Merge pull request #573 from swails/ommparams

merge master

.travis.yml

@@ -8,32 +8,19 @@ addons:
         packages:
             - g++
             - gromacs
-            - pypy
 
 matrix:
   include:
     - { os: linux, env: PYTHON_VERSION=2.7 }
-    - { os: linux, env: PYTHON_VERSION=3.3 MINIMAL_PACKAGES=yes }
     - { os: linux, env: PYTHON_VERSION=3.4 }
+    - { os: linux, env: PYTHON_VERSION=3.5 MINIMAL_PACKAGES=yes }
     - { os: linux, env: PYTHON_VERSION=pypy }
-    - { os: osx, env: PYTHON_VERSION=3.4 MINIMAL_PACKAGES=yes }
+    - { os: osx, env: PYTHON_VERSION=3.5 MINIMAL_PACKAGES=yes }
 
 install:
     - source devtools/travis-ci/install.sh
       # install our package
     - python setup.py install
 
 script:
-    # Skip tests that use a lot of memory so Travis doesn't sporadically kill
-    # them. Also fix the number of running threads to 1.
-    - export PARMED_SKIP_BIG_TESTS=1
-    - export OPENMM_CPU_THREADS=1
-    - echo "Checking parmed source with pyflakes linter"
-    - if [ "$PYTHON_VERSION" = "pypy" ]; then export PYENV_ROOT="${HOME}/.pyenv"; fi
-    - if [ "$PYTHON_VERSION" = "pypy" ]; then export PATH="${PYENV_ROOT}/bin:${PATH}"; fi
-    - if [ "$PYTHON_VERSION" = "pypy" ]; then eval "$(pyenv init -)"; fi
-    - devtools/travis-ci/pyflakes_check.sh
-    - cd test
-    - echo "Using `which nosetests`::"
-    - which nosetests
-    - nosetests -vs --with-timer --timer-ok=5s --timer-warning=12s .
+    - source devtools/travis-ci/runtest.sh

MANIFEST.in

@@ -1,3 +1,3 @@
 graft examples
 graft src
-graft test
+graft parmed

devtools/travis-ci/install.sh

@@ -7,9 +7,9 @@ if [ "$PYTHON_VERSION" = "pypy" ]; then
     pyenv install pypy-4.0.1
     pyenv global pypy-4.0.1
 
-    pypy -m pip install nose coverage pyflakes nose-timer
+    pypy -m pip install nose pyflakes nose-timer
     which pyflakes
-    pypy -m pip install --user git+https://bitbucket.org/pypy/numpy.git
+    pypy -m pip install --user git+https://bitbucket.org/pypy/numpy.git@pypy-4.0.1
 else # Otherwise, CPython... go through conda
     if [ "$TRAVIS_OS_NAME" = "osx" ]; then
         wget http://repo.continuum.io/miniconda/Miniconda-3.7.0-MacOSX-x86_64.sh -O miniconda.sh;
@@ -25,12 +25,13 @@ else # Otherwise, CPython... go through conda
 
     if [ -z "$MINIMAL_PACKAGES" ]; then
         conda create -y -n myenv python=$PYTHON_VERSION \
-            numpy scipy pandas nose openmm pyflakes coverage nose-timer
+            numpy scipy pandas nose openmm pyflakes coverage nose-timer \
+            python-coveralls
         conda update -y -n myenv --all
     else
         # Do not install the full numpy/scipy stack
         conda create -y -n myenv python=$PYTHON_VERSION numpy nose pyflakes \
-            coverage nose-timer
+            coverage nose-timer python-coveralls
     fi
 
     source activate myenv

devtools/travis-ci/runtest.sh

@@ -0,0 +1,36 @@
+#!/bin/sh
+set -e
+
+do_coverage() {
+    echo "Combining coverage data"
+    coverage combine
+    echo "Reporting..."
+    coverage report -m
+}
+
+echo "Checking parmed source with pyflakes linter"
+if [ "$PYTHON_VERSION" = "pypy" ]; then
+    export PYENV_ROOT="${HOME}/.pyenv"
+    export PATH="${PYENV_ROOT}/bin:${PATH}"
+    eval "$(pyenv init -)"
+fi
+sh devtools/travis-ci/pyflakes_check.sh
+cd test
+echo "Using nosetests...:"
+./run_scripts.sh
+if [ "$PYTHON_VERSION" = "pypy" ]; then
+    # Disable coverage with pypy, since it multiplies the time taken by 6 or
+    # something ridiculous like that
+    nosetests -vs --with-timer --timer-ok=5s --timer-warning=12s \
+              --timer-filter=warning,error .
+else
+    # Run nose under coverage, since that allows getting the full flexibility of
+    # the coverage package without sacrificing nose functionality
+    coverage run --source=parmed --parallel-mode -m \
+        nose -vs --with-timer --timer-ok=5s --timer-warning=12s \
+             --timer-filter=warning,error .
+fi
+test -z `which coverage 2>/dev/null` || do_coverage
+echo "Running coveralls"
+test -z `which coveralls` || coveralls
+echo "Done!"

doc/devdoc.rst

@@ -23,9 +23,9 @@ is clearly not being run, or not being run correctly (which means there is no
 way that your test could prevent a breakage in the future).
 
