Add checks for dependencies

setup.py

-"""pdbfixer Fixes problems in PDB files
+"""pdbfixer: Fixes problems in PDB files
 
+Protein Data Bank (PDB) files often have a number of problems that must be
+fixed before they can be used in a molecular dynamics simulation. The details
+vary depending on how the file was generated. Here are some of the most common
+ones:
+
+- If the structure was generated by X-ray crystallography, most or all of the 
+- hydrogen atoms will usually be missing.
+- There may also be missing heavy atoms in flexible regions that could not be
+  clearly resolved from the electron density. This may include anything from a
+  few atoms at the end of a sidechain to entire loops.
+- Many PDB files are also missing terminal atoms that should be present at the 
+  ends of chains.
+- The file may include nonstandard residues that were added for crystallography
+  purposes, but are not present in the naturally occurring molecule you want to
+  simulate.
+- The file may include more than what you want to simulate. For example, there
+  may be salts, ligands, or other molecules that were added for experimental
+  purposes. Or the crystallographic unit cell may contain multiple copies of a
+  protein, but you only want to simulate a single copy.
+- There may be multiple locations listed for some atoms.
+- If you want to simulate the structure in explicit solvent, you will need to
+  add a water box surrounding it.
+
+PDBFixer can fix all of these problems for you in a fully automated way. You
+simply select a file, tell it which problems to fix, and it does everything else.
 """
 from __future__ import print_function
 import os
+import sys
 from os.path import relpath, join
 from setuptools import setup, find_packages
 DOCLINES = __doc__.split("\n")
@@ -36,6 +62,42 @@ def find_package_data():
     return files
 
 
+def check_dependencies():
+    from distutils.version import StrictVersion
+    found_openmm = True
+    found_openmm_52_or_later = True
+    found_numpy = True
+
+    try:
+        from simtk import openmm
+        openmm_version = StrictVersion(openmm.Platform.getOpenMMVersion())
+        if openmm_version < StrictVersion('5.2'):
+            found_openmm_52_or_later = False
+    except ImportError as err:
+        found_openmm = False
+
+    try:
+        import numpy
+    except:
+        found_numpy = False
+
+    msg = None
+    bar = ('-' * 70) + "\n" + ('-' * 70)
+    if found_openmm:
+        if not found_openmm_52_or_later:
+            msg = [bar, '[Unmet Dependency] PDBFixer requires OpenMM version 5.2 or later. You have version %s.' % openmm_version, bar]
+    else:
+        msg = [bar, '[Unmet Dependency] PDBFixer requires the OpenMM python package. Refer to <http://openmm.org> for details and installation instructions.', bar]
+
+    if not found_numpy:
+        msg = [bar, '[Unmet Dependency] PDBFixer requires the numpy python package. Refer to <http://www.scipy.org/scipylib/download.html> for numpy installation instructions.', bar]
+
+    if msg is not None:
+        import textwrap
+        print()
+        print(os.linesep.join([line for e in msg for line in textwrap.wrap(e)]), file=sys.stderr)
+        #print('\n'.join(list(textwrap.wrap(e) for e in msg)))
+
 setup(
     name='pdbfixer',
     author='Peter Eastman',
@@ -50,4 +112,5 @@ setup(
     package_data={'pdbfixer': find_package_data()},
     zip_safe=False,
     entry_points={'console_scripts': ['pdbfixer = pdbfixer.pdbfixer:main']})
-    
\ No newline at end of file
+
+check_dependencies()