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

tests/test_pdb_splitseg.py

@@ -1,251 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Copyright 1118 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_splitseg`.
-"""
-
-import os
-import shutil
-import sys
-import tempfile
-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_splitseg'
-        self.module = __import__(name, fromlist=[''])
-        self.tempdir = tempfile.mkdtemp()  # set temp dir
-        os.chdir(self.tempdir)
-
-    def tearDown(self):
-        os.chdir(os.path.dirname(os.path.abspath('.')))  # cd ../
-        shutil.rmtree(self.tempdir)
-
-    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_run_fhandler(self):
-        """pdb_splitseg.run(iterable)"""
-        from pdbtools import pdb_splitseg
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'dummy.pdb')
-        dst = os.path.join(self.tempdir, 'dummy.pdb')
-        shutil.copy(src, dst)
-
-        with open(dst, 'r') as fin:
-            pdb_splitseg.run(fin)
-
-        # Read files created by script and then delete
-        ofiles = [f for f in os.listdir(self.tempdir) if f.startswith('dummy')]
-        self.assertEqual(len(ofiles), 2 + 1)  # ori + 2 segments
-
-        # Make sure each file has the chain it should have
-        records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
-        for fpath in ofiles:
-            if fpath == 'dummy.pdb':
-                continue
-
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                fname_seg = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_segids = [l[72:76].strip() for l in handle
-                              if l.startswith(records)]
-
-                self.assertEqual(fname_seg, list(set(pdb_segids))[0])
-
-    def test_run_iterable_with_name(self):
-        """pdb_splitseg.run(iterable, outname='newname')"""
-        from pdbtools import pdb_splitseg
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'dummy.pdb')
-        dst = os.path.join(self.tempdir, 'dummy.pdb')
-        shutil.copy(src, dst)
-
-        with open(dst, 'r') as fin:
-            lines = fin.readlines()
-
-        pdb_splitseg.run(lines, outname='newname')
-
-        # Read files created by script and then delete
-        ofiles = [f for f in os.listdir(self.tempdir) if f.startswith('newname')]
-        self.assertEqual(len(ofiles), 2)
-
-        # Make sure each file has the chain it should have
-        records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
-        for fpath in ofiles:
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                fname_seg = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_segids = [l[72:76].strip() for l in handle
-                              if l.startswith(records)]
-
-                self.assertEqual(fname_seg, list(set(pdb_segids))[0])
-
-    def test_run_iterable(self):
-        """pdb_splitseg.run(fhandler)"""
-        from pdbtools import pdb_splitseg
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'dummy.pdb')
-        dst = os.path.join(self.tempdir, 'dummy.pdb')
-        shutil.copy(src, dst)
-
-        with open(dst, 'r') as fin:
-            lines = fin.readlines()
-
-        pdb_splitseg.run(lines)
-
-        # Read files created by script and then delete
-        ofiles = [
-            f
-            for f in os.listdir(self.tempdir)
-            if f.startswith('splitsegs')]
-        self.assertEqual(len(ofiles), 2)
-
-        # Make sure each file has the chain it should have
-        records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
-        for fpath in ofiles:
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                fname_seg = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_segids = [l[72:76].strip() for l in handle
-                              if l.startswith(records)]
-
-                self.assertEqual(fname_seg, list(set(pdb_segids))[0])
-
-    def test_default(self):
-        """$ pdb_splitseg data/dummy.pdb"""
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'dummy.pdb')
-        dst = os.path.join(self.tempdir, 'dummy.pdb')
-        shutil.copy(src, dst)
-        sys.argv = ['', dst]
-
-        # Execute the script
-        self.exec_module()
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        # Read files created by script and then delete
-        ofiles = [f for f in os.listdir(self.tempdir) if f.startswith('dummy')]
-        self.assertEqual(len(ofiles), 2 + 1)  # ori + 2 segments
-
-        # Make sure each file has the chain it should have
-        records = (('ATOM', 'HETATM', 'TER', 'ANISOU'))
-        for fpath in ofiles:
-            if fpath == 'dummy.pdb':
-                continue
-
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                fname_seg = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_segids = [l[72:76].strip() for l in handle
-                              if l.startswith(records)]
-
-                self.assertEqual(fname_seg, list(set(pdb_segids))[0])
-
-    def test_file_not_found(self):
-        """$ pdb_splitseg 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_splitseg -10"""
-
-        sys.argv = ['', '-10']
-
-        self.exec_module()
-
-        self.assertEqual(self.retcode, 1)
-        self.assertEqual(len(self.stdout), 0)  # no output
-        self.assertEqual(self.stderr[0][:38],
-                         "ERROR!! File not found or not readable")
-
-    @unittest.skipIf(os.getenv('SKIP_TTY_TESTS'), 'skip on GHA - no TTY')
-    def test_helptext(self):
-        """$ pdb_splitseg"""
-
-        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_splitseg -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][:22],
-                         "ERROR!! Script takes 1")  # proper error message
-
-
-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_tidy.py

@@ -1,312 +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_tidy`.
