Decreasing the number of dynamically shadowed bindings

[JackMaguire]

Nowhere near ready for review...

[JackMaguire]

@lyskov Why did -class protocols::mean_field::jagged_array< protocols::mean_field::AAProb > not work? I'm still seeing that the class got bound in the failed unit tests:

CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::assign` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::assign` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::capacity` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::clear` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::empty` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::max_size` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::pop_back` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::reserve` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'int'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>, <class 'int'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::resize` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'int'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>, <class 'int'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::size` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>]`
CONFLICT `<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>::swap` --- `[<class 'pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t'>, <class 'pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_t'>]` --- `[<class 'pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_t'>, <class 'pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_t'>]`

Edit: This isn't urgent. I found a workaround. I'm more just curious about why it failed than how to fix it

[JackMaguire]

Down from 276 to 182

[lyskov]

@lyskov Why did -class protocols::mean_field::jagged_array< protocols::mean_field::AAProb > not work? I'm still seeing that the class got bound in the failed unit tests:

-- one need to use full C++ class/function name with all template arguments. Easiest way to find such name is to look at generated C++ sources (see source/build/PyRosetta dir if you build locally). For this particular case full name is probably something like:

protocols::mean_field::jagged_array<protocols::mean_field::AAProb,std::allocator<protocols::mean_field::AAProb>>