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

tests/test_pdb_tocif.py

@@ -1,238 +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_tocif`.
-"""
-
-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_tocif'
-        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_model_run_iterable(self):
-        """$ pdb_tocif.run(iterable)"""
-        from pdbtools import pdb_tocif
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        with open(fpath, 'r') as fin:
-            lines = fin.readlines()
-
-        newlines = list(pdb_tocif.run(lines))
-
-        # Check no of records
-        n_ATOM = sum(1 for l in newlines if l.startswith('ATOM'))
-        n_HETATM = sum(1 for l in newlines if l.startswith('HETATM'))
-        n_coord = n_ATOM + n_HETATM
-        self.assertEqual(n_ATOM, 176)
-        self.assertEqual(n_HETATM, 9)
-        self.assertEqual(n_coord, 185)
-
-        # check name
-        self.assertEqual(newlines[2], 'data_cell\n')
-
-    def test_single_model_run_iterable_with_name(self):
-        """$ pdb_tocif.run(iterable)"""
-        from pdbtools import pdb_tocif
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        with open(fpath, 'r') as fin:
-            lines = fin.readlines()
-
-        newlines = list(pdb_tocif.run(lines, outname='newcif'))
-
-        # Check no of records
-        n_ATOM = sum(1 for l in newlines if l.startswith('ATOM'))
-        n_HETATM = sum(1 for l in newlines if l.startswith('HETATM'))
-        n_coord = n_ATOM + n_HETATM
-        self.assertEqual(n_ATOM, 176)
-        self.assertEqual(n_HETATM, 9)
-        self.assertEqual(n_coord, 185)
-
-        # check name
-        self.assertEqual(newlines[2], 'data_newcif\n')
-
-    def test_single_model_run_fhandler(self):
-        """$ pdb_tocif.run(fhandler)"""
-        from pdbtools import pdb_tocif
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        with open(fpath, 'r') as fin:
-            newlines = list(pdb_tocif.run(fin))
-
-        # Check no of records
-        n_ATOM = sum(1 for l in newlines if l.startswith('ATOM'))
-        n_HETATM = sum(1 for l in newlines if l.startswith('HETATM'))
-        n_coord = n_ATOM + n_HETATM
-        self.assertEqual(n_ATOM, 176)
-        self.assertEqual(n_HETATM, 9)
-        self.assertEqual(n_coord, 185)
-
-        # check name
-        self.assertEqual(newlines[2], 'data_dummy\n')
-
-    def test_single_model_run_fhandler_name(self):
-        """$ pdb_tocif.run(fhandler)"""
-        from pdbtools import pdb_tocif
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        with open(fpath, 'r') as fin:
-            newlines = list(pdb_tocif.run(fin, outname='newname'))
-
-        # Check no of records
-        n_ATOM = sum(1 for l in newlines if l.startswith('ATOM'))
-        n_HETATM = sum(1 for l in newlines if l.startswith('HETATM'))
-        n_coord = n_ATOM + n_HETATM
-        self.assertEqual(n_ATOM, 176)
-        self.assertEqual(n_HETATM, 9)
-        self.assertEqual(n_coord, 185)
-
-        # check name
-        self.assertEqual(newlines[2], 'data_newname\n')
-
-    def test_single_model(self):
-        """$ pdb_tocif 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)
-        self.assertEqual(len(self.stdout), 212)
-        self.assertEqual(len(self.stderr), 0)
-
-        # Check no of records
-        n_ATOM = len([l for l in self.stdout if l.startswith('ATOM')])
-        n_HETATM = len([l for l in self.stdout if l.startswith('HETATM')])
-        n_coord = n_ATOM + n_HETATM
-        self.assertEqual(n_ATOM, 176)
-        self.assertEqual(n_HETATM, 9)
-        self.assertEqual(n_coord, 185)
-
-    def test_multi_model(self):
-        """$ pdb_tocif 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)
-        self.assertEqual(len(self.stdout), 31)
-        self.assertEqual(len(self.stderr), 0)
-
-        # Check no of records
-        n_ATOM = len([l for l in self.stdout if l.startswith('ATOM')])
-        n_HETATM = len([l for l in self.stdout if l.startswith('HETATM')])
-        n_coord = n_ATOM + n_HETATM
-        self.assertEqual(n_ATOM, 4)
-        self.assertEqual(n_HETATM, 0)
-        self.assertEqual(n_coord, 4)
-
-        # Check model numbers
-        records = (('ATOM', 'HETATM'))
-        models = [l.split()[-1] for l in self.stdout if l.startswith(records)]
-        self.assertEqual(models, ['1', '1', '2', '2'])
-
-        # Check number of fields
-        atom_lines = [l for l in self.stdout if l.startswith(records)]
-        n_fields = list(set(map(lambda x: len(x.split()), atom_lines)))
-        self.assertEqual(n_fields, [21])
-
-    def test_file_not_found(self):
-        """$ pdb_tocif 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_tocif"""
-
-        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_tocif -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_tofasta.py

