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

tests/test_pdb_chain.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_chain`.
-"""
-
-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_chain'
-        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_chain 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)]
-        unique_chain_ids = list(set(chain_ids))
-        self.assertEqual(unique_chain_ids, [' '])
-
-    def test_two_options(self):
-        """$ pdb_chain -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'))
-        chain_ids = [l[21] for l in self.stdout if l.startswith(records)]
-        unique_chain_ids = list(set(chain_ids))
-        self.assertEqual(unique_chain_ids, ['X'])
-
-    def test_file_not_found(self):
-        """$ pdb_chain -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_chain -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_chain"""
-
-        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_chain -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_chain 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_chainbows.py

@@ -1,140 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Copyright 2020 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_chainbows`.
-"""
-
-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_chainbows'
-        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_chainbows 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.
-        # CONECTs are ignored by issue #72, expected only 204 lines
-        self.assertEqual(len(self.stdout), 204)
-        self.assertEqual(len(self.stderr), 0)  # no warnings/errors
-
-        # Check chains were reassigned properly
-        expected = ['A'] * 51 + ['B'] * 56 + ['C'] * 49 + ['D'] * 20
-        chains = [
-            l[21] for l in self.stdout if l.startswith('ATOM')
-        ]
-        self.assertEqual(chains, expected)
-
-        # Check TERs
-        expected = ['A', 'B', 'C']
-        chains = [
-            l[21] for l in self.stdout if l.startswith('TER')
-        ]
-        self.assertEqual(chains, expected)
-
-        # Check HETATM were reassigned properly
-        expected = ['B', 'B', 'B', 'A', 'C', 'C', 'C', 'C', 'C']
-        chains = [
-            l[21] for l in self.stdout if l.startswith('HETATM')
-        ]
-        self.assertEqual(chains, expected)
-
-    def test_file_not_found(self):
-        """$ pdb_chainbows 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_chainbows"""
-
-        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_chainbows -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_chainxseg.py

@@ -1,156 +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_chainxseg`.
-"""
-
-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_chainxseg'
-        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_chainxseg 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[72:76] for l in self.stdout if l.startswith(records)]
-
-        # Test content
-        unique_chain_ids = sorted(set(map(str.strip, chain_ids)))
-        self.assertEqual(unique_chain_ids, ['A', 'B', 'C', 'D'])
-
-        # Test order
-        segid_list = ['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   ', '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   ', '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, segid_list)
-
-    def test_file_not_found(self):
-        """$ pdb_chainxseg 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_chainxseg"""
-
-        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_chainxseg -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_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()