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

tests/test_pdb_rplresname.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_rplresname`.
-"""
-
-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_rplresname'
-        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_rplresname -MET:DRG data/dummy.pdb"""
-
-        sys.argv = ['', '-MET:DRG', 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', 'TER'))
-        res_list = set([l[17:20] for l in self.stdout if l.startswith(records)])
-        self.assertTrue('DRG' in res_list)
-        self.assertTrue('MET' not in res_list)
-
-    def test_option_2(self):
-        """$ pdb_rplresname -DT:DA data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-DT:DA', 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', 'TER'))
-        res_list = set([l[17:20] for l in self.stdout if l.startswith(records)])
-        self.assertTrue(' DA' in res_list)
-        self.assertTrue(' DT' not in res_list)
-
-    def test_file_not_found(self):
-        """$ pdb_rplresname -DA:DT not_existing.pdb"""
-
-        afile = os.path.join(data_dir, 'not_existing.pdb')
-        sys.argv = ['', '-DA:DT', 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_rplresname -DA"""
-
-        sys.argv = ['', '-DA']
-
-        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_rplresname"""
-
-        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_rplresname -HIS data/dummy.pdb"""
-
-        sys.argv = ['', '-HIS', 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: 'HIS")
-
-    def test_invalid_option_2(self):
-        """$ pdb_rplresname -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!! Residue names must have one to three ch")
-
-    def test_not_an_option(self):
-        """$ pdb_rplresname 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()

tests/test_pdb_seg.py

@@ -1,160 +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_seg`.
-"""
-
-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_seg'
-        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_seg data/dummy.pdb"""
-
-        # Simulate input
-        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'))
-        seg_ids = [l[72:76] for l in self.stdout if l.startswith(records)]
-        unique_seg_ids = list(set(seg_ids))
-        self.assertEqual(unique_seg_ids, ['    '])
-
-    def test_two_options(self):
-        """$ pdb_seg -X data/dummy.pdb"""
-
-        sys.argv = ['', '-X', 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'))
-        seg_ids = [l[72:76] for l in self.stdout if l.startswith(records)]
-        unique_seg_ids = list(set(seg_ids))
-        self.assertEqual(unique_seg_ids, ['X   '])
-
-    def test_file_not_found(self):
-        """$ pdb_seg -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_seg -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_seg"""
-
-        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_seg -AHASX data/dummy.pdb"""
-
-        sys.argv = ['', '-AHASX', 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!! Segment id must be max. four characters")
-
-    def test_not_an_option(self):
-        """$ pdb_seg 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()

tests/test_pdb_segxchain.py

@@ -1,146 +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_segxchain`.
-"""
-
-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_segxchain'
-        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_segxchain data/dummy.pdb"""
-
-        # Simulate input
-        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'))
-        chain_ids = [l[21] for l in self.stdout if l.startswith(records)]
-
-        # Test content
-        unique_chain_ids = sorted(set(chain_ids))
-        self.assertEqual(unique_chain_ids, [' ', 'A', 'Z'])
-
-        # Test order
-        chain_list = [' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',
-                      ' ', 'A', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z',
-                      'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z',
-                      ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ']
-
-        self.assertEqual(chain_ids, chain_list)
-
-    def test_file_not_found(self):
-        """$ pdb_segxchain 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)  # 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_helptext(self):
-        """$ pdb_segxchain"""
-
-        sys.argv = ['']
-
-        # Execute the script
-        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_segxchain -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!! Script takes 1 argument, not")
-
-
-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()