 Once you have a failing test case, write code until the test case passes. Then
-add more test until the test case fails again. Then update the test case until
-it fails again. Rinse-and-repeat until the functionality you are adding is
-complete.
+add more test until the test case fails again. Then update the code until the
+test passes again. Rinse-and-repeat until the functionality you are adding is
+complete and fully-tested.
 
 Coding Style
 ------------
@@ -40,7 +40,7 @@ the following I consider very important (and will block any PRs):
     - Please make sure comments and docstrings are written in English
     - Use only absolute imports or *explicit* relative imports
     - Always use ``print`` as a function (via the ``print_function`` futures
-      import)
+      import) -- see below for why this is a hard requirement.
 
 Things I would like to see, but are not as important:
 
@@ -62,8 +62,8 @@ package, and all components should be imported from there.
 In particular, the ``range`` and ``zip`` builtins should be imported from
 ``parmed.utils.six.moves`` rather than relying on the standard versions. This is
 because in Python 3, ``range`` and ``zip`` return efficient iterators, while in
-Python 2 they return (sometimes *very* inefficient lists). The Python
-2-equivalent versions of the ``range`` and ``zip`` iterators are ``xrange`` and
+Python 2 they return potentially inefficient lists. The Python 2-equivalent
+versions of the ``range`` and ``zip`` iterators are ``xrange`` and
 ``itertools.izip``, respectively, which are the *actual* functions defined
 within ``parmed.utils.six.moves`` for Python 2.
 
@@ -108,14 +108,14 @@ Obviously in this case, ``test_parmed_structure.py`` is replaced with whichever
 test module you are working on. You can select *specific* tests using the ``-m``
 flag specifying a regex that matches the test case method.  For example::
 
-    nosetests -vs test/test_parmed_structure.py -m AddAtom
+    nosetests -vs test/test_parmed_structure.py -m add_atom
 
-will test both the ``tesAddAtom`` and ``testAddAtomToResidue`` methods. This is
-an easy way to run tests quickly while working on new methods *without* having
-to run ``python setup.py install`` after every change. Note that when you run
-tests from the root ParmEd directory, however, the imported ParmEd repository
-will not have any Python extensions installed (meaning that the tests relying on
-them -- like the test for the Amber optimized reader -- will fail).
+will test both the ``test_add_atom`` and ``test_add_atom_to_residue`` methods.
+This is an easy way to run tests quickly while working on new methods *without*
+having to run ``python setup.py install`` after every change. Note that when you
+run tests from the root ParmEd directory, however, the imported ParmEd
+repository will not have any Python extensions installed (meaning that the tests
+relying on them -- like the test for the Amber optimized reader -- will fail).
 
 ParmEd utilizes the Travis continuous integration server to perform automatic
 tests of all pull requests. Tests generally must pass these tests before being

doc/index.rst

@@ -151,9 +151,9 @@ A simple example demonstrating the file conversion capabilities is to convert a
 PDBx/mmCIF file into the more commonly supported PDB format::
 
     >>> import parmed as pmd
-    >>> pmd.write_PDB(pmd.download_CIF('4lzt'), '4lzt.pdb')
+    >>> pmd.download_CIF('4lzt').save('4lzt.pdb')
     >>> # Now read in the PDB file we just created
-    ... pmd.read_PDB('4lzt.pdb')
+    ... pmd.load_file('4lzt.pdb')
     <Structure 1164 atoms; 274 residues; 0 bonds; PBC; NOT parametrized>
 
 Program and API Reference

parmed/__init__.py

@@ -6,7 +6,7 @@
 # Version format should be "major.minor.patch". For beta releases, attach
 # "-beta#" to the end. The beta number will be turned into another number in the
 # version tuple
-__version__ = '2.1.6'
+__version__ = '2.1.11'
 __author__ = 'Jason Swails'
 
