- 19 Nov, 2014 4 commits
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Jason Swails authored
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Jason Swails authored
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Jason Swails authored
SyntaxWarning otherwise). So move those imports back to the module level and save any error messages for when the tests are actually run (if ever). python -m simtk.testInstallation runs the tests, whereas python -c "import simtk.testInstallation" does not.
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Jason Swails authored
Also copy the test PDB file to the data/ directory, since we rather need it...
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- 18 Nov, 2014 4 commits
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Jason Swails authored
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Jason Swails authored
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Jason Swails authored
most important and we don't want false positives.
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Jason Swails authored
At some point, at least, TP4 was the residue label for water (I think tleap currently translates most of the water residue labels to WAT, but there are at least some -- like $AMBERHOME/test/tip4p/prmtop -- that use older labels).
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- 17 Nov, 2014 1 commit
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Jason Swails authored
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- 14 Nov, 2014 3 commits
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Jason Swails authored
Make sure files are appropriately closed by PDBFile()
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Jason Swails authored
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Jason Swails authored
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- 13 Nov, 2014 2 commits
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Jason Swails authored
can't validate the that this object does anything more than simply write without exceptions (i.e., we can't tell if the DCD file is actually _valid_)
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Jason Swails authored
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- 10 Nov, 2014 2 commits
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Matthew Harrigan authored
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Matthew Harrigan authored
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- 07 Nov, 2014 1 commit
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peastman authored
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- 06 Nov, 2014 1 commit
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peastman authored
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- 05 Nov, 2014 2 commits
- 04 Nov, 2014 2 commits
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Jason Swails authored
Add a test for the various numpy attributes (and the arguments they take) for the unit module.
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Jason Swails authored
Traceback (most recent call last): File ".../python/tests/TestNumpyCompatibility.py", line 87, in testNumpyAttributes d = self.data.reshape((100, 3)) File ".../simtk/unit/quantity.py", line 575, in reshape return Quantity(self._value.reshape(shape, order=order)) File ".../simtk/unit/quantity.py", line 142, in __init__ if value == first_item: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() Also add a test for new unit numpy capabilities.
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- 03 Nov, 2014 2 commits
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Jason Swails authored
underlying numpy array. This function would be used in instances where, for instance, a certain API would send a flattened array of coordinates or velocities with units attached, and you wanted to reshape the array into (natom, 3) to be consistent with OpenMM's Context object.
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Jason Swails authored
arguments and pass them to the numpy function if applicable. That way, users get the full flexibility of the numpy API on those particular methods AND get the added benefit that the result has the correct units (and it all runs fast).
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- 23 Oct, 2014 4 commits
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Peter Eastman authored
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peastman authored
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Peter Eastman authored
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Peter Eastman authored
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- 22 Oct, 2014 3 commits
- 15 Oct, 2014 1 commit
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Peter Eastman authored
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- 13 Oct, 2014 1 commit
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peastman authored
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- 06 Oct, 2014 4 commits
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Jason Swails authored
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Jason Swails authored
it. Not only that, I got this FutureWarning: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simtk/unit/quantity.py:170: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future. if value == None:
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Jason Swails authored
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Jason Swails authored
sqrt of the variance), and average, returning a Quantity with the proper units. This should be reasonably efficient, as it takes advantage of numpy-accelerated methods if they're present.
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- 03 Oct, 2014 1 commit
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peastman authored
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- 01 Oct, 2014 2 commits
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kyleabeauchamp authored
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kyleabeauchamp authored
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