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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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check for redundant frames in Trajectory.py minor bug #268

Closed mlawrenz closed 10 years ago

mlawrenz commented 10 years ago

Loading in a trajectory - which had some redundant frames - gave this error because num_redundant was not initialized in the loop for "if not JustInspect:" Adding num_redundant=0 here fixed this.

dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "new-Cluster-Macrostates.py", line 109, in main(frames=options.frames, rmsdcutoff=options.rmsdcutoff, traj=options.traj, atomindices=options.atomindices, dir=options.dir) File "new-Cluster-Macrostates.py", line 59, in main t=Trajectory.load_from_dcd(traj, Conf=reference) File "/home/mlawrenz/epd-7.1-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 435, in load_from_dcd num_redundant += 1 UnboundLocalError: local variable 'num_redundant' referenced before assignment

rmcgibbo commented 10 years ago

Nice spot.

Do you know how to make a pull request? Since you already made the fix, checking it in to the repo should be really easy.

Sent from my iPhone

On Dec 28, 2013, at 12:15 PM, mlawrenz notifications@github.com wrote:

Loading in a trajectory - which had some redundant frames - gave this error because num_redundant was not initialized in the loop for "if not JustInspect:" Adding num_redundant=0 here fixed this.

dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "new-Cluster-Macrostates.py", line 109, in main(frames=options.frames, rmsdcutoff=options.rmsdcutoff, traj=options.traj, atomindices=options.atomindices, dir=options.dir) File "new-Cluster-Macrostates.py", line 59, in main t=Trajectory.load_from_dcd(traj, Conf=reference) File "/home/mlawrenz/epd-7.1-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 435, in load_from_dcd num_redundant += 1 UnboundLocalError: local variable 'num_redundant' referenced before assignment

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mlawrenz commented 10 years ago

yes, pull request sent.

On Dec 28, 2013, at 3:35 PM, Robert McGibbon wrote:

Nice spot.

Do you know how to make a pull request? Since you already made the fix, checking it in to the repo should be really easy.

Sent from my iPhone

On Dec 28, 2013, at 12:15 PM, mlawrenz notifications@github.com wrote:

Loading in a trajectory - which had some redundant frames - gave this error because num_redundant was not initialized in the loop for "if not JustInspect:" Adding num_redundant=0 here fixed this.

dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "new-Cluster-Macrostates.py", line 109, in main(frames=options.frames, rmsdcutoff=options.rmsdcutoff, traj=options.traj, atomindices=options.atomindices, dir=options.dir) File "new-Cluster-Macrostates.py", line 59, in main t=Trajectory.load_from_dcd(traj, Conf=reference) File "/home/mlawrenz/epd-7.1-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 435, in load_from_dcd num_redundant += 1 UnboundLocalError: local variable 'num_redundant' referenced before assignment

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rmcgibbo commented 10 years ago

Sweet. Merged.

Sent from my iPhone

On Dec 28, 2013, at 2:06 PM, mlawrenz notifications@github.com wrote:

yes, pull request sent.

On Dec 28, 2013, at 3:35 PM, Robert McGibbon wrote:

Nice spot.

Do you know how to make a pull request? Since you already made the fix, checking it in to the repo should be really easy.

Sent from my iPhone

On Dec 28, 2013, at 12:15 PM, mlawrenz notifications@github.com wrote:

Loading in a trajectory - which had some redundant frames - gave this error because num_redundant was not initialized in the loop for "if not JustInspect:" Adding num_redundant=0 here fixed this.

dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Traceback (most recent call last): File "new-Cluster-Macrostates.py", line 109, in main(frames=options.frames, rmsdcutoff=options.rmsdcutoff, traj=options.traj, atomindices=options.atomindices, dir=options.dir) File "new-Cluster-Macrostates.py", line 59, in main t=Trajectory.load_from_dcd(traj, Conf=reference) File "/home/mlawrenz/epd-7.1-1-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.7.dev-py2.7-linux-x86_64.egg/msmbuilder/Trajectory.py", line 435, in load_from_dcd num_redundant += 1 UnboundLocalError: local variable 'num_redundant' referenced before assignment

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