-"""
-
-try:
-    from StringIO import StringIO  # python 2.7
-except ImportError:
-    from io import StringIO  # python 3.x
-
-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_tidy'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self, stdin=None):
-        """
-        Execs module.
-        """
-
-        if stdin is not None:
-            sys.stdin = StringIO(stdin)
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        sys.stdin = sys.__stdin__  # restore
-
-        return
-
-    def test_default(self):
-        """$ pdb_tidy 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 205 lines
-        self.assertEqual(len(self.stdout), 205)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        # Check if we added TER statements correctly
-        n_ter = len([r for r in self.stdout if r.startswith('TER')])
-        self.assertEqual(n_ter, 5)
-
-        # Check no CONECT in output
-        c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
-        self.assertEqual(c_conect, 0)
-
-        # Check if we added END statements correctly
-        self.assertTrue(self.stdout[-1].startswith('END'))
-
-    def test_default_in_lib(self):
-        """
-        Test command-line versus lib.
-
-        $ pdb_tidy data/dummy.pdb
-
-        >>> original_lines = open('dummy.pdb').readlines()
-        >>> lines = list(pdb_tidy.run(original_lines))
-
-        `lines` and the result from the command-line must be the same.
-        """
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', fpath]
-
-        # Execute the script
-        self.exec_module()
-
-        fin = open(os.path.join(data_dir, 'dummy.pdb'))
-        original_lines = fin.readlines()
-        fin.close()
-        lines = list(self.module.run(original_lines))
-
-        self.assertEqual(len(lines), 205)
-        # Check if we added TER statements correctly
-        n_ter = len([r for r in lines if r.startswith('TER')])
-        self.assertEqual(n_ter, 5)
-
-        # Check no CONECT in output
-        c_conect = sum(1 for i in lines if i.startswith('CONECT'))
-        self.assertEqual(c_conect, 0)
-
-        # Check if we added END statements correctly
-        self.assertTrue(lines[-1].startswith('END'))
-
-        self.assertTrue(lines, self.stdout)
-
-    def test_tidy_removes_master(self):
-        """Test pdb_tidy removes MASTER lines as well."""
