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

{pdb_tools-2.5.0.dist-info → pdb_tools-2.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pdb-tools
-Version: 2.5.0
+Version: 2.5.1
 Summary: A swiss army knife for PDB files.
 Home-page: http://bonvinlab.org/pdb-tools
 Author: Joao Rodrigues
@@ -9,20 +9,30 @@ License: Apache Software License, version 2
 Project-URL: Bug Reports, https://github.com/haddocking/pdb-tools/issues
 Project-URL: Source, https://github.com/haddocking/pdb-tools
 Keywords: bioinformatics protein structural-biology pdb
-Platform: UNKNOWN
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: summary
 
 # pdb-tools
 
@@ -176,5 +186,3 @@ or a new tools, read our `CONTRIBUTING` instructions [here](https://github.com/h
 ## License
 `pdb-tools` are open-source and licensed under the Apache License, version 2.0.
 For details, see the LICENSE file.
-
-

pdb_tools-2.5.1.dist-info/RECORD

@@ -0,0 +1,55 @@
+pdb_tools-2.5.1.dist-info/licenses/LICENSE,sha256=cT2RbiAZ-YA-Vr_FpRv5cgvS3zh_KjQlBnvoewjElNQ,11350
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+pdb_tools-2.5.1.dist-info/top_level.txt,sha256=VJ80Sd0ldoM5Fb0EG_JRbs2GmslbFIKBL8Y0Rok8q-U,9
+pdb_tools-2.5.1.dist-info/RECORD,,

{pdb_tools-2.5.0.dist-info → pdb_tools-2.5.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.37.1)
+Generator: setuptools (80.10.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{pdb_tools-2.5.0.dist-info → pdb_tools-2.5.1.dist-info}/entry_points.txt

@@ -48,4 +48,3 @@ pdb_tofasta = pdbtools.pdb_tofasta:main
 pdb_uniqname = pdbtools.pdb_uniqname:main
 pdb_validate = pdbtools.pdb_validate:main
 pdb_wc = pdbtools.pdb_wc:main
-

{pdb_tools-2.5.0.dist-info → pdb_tools-2.5.1.dist-info}/top_level.txt

@@ -1,2 +1 @@
 pdbtools
-tests

pdbtools/pdb_tidy.py

@@ -44,6 +44,8 @@ effort to maintain and compile. RIP.
 
 import os
 import sys
+import re
+import textwrap
 
 __author__ = "Joao Rodrigues"
 __email__ = "j.p.g.l.m.rodrigues@gmail.com"
@@ -108,7 +110,7 @@ def check_input(args):
 
 def run(fhandle, strict=False):
     """
-    Add TER/END statements and pads all lines to 80 characters.
+    Add TER/END statements and truncates/pads all lines to 80 characters.
 
     This function is a generator.
 
@@ -161,8 +163,14 @@ def run(fhandle, strict=False):
         if line.startswith(ignored):  # to avoid matching END _and_ ENDMDL
             continue
 
-        # Check line length
-        line = "{:<80}\n".format(line)
+        # Check line length, wrapping and padding as necessary
+        # preserve the line prefix for wrapping
+        prefix = re.match(r"\S+\s*", line).group(0)
+        content = line[len(prefix):].lstrip()
+
+        line = "".join(
+            f"{prefix}{part:<{80 - len(prefix)}}\n"
+            for part in textwrap.wrap(content, width=80 - len(prefix)))
 
         yield line
 
@@ -214,9 +222,9 @@ def run(fhandle, strict=False):
             if atom_section:
                 atom_section = False
                 yield make_TER(prev_line)
-                if in_model:
-                    yield "{:<80}\n".format("ENDMDL")
-                    in_model = False
+            if in_model:
+                yield "{:<80}\n".format("ENDMDL")
+                in_model = False
 
             if line.startswith('MODEL'):
                 line = "MODEL " + "    " + str(num_models).rjust(4)
@@ -240,9 +248,9 @@ def run(fhandle, strict=False):
             # Add last TER statement
             atom_section = False
             yield make_TER(prev_line)
-            if in_model:
-                yield "{:<80}\n".format("ENDMDL")
-                in_model = False
+        if in_model:
+            yield "{:<80}\n".format("ENDMDL")
+            in_model = False
 
     # Add END statement
     yield "{:<80}\n".format("END")

pdb_tools-2.5.0.dist-info/RECORD

@@ -1,105 +0,0 @@
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tests/__init__.py

@@ -1,38 +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 all pdb-tools scripts
-"""
-
-import os
-import sys
-import unittest
-
-from .config import test_dir
-
-
-def test_all():
-    mpath = os.path.abspath(os.path.join(test_dir, '..'))
-    sys.path.insert(0, mpath)  # so we load dev files before  any installation
-
-    loader = unittest.defaultTestLoader
-
-    tpath = os.path.join(mpath, 'tests')
-    suite = loader.discover(tpath)
-
-    return suite

tests/config.py

@@ -1,25 +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.
-
-"""
-Configuration settings for the Tests.
-"""
-
-import os
-
-test_dir = os.path.dirname(os.path.abspath(__file__))
-data_dir = os.path.join(test_dir, 'data')

tests/test_pdb_b.py

@@ -1,161 +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_b`.
-"""
-
-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_b'
-        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_b data/dummy.pdb"""
-
-        # Simulate input
-        # pdb_b -20 dummy.pdb
-        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'))
-        bfactors = [l[60:66] for l in self.stdout if l.startswith(records)]
-        unique_bfac = list(set(map(float, bfactors)))
-        self.assertEqual(unique_bfac, [10.00])  # all bfactors changed
-
-    def test_two_options(self):
-        """$ pdb_b -20 data/dummy.pdb"""
-
-        sys.argv = ['', '-20.0', 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'))
-        bfactors = [l[60:66] for l in self.stdout if l.startswith(records)]
-        unique_bfac = list(set(map(float, bfactors)))
-        self.assertEqual(unique_bfac, [20.00])
-
-    def test_file_not_found(self):
-        """$ pdb_b not_existing.pdb"""
-
-        afile = os.path.join(data_dir, 'not_existing.pdb')
-        sys.argv = ['', '-10.0', 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_b -10"""
-
-        sys.argv = ['', '-10.0']
-
-        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_b"""
-
-        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_b -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][:47],
-                         "ERROR!! You provided an invalid b-factor value:")
-
-    def test_not_an_option(self):
-        """$ pdb_b 20 data/dummy.pdb"""
-
-        sys.argv = ['', '20', 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: '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()