- IMP-dev - salilab.org

doc cleanup
by Daniel Russel 10 Dec '08

10 Dec '08

This patch removes the docbook files since all their content is now in the wiki and doxygen. It also renames the documentation directories to be more obvious: the doxygen config is now in doc/doxygen and the produced documentation goes in doc/html.

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cleanup patches
by Daniel Russel 10 Dec '08

10 Dec '08

optimizer states should be ref counted clean up the keys in doxygen so that there are not so many keybase listings in the class hierarchy

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fix bug in pointer
by Daniel Russel 09 Dec '08

09 Dec '08

Fix a bug in pointer where bad things would happen if you assigned a value to a pointer that equaled its old value. Check for this and skip the increment and decrement.

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covering particles with balls and rigid bodies
by Daniel Russel 09 Dec '08

09 Dec '08

There is now some code to use SingletonModifiers and a ScoreState and ParticleRefiners to, for example, make sure that each residue defines a sphere which contains all its atoms and that derivatives are propagated properly. Such would probably also make a good model for rigid bodies as all we would have to write would be four very simple classes: - a RigidBodyDecorator which inherits from XYZDecorator and adds a quaternion - a RigidBodyComponentDecorator which inherits from XYZDecorator and adds a set of coordinates relative to its original frame - a TorquesFromRefinedSingletonModifier (like DerivativesFromRefinedSingletonModifier) which uses the derivatives of the particles produced by a particle refiner to apply torques to a rigid body - a TransformComponentsSingletonModifier which applies the transform in a RigidBodyDecorator particle to each of the RigidBodyComponentDecorator particles produced by a particle refiner Then they could be tied together just as in the residue cover example and the rigid bodies could be trivially defined through a molecular hierarchy or any other particle refiner you want to use.

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Define internal namespace in imp_module.py
by Daniel Russel 09 Dec '08

09 Dec '08

Move the definition of the core::internal namespace to imp_module.py. Now all modules have a uniform internal namespace called modulename::internal to go along with the internal include directory. There are lots of extra includes of macros.h in core due to it being defined elsewhere before, but those can wait.

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minor patch to .is
by Daniel Russel 09 Dec '08

09 Dec '08

This removes the IMPCORE_OWN_FIRST... macros and makes the kernel ones check so that they can handle optional and null arguments.

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patch to fix test error message paths
by Daniel Russel 09 Dec '08

09 Dec '08

This patch makes run-all-tests.py run from the IMP root directory so error messages work in emacs and IDEs.

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MSVC has trouble with friends
by Daniel Russel 06 Dec '08

06 Dec '08

VC seems to have issues with friends. So this patch turns off the protected destructors when building with that compiler.

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adjust module documentation
by Daniel Russel 05 Dec '08

05 Dec '08

This patch moves the namespace documentation to the respective module/ doc/module.dox file (and adds such files for other modules). Here is an unrelated patch to allow entries to be added to the scons PATH so that I can build the docs on my mac without hacking the install scripts:

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Cleanups to kernel and doxygen.conf
by Daniel Russel 04 Dec '08

04 Dec '08

The patch has some more changes to the kernel documentation as well as cleaning up the doxygen.conf file to remove extraneous stuff. If you want to see doxygen information involving .cpp files (which are not documented in general), use the doxygen.conf in kernel/doc/internal (although you may want to wait until to check more tomorrow). I can't imagine why you would want to use those other docs though :-)

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