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

tests/test_pdb_delres.py

@@ -1,241 +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_delres`.
-"""
-
-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_delres'
-        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_range_1(self):
-        """$ pdb_delres -1:5 data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-1:5', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 60)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_range_2(self):
-        """$ pdb_delres -1: data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-1:', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 25)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_range_3(self):
-        """$ pdb_delres -:-1 data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-:-1', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 195)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_range_4(self):
-        """$ pdb_delres -::5 data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-::5', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 160)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_invalid_range_1(self):
-        """$ pdb_delres --9998:: data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '--9998::', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! Starting value")
-
-    def test_invalid_range_2(self):
-        """$ pdb_delres -:10000: data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-:10000:', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! End value must")
-
-    def test_invalid_range_3(self):
-        """$ pdb_delres -::: 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, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:21],
-                         "ERROR!! Residue range")
-
-    def test_invalid_range_4(self):
-        """$ pdb_delres -5:1:: data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-5:1::', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:21],
-                         "ERROR!! Residue range")
-
-    def test_file_not_found(self):
-        """$ pdb_delres 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_delres -1:10"""
-
-        sys.argv = ['', '-1:10']
-
-        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_delres"""
-
-        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_delres -A:B data/dummy.pdb"""
-
-        sys.argv = ['', '-A:B', 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][:39],
-                         "ERROR!! Starting value must be numerica")
-
-    def test_not_an_option(self):
-        """$ pdb_delres 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_delresname.py

@@ -1,171 +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_delresname`.
-"""
-
-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_delresname'
-        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_single_sele(self):
-        """$ pdb_delresname -ARG data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-ARG', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 128)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_multiple_sele(self):
-        """$ pdb_delresname -ARG,CA data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-ARG,CA', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 127)
-        self.assertEqual(len(self.stderr), 0)
-
-    def test_empty_sele(self):
-        """$ pdb_delresname - 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, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! Residue name s")
-
-    def test_invalid_sele(self):
-        """$ pdb_delresname -ABCD data/dummy.pdb"""
-
-        # Simulate input
-        sys.argv = ['', '-ABCD', os.path.join(data_dir, 'dummy.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! Residue name i")
-
-    def test_file_not_found(self):
-        """$ pdb_delresname 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_delresname -ARG"""
-
-        sys.argv = ['', '-ARG']
-
-        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_delresname"""
-
-        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_not_an_option(self):
-        """$ pdb_delresname 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_element.py

@@ -1,151 +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_element`.
-"""
-
-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_element'
-        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_element 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
-
-        element_cols = [l[76:78] for l in self.stdout]
-
-        # Test content
-        assigned = [l for l in element_cols if l.strip()]
-        self.assertEqual(len(assigned), 185)  # ignore TER/END & headers
-
-        # Test order
-        element_list = ['  ', '  ', '  ', '  ', '  ', '  ', '', '', '', '', '',
-                        '', '', ' N', ' H', ' H', ' H', ' C', ' H', ' C', ' H',
-                        ' H', ' C', ' H', ' H', ' C', ' H', ' H', ' N', ' H',
-                        ' C', ' N', ' H', ' H', ' N', ' H', ' H', ' C', ' O',
-                        ' N', ' H', ' C', ' H', ' C', ' H', ' H', ' C', ' H',
-                        ' H', ' C', ' O', ' O', ' C', ' O', ' N', ' H', ' C',
-                        ' H', ' C', ' H', ' H', ' H', ' C', ' O', '', ' N',
-                        ' H', ' H', ' H', ' C', ' C', ' H', ' C', ' H', ' H',
-                        ' C', ' O', ' N', ' H', ' H', ' C', ' O', ' N', ' H',
-                        ' C', ' H', ' C', ' H', ' H', ' C', ' H', ' H', ' C',
-                        ' H', ' H', ' N', ' H', ' C', ' N', ' H', ' H', ' N',
-                        ' H', ' H', ' C', ' O', ' N', ' H', ' C', ' H', ' C',
-                        ' H', ' H', ' C', ' H', ' H', ' C', ' O', ' O', ' C',
-                        ' O', '  ', ' N', ' H', ' H', ' H', ' C', ' H', ' C',
-                        ' H', ' H', ' C', ' H', ' H', ' C', ' H', ' H', ' N',
-                        ' H', ' C', ' N', ' H', ' H', ' N', ' H', ' H', ' C',
-                        ' O', ' N', ' H', ' C', ' H', ' C', ' H', ' H', ' C',
-                        ' H', ' H', ' C', ' O', ' O', ' C', ' O', ' N', ' C',
-                        ' C', ' O', ' C', ' C', ' S', ' C', '  ', ' P', ' O',
-                        ' O', ' O', ' C', ' C', ' O', ' C', ' O', ' C', ' C',
-                        ' N', ' C', ' O', ' N', ' C', ' O', ' C', ' C', ' C',
-                        'CA', ' O', ' O', ' O', ' O', ' O', ' O', ' O', ' O',
-                        '  ', '', '']
-
-        self.assertEqual(element_cols, element_list)
-
-    def test_file_not_found(self):
-        """$ pdb_element 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_element"""
-
-        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_element -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()