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

tests/test_pdb_splitchain.py

@@ -1,242 +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_splitchain`.
-"""
-
-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_splitchain'
-        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_default(self):
-        """$ pdb_splitchain 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), 4 + 1)  # ori + 4 chains
-
-        # 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_chain = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_chains = [l[21] for l in handle if l.startswith(records)]
-
-                self.assertEqual(fname_chain, list(set(pdb_chains))[0])
-
-    def test_run_fhandler(self):
-        """pdb_splitchain.run(fhandler)"""
-        from pdbtools import pdb_splitchain
-
-        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_splitchain.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), 4 + 1)  # ori + 4 chains
-
-        # 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_chain = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_chains = [l[21] for l in handle if l.startswith(records)]
-
-                self.assertEqual(fname_chain, list(set(pdb_chains))[0])
-
-    def test_run_iterable(self):
-        """pdb_splitchain.run(iterable)"""
-        from pdbtools import pdb_splitchain
-
-        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_splitchain.run(lines)
-
-        # Read files created by script and then delete
-        ofiles = [
-            f
-            for f in os.listdir(self.tempdir)
-            if f.startswith('splitchains')
-            ]
-        self.assertEqual(len(ofiles), 4)  # 4 chains
-
-        # 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_chain = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_chains = [l[21] for l in handle if l.startswith(records)]
-
-                self.assertEqual(fname_chain, list(set(pdb_chains))[0])
-
-    def test_run_iterable_with_name(self):
-        """pdb_splitchain.run(iterable)"""
-        from pdbtools import pdb_splitchain
-
-        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_splitchain.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), 4)  # 4 chains
-
-        # 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_chain = fpath.split('_')[1][:-4]  # xxx_(X).pdb
-                pdb_chains = [l[21] for l in handle if l.startswith(records)]
-
-                self.assertEqual(fname_chain, list(set(pdb_chains))[0])
-
-    def test_file_not_found(self):
-        """$ pdb_splitchain 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_splitchain -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_splitchain"""
-
-        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_splitchain -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_splitmodel.py

@@ -1,235 +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_splitmodel`.
-"""
-
-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_splitmodel'
-        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_default(self):
-        """$ pdb_splitmodel data/ensemble_OK.pdb"""
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'ensemble_OK.pdb')
-        dst = os.path.join(self.tempdir, 'ensemble_OK.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
-        ofiles = [f for f in os.listdir(self.tempdir)
-                  if f.startswith('ensemble_OK')]
-        self.assertEqual(len(ofiles), 2 + 1)  # ori + 2 models
-
-        for fpath in ofiles:
-            if fpath == 'ensemble_OK.pdb':
-                continue
-
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                n_lines = len(handle.readlines())
-                self.assertEqual(n_lines, 2)
-
-    def test_run_iterable(self):
-        """pdb_splitmodel.run(iterable)"""
-        from pdbtools import pdb_splitmodel
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'ensemble_OK.pdb')
-        dst = os.path.join(self.tempdir, 'ensemble_OK.pdb')
-        shutil.copy(src, dst)
-
-        with open(dst, 'r') as fin:
-            lines = fin.readlines()
-
-        pdb_splitmodel.run(lines)
-
-        # Read files created by script
-        ofiles = [f for f in os.listdir(self.tempdir)
-                  if f.startswith('splitmodels')]
-        self.assertEqual(len(ofiles), 2)
-
-        for fpath in ofiles:
-            if fpath == 'ensemble_OK.pdb':
-                continue
-
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                n_lines = len(handle.readlines())
-                self.assertEqual(n_lines, 2)
-
-    def test_run_iterable_with_name(self):
-        """pdb_splitmodel.run(iterable)"""
-        from pdbtools import pdb_splitmodel
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'ensemble_OK.pdb')
-        dst = os.path.join(self.tempdir, 'ensemble_OK.pdb')
-        shutil.copy(src, dst)
-
-        with open(dst, 'r') as fin:
-            lines = fin.readlines()
-
-        pdb_splitmodel.run(lines, outname='newname')
-
-        # Read files created by script
-        ofiles = [f for f in os.listdir(self.tempdir)
-                  if f.startswith('newname')]
-        self.assertEqual(len(ofiles), 2)
-
-        for fpath in ofiles:
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                n_lines = len(handle.readlines())
-                self.assertEqual(n_lines, 2)
-
-    def test_run_fhandler(self):
-        """pdb_splitmodel.run(fhandler)"""
-        from pdbtools import pdb_splitmodel
-
-        # Copy input file to tempdir
-
-        # Simulate input
-        src = os.path.join(data_dir, 'ensemble_OK.pdb')
-        dst = os.path.join(self.tempdir, 'ensemble_OK.pdb')
-        shutil.copy(src, dst)
-
-        with open(dst, 'r') as fin:
-            pdb_splitmodel.run(fin)
-
-        # Read files created by script
-        ofiles = [f for f in os.listdir(self.tempdir)
-                  if f.startswith('ensemble_OK')]
-        self.assertEqual(len(ofiles), 2 + 1)  # ori + 2 models
-
-        for fpath in ofiles:
-            if fpath == 'ensemble_OK.pdb':
-                continue
-
-            with open(os.path.join(self.tempdir, fpath), 'r') as handle:
-                n_lines = len(handle.readlines())
-                self.assertEqual(n_lines, 2)
-
-    def test_file_not_found(self):
-        """$ pdb_splitmodel 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_splitmodel -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_splitmodel"""
-
-        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_splitmodel -A data/ensemble_OK.pdb"""
-
-        sys.argv = ['', '-A', os.path.join(data_dir, 'ensemble_OK.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()