pdb-tools 2.4.12__py3-none-any.whl → 2.5.1__py3-none-any.whl

tests/test_pdb_chkensemble.py

@@ -1,191 +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_chkensemble`.
-"""
-
-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_chkensemble'
-        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_valid_ensemble(self):
-        """$ pdb_chkensemble data/ensemble_OK.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_OK.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), 1)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout[0],
-                         "Ensemble of 2 models *seems* OK")
-
-    def test_ensemble_diffatom(self):
-        """$ pdb_chkensemble data/ensemble_error_1.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_error_1.pdb')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(len(self.stderr), 3)
-
-        self.assertEqual(self.stderr,
-                         ["Models 1 and 2 differ:",
-                          "Atoms in model 1 only:",
-                          "    2  H   ASN A   1 "])
-
-    def test_ensemble_nomodel(self):
-        """$ pdb_chkensemble data/ensemble_error_2.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_error_2.pdb')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(len(self.stderr), 1)
-
-        self.assertEqual(self.stderr[0],
-                         "ERROR!! MODEL record missing before ATOM at line '3'")
-
-    def test_ensemble_noendmdl(self):
-        """$ pdb_chkensemble data/ensemble_error_3.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_error_3.pdb')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(len(self.stderr), 1)
-
-        self.assertEqual(self.stderr[0],
-                         "ERROR!! ENDMDL record missing at line '10'")
-
-    def test_ensemble_noendmdl2(self):
-        """$ pdb_chkensemble data/ensemble_error_4.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_error_4.pdb')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(len(self.stderr), 1)
-
-        self.assertEqual(self.stderr[0],
-                         "ERROR!! MODEL record found before ENDMDL at line '6'")
-
-    def test_file_not_found(self):
-        """$ pdb_chkensemble 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_chkensemble"""
-
-        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_chkensemble -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()

tests/test_pdb_delchain.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_delchain`.
-"""
-
-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_delchain'
-        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_delchain -A data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_delchain dummy.pdb
-        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), 144)  # deleted chain A (60 atoms)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-    def test_multiple(self):
-        """
-        $ pdb_delchain -A,B data/dummy.pdb
-        """
-
-        sys.argv = ['', '-A,B', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 91)  # deleted chains A+B (153 atoms)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-    def test_file_not_found(self):
-        """$ pdb_delchain 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_delchain -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_delchain"""
-
-        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_delchain 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 chain ide")
-
-    def test_invalid_option_2(self):
-        """$ pdb_delchain -AB data/dummy.pdb"""
-
-        sys.argv = ['', '-AB', 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!! Chain identifier name is invalid")
-
-    def test_not_an_option(self):
-        """$ pdb_delchain 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_delelem.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_delelem`.
-"""
-
-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_delelem'
-        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_delelem -H data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_delelem dummy.pdb
-        sys.argv = ['', '-H', 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), 130)  # deleted 74 protons
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-    def test_multiple(self):
-        """
-        $ pdb_delelem -C,H data/dummy.pdb
-        """
-
-        sys.argv = ['', '-C,H', os.path.join(data_dir, 'dummy.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 89)  # deleted protons and 41 carbons
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-    def test_file_not_found(self):
-        """$ pdb_delelem 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_delelem -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_delelem"""
-
-        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_delelem 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 element n")
-
-    def test_invalid_option_2(self):
-        """$ pdb_delelem -ABD data/dummy.pdb"""
-
-        sys.argv = ['', '-ABC', 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][:32],
-                         "ERROR!! Element name is invalid:")
-
-    def test_not_an_option(self):
-        """$ pdb_delelem 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_delhetatm.py

@@ -1,115 +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_delhetatm`.
-"""
-
-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_delhetatm'
-        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_delhetatm data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_delhetatm 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), 194)  # 9 HETATM records + 2 CONECT
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-    def test_file_not_found(self):
-        """$ pdb_delhetatm 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_helptext(self):
-        """$ pdb_delhetatm"""
-
-        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_delhetatm -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!! 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()