 __all__ = ['exceptions', 'periodic_table', 'residue', 'unit', 'utils',
@@ -23,11 +23,12 @@
 from parmed import formats
 from parmed.vec3 import Vec3
 from parmed.parameters import ParameterSet
+from parmed.utils.decorators import deprecated as _deprecated
 load_file = formats.load_file
 read_PDB = formats.PDBFile.parse
 read_CIF = formats.CIFFile.parse
-write_PDB = formats.PDBFile.write
-write_CIF = formats.CIFFile.write
+write_PDB = _deprecated(formats.PDBFile.write)
+write_CIF = _deprecated(formats.CIFFile.write)
 load_rosetta = rosetta.RosettaPose.load
 
 download_PDB = formats.PDBFile.download

parmed/amber/_amberparm.py

@@ -842,12 +842,12 @@ def has_NBFIX(self):
             If True, off-diagonal elements in the combined Lennard-Jones matrix
             exist. If False, they do not.
         """
+        assert self.combining_rule in ('lorentz', 'geometric'), \
+                "Unrecognized combining rule"
         if self.combining_rule == 'lorentz':
             comb_sig = lambda sig1, sig2: 0.5 * (sig1 + sig2)
         elif self.combining_rule == 'geometric':
             comb_sig = lambda sig1, sig2: sqrt(sig1 * sig2)
-#       else:
-        assert self.combining_rule in ('lorentz', 'geometric'), "Unrecognized combining rule"
         fac = 2**(-1/6) * 2
         LJ_sigma = [x*fac for x in self.LJ_radius]
         pd = self.parm_data
@@ -978,6 +978,8 @@ def omm_nonbonded_force(self, nonbondedMethod=None,
         hasnbfix = self.has_NBFIX()
         has1264 = 'LENNARD_JONES_CCOEF' in self.flag_list
         if not hasnbfix and not has1264 and not has1012:
+            if self.chamber:
+                self._modify_nonb_exceptions(nonbfrc, None)
             return nonbfrc
 
         # If we have NBFIX, omm_nonbonded_force returned a tuple
@@ -1741,8 +1743,9 @@ def _modify_nonb_exceptions(self, nonbfrc, customforce):
         exclusions. The exceptions on the nonbonded force might need to be
         adjusted if off-diagonal modifications on the L-J matrix are present
         """
-        # To get into this routine, we already needed to know that nbfix is
-        # present
+        # To get into this routine, either NBFIX is present OR this is a chamber
+        # prmtop and we need to pull the 1-4 L-J parameters from the
+        # LENNARD_JONES_14_A/BCOEF arrays
         length_conv = u.angstroms.conversion_factor_to(u.nanometers)
         ene_conv = u.kilocalories.conversion_factor_to(u.kilojoules)
         atoms = self.atoms
@@ -1762,7 +1765,8 @@ def _modify_nonb_exceptions(self, nonbfrc, customforce):
                     ee.value_in_unit(u.kilocalories_per_mole) == 0):
                 # Copy this exclusion as-is... no need to modify the nonbfrc
                 # exception parameters
-                customforce.addExclusion(i, j)
+                if customforce is not None:
+                    customforce.addExclusion(i, j)
                 continue
             # Figure out what the 1-4 scaling parameters were for this pair...
             unscaled_ee = sqrt(self.atoms[i].epsilon_14 *
@@ -1788,7 +1792,8 @@ def _modify_nonb_exceptions(self, nonbfrc, customforce):
                 epsilon = b / (2 * rmin**6) * ene_conv * one_scnb
                 sigma = rmin * sigma_scale
             nonbfrc.setExceptionParameters(ii, i, j, qq, sigma, epsilon)
-            customforce.addExclusion(i, j)
+            if customforce is not None:
+                customforce.addExclusion(i, j)
 
     #===================================================
 
@@ -1862,12 +1867,11 @@ def _add_missing_13_14(self, ignore_inconsistent_vdw=False):
                         scee = 1e10
                     else:
                         scee = 1 / pair.type.chgscale
-                    if (abs(rref - pair.type.rmin) > SMALL and
+                    if ignore_inconsistent_vdw:
+                        scnb = 1.0
+                    elif (abs(rref - pair.type.rmin) > SMALL and
                             pair.type.epsilon != 0):
-                        if ignore_inconsistent_vdw:
-                            scnb = 1.0
-                        else:
-                            raise TypeError('Cannot translate exceptions')
+                        raise TypeError('Cannot translate exceptions')
                     if (abs(scnb - dihedral.type.scnb) < SMALL and
                             abs(scee - dihedral.type.scee) < SMALL):
                         continue