@@ -1,158 +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_tofasta`.
-"""
-
-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_tofasta'
-        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_tofasta 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.
-        self.assertEqual(len(self.stdout), 2)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout, ['>1DUM|ABCD', 'REANREREMXXXXXXXXXX'])
-
-    def test_headerless(self):
-        """$ pdb_tofasta data/dummy_nohead.pdb"""
-
-        fpath = os.path.join(data_dir, 'dummy_nohead.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), 2)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout, ['>PDB|ABCD', 'REANREREMXXXXXXXXXX'])
-
-    def test_multi(self):
-        """$ pdb_tofasta -multi data/dummy.pdb"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', '-multi', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 14)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        self.assertEqual(self.stdout, ['>1DUM|B', 'REA',
-                                       '>1DUM|A', 'NRE',
-                                       '>1DUM|C', 'REM',
-                                       '>1DUM|D', 'X',
-                                       '>1DUM|A', 'XXX',
-                                       '>1DUM|B', 'X',
-                                       '>1DUM|C', 'XXXXX'])
-
-    def test_file_not_found(self):
-        """$ pdb_tofasta 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_tofasta"""
-
-        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_tofasta -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!! You provided an invalid opti")
-
-
-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_uniqname.py

@@ -1,156 +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_uniqname`.
-"""
-
-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_uniqname'
-        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_uniqname data/hetatm.pdb"""
-
-        # Simulate input
-        sys.argv = ['', os.path.join(data_dir, 'hetatm.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 19)  # no lines deleted
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        records = ('ATOM', 'HETATM')
-        atnames = [l[12:16] for l in self.stdout if l.startswith(records)]
-
-        self.assertEqual(
-            atnames,
-            [
-                ' C1 ', ' C2 ', ' H1 ', ' C3 ',
-                'CA1 ', 'CA2 ', ' H1 ', ' H2 ',
-                ' C1 ', ' C2 ', ' H  ', ' H  '
-            ]
-        )
-
-    def test_error(self):
-        """$ pdb_uniqname data/hetatm_bad.pdb"""
-
-        # Simulate input
-        sys.argv = ['', os.path.join(data_dir, 'hetatm_bad.pdb')]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 1)  # ensure the program threw an error
-        self.assertEqual(len(self.stdout), 0)  # no output
-
-        self.assertEqual(self.stderr[0][:22],
-                         "ERROR!! No element fou")  # proper error message
-
-    def test_file_not_found(self):
-        """$ pdb_uniqname 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_uniqname"""
-
-        sys.argv = ['']
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(self.stderr[1],
-                         self.module.__doc__.split("\n")[1])
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_helptext(self):
-        """$ pdb_uniqname"""
-
-        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[1],
-                         self.module.__doc__.split("\n")[1])
-
-    def test_invalid_option(self):
-        """$ pdb_uniqname -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[1],
-                         self.module.__doc__.split("\n")[1])
-
-
-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_validate.py

@@ -1,142 +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_validate`.
-"""
-
-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_validate'
-        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_warnings(self):
-        """$ pdb_validate 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, 1)
-        self.assertEqual(len(self.stdout), 253)
-        self.assertEqual(len(self.stderr), 0)
-
-        # Count no. of line length warnings
-        n_warn = len([l for l in self.stdout if 'is short' in l])
-        self.assertEqual(n_warn, 70)
-
-        self.assertEqual(self.stdout[-4],
-                         "[!] Line 203 is short: 26 < 80")
-
-    def test_valid(self):
-        """$ pdb_validate 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.stderr), 0)
-        self.assertEqual(len(self.stdout), 1)  # no errors
-
-        self.assertEqual(self.stdout,
-                         ["It *seems* everything is OK."])
-
-    def test_file_not_found(self):
-        """$ pdb_validate 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_validate"""
-
-        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_validate -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()