Merge branch 'development' into feature/chain

CHANGES.txt

@@ -1,5 +1,11 @@
 Changelog
 ---------
+# 2.3.1
+* fixes in interaction detection with peptide ligands by @kalinni in #153
+* fix in hydrogen bond acceptor identification by @kalinni in #151
+* fixes in waterbridge detection and filtering by @kalinni in #152
+* fix NumPy DeprecationWarning when using numpy.uint32 with negative numbers by @QY0831 in #150
+
 # 2.3.0
 * fixes an issue that caused encoding errors to be thrown
 * salt bridge interaction improved

plip/basic/config.py

@@ -1,4 +1,4 @@
-__version__ = '2.3.0'
+__version__ = '2.3.1'
 __maintainer__ = 'PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai'
 __citation_information__ = "Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. " \
                            "Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294"

setup.py

@@ -1,32 +1,102 @@
 from setuptools import setup, find_packages
+from setuptools.command.build_ext import build_ext
+from setuptools.command.install import install
+from distutils.command.build import build
 
 from plip.basic import config
 
+def install_pkg_via_pip(package):
+        import subprocess
+        subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--user', package])
+
+def build_ob_py_bindings():
+    """ Fix openbabel issue (https://github.com/openbabel/openbabel/issues/2408) manually
+      - Download openbabel bindings from pypi
+      - extract to a tmpdir
+      - fix version in $tmpdir/openbabel-3.1.1.1/openbabel/__init__.py to have 2 dot version only
+      - install the fixed version with setuptools/pip
+      - cleanup the tmpdir
+    """
+    import requests
+    import tarfile
+    import tempfile
+    import shutil
+    import fileinput
+    import subprocess
+    import sys
+
+    openbabel_pypi_url='https://files.pythonhosted.org/packages/9d/3f/f08f5d1422d74ed0e1e612870b343bfcc26313bdf9efec9165c3ea4b3ae2/openbabel-3.1.1.1.tar.gz'
+
+    print (f"Downloading openbabel package from : {openbabel_pypi_url}")
+    obtar=requests.get(openbabel_pypi_url)
+    obtmpdir = tempfile.mkdtemp()
+    obtmp = obtmpdir+'/openbabel-3.1.1.1.tar'
+    open(obtmp,'wb').write(obtar.content)
+    print(f"Saving openbabel tar.gz to {obtmpdir}")
+    versfile = obtmpdir+'/openbabel-3.1.1.1/openbabel/__init__.py'
+
+    with tarfile.open(obtmp,mode='r') as tf:
+        tf.extractall(obtmpdir)
+
+    print ('Fix versions: s/3.1.1.1/3.1.1/ to make StrictVersion() in openbabel\'s setup.py happy')
+    print ('See https://github.com/openbabel/openbabel/issues/2408 for more details')
+    with fileinput.input(files=versfile,inplace=True) as f:
+        for line in f:
+            op = line.replace('__version__ = "3.1.1.1"', '__version__ = "3.1.1"')
+            print(op, end='')
+
+    install_pkg_via_pip(obtmpdir+'/openbabel-3.1.1.1/')
+    print (f"Cleanup tmpdir: {obtmpdir}")
+    shutil.rmtree(obtmpdir)
+
+class CustomBuild(build):
+    """Ensure build_ext runs first in build command."""
+    def run(self):
+        self.run_command('build_ext')
+        build.run(self)
+
+class CustomInstall(install):
+    """Ensure build_ext runs first in install command."""
+    def run(self):
+        self.run_command('build_ext')
+        install.run(self)
+
+class CustomBuildExt(build_ext):
+    """ Check if openbabel bindings are installed || build them """
+    def run(self):
+        try: import openbabel
+        except ModuleNotFoundError:
+            try: import requests
+            except ModuleNotFoundError:
+                install_pkg_via_pip('requests')
+            build_ob_py_bindings()
+        return
+
 setup(name='plip',
-      version=config.__version__,
-      description='PLIP - Fully automated protein-ligand interaction profiler',
-      classifiers=[
-          'Development Status :: 5 - Production/Stable',
-          'Intended Audience :: Science/Research',
-          'Natural Language :: English',
-          'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
-          'Programming Language :: Python :: 3.6',
-          'Topic :: Scientific/Engineering :: Bio-Informatics'
-      ],
-      url='https://github.com/pharmai/plip',
-      author='PharmAI GmbH',
-      author_email='hello@pharm.ai',
-      license='GPLv2',
-      packages=find_packages(),
-      scripts=['plip/plipcmd.py'],
-      install_requires=[
-          'openbabel',
-          'numpy',
-          'lxml'
-      ],
-      entry_points={
-          "console_scripts": [
-              "plip = plip.plipcmd:main"
-          ]
-      },
-      zip_safe=False)
+    version=config.__version__,
+    description='PLIP - Fully automated protein-ligand interaction profiler',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'Natural Language :: English',
+        'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
+        'Programming Language :: Python :: 3.6',
+        'Topic :: Scientific/Engineering :: Bio-Informatics'
+        ],
+    url='https://github.com/pharmai/plip',
+    author='PharmAI GmbH',
+    author_email='hello@pharm.ai',
+    license='GPLv2',
+    packages=find_packages(),
+    scripts=['plip/plipcmd.py'],
+    cmdclass={'build': CustomBuild, 'build_ext': CustomBuildExt, 'install': CustomInstall},
+    install_requires=[
+        'numpy',
+        'lxml'
+        ],
+    entry_points={
+        "console_scripts": [
+            "plip = plip.plipcmd:main"
+            ]
+        },
+    zip_safe=False)