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

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()

tests/test_pdb_fixinsert.py

@@ -1,223 +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_fixinsert`.
-"""
-
-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_fixinsert'
-        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_fixinsert data/dummy_insertions.pdb"""
-
-        # Simulate input
-        # pdb_fixinsert dummy_insertions.pdb
-        sys.argv = ['', os.path.join(data_dir, 'dummy_insertions.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 255)  # no lines deleted
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        # Check if we do not have any insertions
-        records = (('ATOM', 'HETATM', 'TER'))
-        icodes = set(l[26] for l in self.stdout if l.startswith(records))
-        self.assertEqual(icodes, set(' '))
-
-        # Check numbering was corrected
-        resid = [int(l[22:26]) for l in self.stdout if l.startswith(records)]
-        expected = [
-            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, 5, 5, 5, 5, 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7,
-            7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9,
-            9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2,
-            2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 5, 5, 5,
-            5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
-            2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, -1, -1, -1, -1, -1, -1,
-            -1, -1, -1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-            2, 301, 302, 303, 301, 301, 302, 303, 304, 305
-        ]
-        self.assertEqual(resid, expected)
-
-    def test_select_insertion(self):
-        """$ pdb_fixinsert -A1 data/dummy_insertions.pdb"""
-
-        sys.argv = ['', '-A1', os.path.join(data_dir, 'dummy_insertions.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 255)
-        self.assertEqual(len(self.stderr), 0)
-
-        records = (('ATOM', 'HETATM', 'TER'))
-
-        # Check the insertions were deleted specifically
-        for line in self.stdout:
-            if line.startswith(records):
-                icode = line[26]
-                resid = int(line[22:26])
-                if line[17:26] == 'ARG B   4':
-                    self.assertIn(icode, ('A', 'B'))
-                    self.assertEqual(resid, 4)
-                elif line[17:26] == 'GLY B   4':
-                    self.assertEqual(icode, ' ')
-                    self.assertEqual(resid, 4)
-                elif line[17:26] == 'ASN A   1':
-                    self.assertEqual(icode, ' ')
-                    self.assertEqual(resid, 1)
-                elif line[17:26] == 'GLY A   1':
-                    self.assertEqual(icode, ' ')
-                    self.assertEqual(resid, 2)  # should have renumbered
-
-        # Check numbering was corrected overall
-        resid = [int(l[22:26]) for l in self.stdout if l.startswith(records)]
-        expected = [
-            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, 5, 5, 5, 5, 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7,
-            7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9,
-            9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2,
-            2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 5, 5, 5,
-            5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
-            2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, -1, -1, -1, -1, -1, -1,
-            -1, -1, -1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
-            2, 301, 302, 303, 301, 301, 302, 303, 304, 305
-        ]
-
-        self.assertEqual(resid, expected)
-
-    def test_file_not_found(self):
-        """$ pdb_fixinsert 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_fixinsert -A89"""
-
-        sys.argv = ['', '-A89']
-
-        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_fixinsert"""
-
-        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_fixinsert -A data/dummy_insertions.pdb"""
-
-        sys.argv = ['', '-A', os.path.join(data_dir, 'dummy_insertions.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:27],
-                         "ERROR!! Option invalid: 'A'")
-
-    def test_invalid_option_2(self):
-        """$ pdb_fixinsert -12A data/dummy_insertions.pdb"""
-
-        sys.argv = ['', '-12A', os.path.join(data_dir, 'dummy_insertions.pdb')]
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)
-        self.assertEqual(self.stderr[0][:39],
-                         "ERROR!! Option invalid: '12A'")
-
-    def test_not_an_option(self):
-        """$ pdb_fixinsert 20 data/dummy_insertions.pdb"""
-
-        sys.argv = ['', '20', os.path.join(data_dir, 'dummy_insertions.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_fromcif.py

@@ -1,124 +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_fromcif`.
-"""
-
-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_fromcif'
-        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_conversion(self):
-        """$ pdb_fromcif data/ensemble_OK.pdb"""
-
-        fpath = os.path.join(data_dir, 'ensemble_OK.cif')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 9)
-        self.assertEqual(len(self.stderr), 0)
-
-        # Check order of records
-        expected = ['MODEL ', 'ATOM  ', 'ATOM  ', 'ENDMDL',
-                    'MODEL ', 'ATOM  ', 'ATOM  ', 'ENDMDL', 'END   ']
-        records = [l[:6] for l in self.stdout]
-        self.assertEqual(records, expected)
-
-    def test_file_not_found(self):
-        """$ pdb_fromcif 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_fromcif"""
-
-        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_fromcif -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_gap.py

@@ -1,125 +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_gap`.
-"""
-
-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_gap'
-        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_gap 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), 5)  # no lines deleted
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout,
-                         ["B:ARG4 < Seq. Gap > B:GLU6",
-                          "A:ASN1 <    9.42A > A:ASN1",
-                          "C:ARG5 < Seq. Gap > C:GLU2",
-                          "C:GLU2 <   95.75A > C:MET-1",
-                          "Found 4 gap(s) in the structure"])
-
-    def test_file_not_found(self):
-        """$ pdb_gap 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_gap"""
-
-        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_gap -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()