more stuff

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+docs/_build/

pdbfixer.py → pdbfixer/pdbfixer.py

@@ -626,7 +626,7 @@ class PDBFixer(object):
         return nearest
 
 
-if __name__=='__main__':
+def main():
     if len(sys.argv) < 2:
         # Display the UI.
         
@@ -674,3 +674,6 @@ if __name__=='__main__':
         if options.box is not None:
             fixer.addSolvent(options.box*unit.nanometer, options.positiveIon, options.negativeIon, options.ionic*unit.molar)
         app.PDBFile.writeFile(fixer.topology, fixer.positions, open(options.output, 'w'))
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

ui.py → pdbfixer/ui.py

@@ -204,4 +204,6 @@ def launchUI():
     uiserver.beginServing()
     uiserver.setCallback(controlsCallback, "/controls")
     displayStartPage()
-    webbrowser.open('http://localhost:'+str(uiserver.server.server_address[1]))
+    url = 'http://localhost:'+str(uiserver.server.server_address[1])
+    print("PDBFixer running: %s " % url)
+    webbrowser.open(url)

setup.py

+"""pdbfixer Fixes problems in PDB files
+
+"""
+from __future__ import print_function
+import os
+from os.path import relpath, join
+from setuptools import setup, find_packages
+DOCLINES = __doc__.split("\n")
+
+########################
+__version__ = '1.0'
+VERSION = __version__
+ISRELEASED = False
+########################
+CLASSIFIERS = """\
+Development Status :: 3 - Alpha
+Intended Audience :: Science/Research
+Intended Audience :: Developers
+License :: OSI Approved :: MIT License
+Programming Language :: Python
+Programming Language :: Python :: 3
+Topic :: Scientific/Engineering :: Bio-Informatics
+Topic :: Scientific/Engineering :: Chemistry
+Operating System :: Microsoft :: Windows
+Operating System :: POSIX
+Operating System :: Unix
+Operating System :: MacOS
+"""
+
+
+def find_package_data():
+    files = []
+    for root, dirnames, filenames in os.walk('pdbfixer'):
+        for fn in filenames:
+            files.append(relpath(join(root, fn), 'pdbfixer'))
+    return files
+
+
+setup(
+    name='pdbfixer',
+    author='Peter Eastman',
+    description=DOCLINES[0],
+    long_description="\n".join(DOCLINES[2:]),
+    version=__version__,
+    license='MIT',
+    url='https://github.com/peastman/pdbfixer',
+    platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'],
+    classifiers=CLASSIFIERS.splitlines(),
+    packages=find_packages(),
+    package_data={'pdbfixer': find_package_data()},
+    zip_safe=False,
+    entry_points={'console_scripts': ['pdbfixer = pdbfixer.pdbfixer:main']})
+    
\ No newline at end of file