parmed/amber/_chamberparm.py

@@ -193,10 +193,10 @@ def from_structure(cls, struct, copy=False):
         inst.LJ_14_radius = [0 for i in range(ntyp)]
         inst.LJ_14_depth = [0 for i in range(ntyp)]
         for atom in inst.atoms:
-            inst.LJ_radius[atom.nb_idx-1] = atom.atom_type.rmin
-            inst.LJ_depth[atom.nb_idx-1] = atom.atom_type.epsilon
-            inst.LJ_14_radius[atom.nb_idx-1] = atom.atom_type.rmin_14
-            inst.LJ_14_depth[atom.nb_idx-1] = atom.atom_type.epsilon_14
+            inst.LJ_radius[atom.nb_idx-1] = atom.rmin
+            inst.LJ_depth[atom.nb_idx-1] = atom.epsilon
+            inst.LJ_14_radius[atom.nb_idx-1] = atom.rmin_14
+            inst.LJ_14_depth[atom.nb_idx-1] = atom.epsilon_14
         inst._add_standard_flags()
         inst.pointers['NATOM'] = len(inst.atoms)
         inst.parm_data['POINTERS'][NATOM] = len(inst.atoms)
@@ -684,33 +684,23 @@ def _set_nonbonded_tables(self, nbfixes=None):
         for i in range(len(data['LENNARD_JONES_14_ACOEF'])):
             data['LENNARD_JONES_14_ACOEF'][i] = None
             data['LENNARD_JONES_14_BCOEF'][i] = None
-        atom_types_assigned_unique_idx = set()
         ii = 0
         while True:
             needed_split = False
             for pair in self.adjusts:
                 a1, a2 = pair.atom1, pair.atom2
                 i, j = sorted([a1.nb_idx - 1, a2.nb_idx - 1])
                 idx = data['NONBONDED_PARM_INDEX'][ntypes*i+j] - 1
-                eps = sqrt(a1.epsilon_14 * a2.epsilon_14)
-                rmin = a1.rmin_14 + a2.rmin_14
+                eps = pair.type.epsilon
+                rmin = pair.type.rmin
                 rmin6 = rmin * rmin * rmin * rmin * rmin * rmin
                 acoef = eps * rmin6*rmin6
                 bcoef = 2 * eps * rmin6
                 if data['LENNARD_JONES_14_ACOEF'][idx] is not None:
                     if abs(data['LENNARD_JONES_14_ACOEF'][idx] - acoef) > SMALL:
                         # Need to split out another type
                         needed_split = True
-                        if a1.type in atom_types_assigned_unique_idx:
-                            if a2.type in atom_types_assigned_unique_idx:
-                                # Ugh. Split out this atom by itself
-                                mask = '@%d' % (a1.idx + 1)
-                            else:
-                                mask = '@%%%s' % a2.type
-                                atom_types_assigned_unique_idx.add(a2.type)
-                        else:
-                            atom_types_assigned_unique_idx.add(a1.type)
-                            mask = '@%%%s' % a1.type
+                        mask = '@%d' % (a1.idx + 1)
                         addLJType(self, mask, radius_14=0,
                                   epsilon_14=0).execute()
                         ntypes += 1
@@ -731,7 +721,6 @@ def _set_nonbonded_tables(self, nbfixes=None):
             # The following should never happen
             assert ii <= len(self.atoms), 'Could not resolve all exceptions. ' \
                     'Some unexpected problem with the algorithm'
-            # TODO delete
         # Now go through and change all None's to 0s, as these terms won't be
         # used for any exceptions, anyway
         for i, item in enumerate(data['LENNARD_JONES_14_ACOEF']):

parmed/gromacs/_cpp.py

@@ -328,6 +328,13 @@ def _pp_undef(self, args):
         elif len(words) == 0:
             raise PreProcessorError('Nothing defined in #undef')
 
+    # Context manager protocol
+    def __exit__(self, type, value, traceback):
+        self.close()
+
+    def __enter__(self):
+        return self
+
     _ppcmdmap = {'if' : _pp_if, 'elif' : _pp_elif, 'ifdef' : _pp_ifdef,
                  'else' : _pp_else, 'define' : _pp_define, 'undef' : _pp_undef,
                  'include' : _pp_include, 'endif' : _pp_endif,
@@ -340,7 +347,7 @@ def _pp_undef(self, args):
     parser = argparse.ArgumentParser()
     parser.add_argument('-i', '--input-file', dest='input', metavar='FILE',
                 required=True, help='''Input file to pre-process. Either a file
-                name or, if '--' is given, from standard input.''')
+                name or, if '-' is given, from standard input.''')
     parser.add_argument('-o', '--output-file', dest='output', metavar='FILE',
                 default=None, help='''Output file with preprocessed results.
                 Default is standard output''')
@@ -361,15 +368,19 @@ def _pp_undef(self, args):
             val = '1'
         defines[define] = val
 
-    if opt.input == '--':
+    if opt.input == '-':
         f = sys.stdin
     else:
         f = opt.input
     pp = CPreProcessor(f, defines=defines, includes=opt.includes)
     if opt.output is None:
         output = sys.stdout
+        own_handle = False
     else:
         output = genopen(opt.output, 'w')
+        own_handle = True
 
     for line in pp:
         output.write(line)
+    if own_handle:
+        output.close()