-        sys.argv = ['']
-        self.exec_module(
-            'MASTER      378    0    9    5    3    '
-            '0   29    6  847    1   76    7'
-            )
-
-        # Check no MASTER in output
-        m_master = sum(1 for i in self.stdout if i.startswith('MASTER'))
-        self.assertEqual(m_master, 0)
-
-    def test_default_stdin(self):
-        """$ cat data/dummy.pdb | pdb_tidy"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['']
-
-        # Execute the script with file as stdin
-        with open(fpath) as fp:
-            self.exec_module(fp.read())
-
-        # Validate results
-        self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        # CONECTs are ignored by issue #72, expected only 205 lines
-        self.assertEqual(len(self.stdout), 205)
-        self.assertEqual(len(self.stderr), 0)  # no errors
-
-        # Check if we added TER statements correctly
-        n_ter = len([r for r in self.stdout if r.startswith('TER')])
-        self.assertEqual(n_ter, 5)
-
-        # Check no CONECT in output
-        c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
-        self.assertEqual(c_conect, 0)
-
-        # Check if we added END statements correctly
-        self.assertTrue(self.stdout[-1].startswith('END'))
-
-    def test_default_strict(self):
-        """$ pdb_tidy -strict data/dummy.pdb"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', '-strict', 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 errors
-
-        # Check if we added TER statements correctly
-        n_ter = len([r for r in self.stdout if r.startswith('TER')])
-        self.assertEqual(n_ter, 4)
-
-        # Check no CONECT in output
-        c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
-        self.assertEqual(c_conect, 0)
-
-        # Check if we added END statements correctly
-        self.assertTrue(self.stdout[-1].startswith('END'))
-
-    def test_default_strict_stdin(self):
-        """$ cat data/dummy.pdb | pdb_tidy -strict"""
-
-        fpath = os.path.join(data_dir, 'dummy.pdb')
-        sys.argv = ['', '-strict']
-
-        # Execute the script
-        with open(fpath) as fp:
-            self.exec_module(fp.read())
-
-        # 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 errors
-
-        # Check if we added TER statements correctly
-        n_ter = len([r for r in self.stdout if r.startswith('TER')])
-        self.assertEqual(n_ter, 4)
-
-        # Check no CONECT in output
-        c_conect = sum(1 for i in self.stdout if i.startswith('CONECT'))
-        self.assertEqual(c_conect, 0)
-
-        # Check if we added END statements correctly
-        self.assertTrue(self.stdout[-1].startswith('END'))
-
-    def test_corrects_model_format_and_numbers(self):
-        """Correct MODEL lines."""
-        fpath = os.path.join(data_dir, 'ensemble_error_MODEL.pdb')
-        sys.argv = ['', fpath]
-        self.exec_module()
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 16)
-        self.assertEqual(len(self.stderr), 0)
-        self.assertEqual(len(self.stdout[5].strip()), 14)
-        self.assertEqual(len(self.stdout[5]), 80)
-        self.assertEqual(len(self.stdout[10].strip()), 14)
-        self.assertEqual(len(self.stdout[10]), 80)
-        self.assertEqual(self.stdout[5].strip(), "MODEL        1")
-        self.assertEqual(self.stdout[10].strip(), "MODEL        2")
-
-    def test_corrects_model_ENDMDL(self):
-        """Correct MODEL lines."""
-        fpath = os.path.join(data_dir, 'ensemble_error_4.pdb')
-        sys.argv = ['', fpath]
-        self.exec_module()
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 14)
-        self.assertEqual(len(self.stderr), 0)
-
-        # MODEL lines
-        self.assertEqual(len(self.stdout[3].strip()), 14)
-        self.assertEqual(len(self.stdout[3]), 80)
-        self.assertEqual(len(self.stdout[3].strip()), 14)
-        self.assertEqual(len(self.stdout[8]), 80)
-        self.assertEqual(self.stdout[3].strip(), "MODEL        1")
-        self.assertEqual(self.stdout[8].strip(), "MODEL        2")
-
-        # ENDMDL LINES
-        self.assertEqual(len(self.stdout[7]), 80)
-        self.assertEqual(len(self.stdout[12]), 80)
-        self.assertEqual(self.stdout[7].strip(), "ENDMDL")
-        self.assertEqual(self.stdout[12].strip(), "ENDMDL")
-
-        # END LINES
-        self.assertEqual(self.stdout[-1].strip(), "END")
-        self.assertEqual(len(self.stdout[-1]), 80)
-
-
-    def test_file_not_found(self):
-        """$ pdb_tidy 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_tidy"""
-
-        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_tidy -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! First argument is not a valid")
-
-
-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()