', 'HETATM')
-        resid_list = [int(l[22:26]) for l in self.stdout
-                      if l.startswith(records)]
-
-        expected = [4, 4, 5, 5, 4, 4]
-        self.assertEqual(resid_list, expected)
-
-        models = ('MODEL',)
-        models_int = [int(l[5:]) for l in self.stdout if l.startswith(models)]
-        models_expected = [1, 2]
-        self.assertEqual(models_int, models_expected)
-
-    def test_too_many_residues(self):
-        """$ pdb_reres -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_reres -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_reres -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_reres"""
-
-        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_reres -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][:47],
-                         "ERROR!! You provided an invalid residue number:")
-
-    def test_not_an_option(self):
-        """$ pdb_reres 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_rplchain.py

@@ -1,172 +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_rplchain`.
-"""
-
-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_rplchain'
-        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_option_1(self):
-        """$ pdb_rplchain -D:Z data/dummy.pdb"""
-
-        sys.argv = ['', '-D:Z', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 204)
-        self.assertEqual(len(self.stderr), 0)
-
-        records = (('ATOM', 'HETATM'))
-        chain_ids = set([l[21] for l in self.stdout if l.startswith(records)])
-        self.assertTrue('Z' in chain_ids)
-        self.assertTrue('D' not in chain_ids)
-
-    def test_option_2(self):
-        """$ pdb_rplchain -A: data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-A:', 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'))
-        chain_ids = set([l[21] for l in self.stdout if l.startswith(records)])
-        self.assertTrue(' ' in chain_ids)
-        self.assertTrue('A' not in chain_ids)
-
-    def test_file_not_found(self):
-        """$ pdb_rplchain -A not_existing.pdb"""
-
-        afile = os.path.join(data_dir, 'not_existing.pdb')
-        sys.argv = ['', '-A', 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_rplchain -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_rplchain"""
-
-        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_1(self):
-        """$ pdb_rplchain -AH data/dummy.pdb"""
-
-        sys.argv = ['', '-AH', 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][:34],
-                         "ERROR!! Invalid option value: 'AH'")
-
-    def test_invalid_option_2(self):
-        """$ pdb_rplchain -AH: data/dummy.pdb"""
-
-        sys.argv = ['', '-AH:', 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!! Chain identifiers must be a single char")
-
-    def test_not_an_option(self):
-        """$ pdb_rplchain 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],
-                         "ERROR! First argument is not an option: '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()