Aleaverfay/sparse dispatch dslf #328
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Torch 2.5.0, 2.5.1, and 2.7 also seem to work just fine for tmol; Torch 2.4 does not work. Also updating the code relying on cattrs.structure The newest versions of cattrs (>=24.1.0) throw errors that previously were not errors or that could be worked around or something so that now the code in tmol/chemical/restypes.py produces errors that weren't there before. One small issue: numpy.array cannot be used as a type name for attrs and this produces a weird complaint out of cattrs. numpy.array is for creating ndrarrays; ndarrays are the types, array is the function
…dd to packer tests
Nicely enough, termini variants are being properly handled already; the tests simply had to be updated.
Now the sampler is responsible for mapping their samples onto the DOFs that define the conformations, allowing samplers to define more than only the chi DOFs for the samples; e.g., if I want to build hydroxyl rotamers onto the heavy-atom coordinates of an existing SER
This code is "used" by the on-the-fly RPE calculation code which itself is not really used
This allows me to talk about global-block-type index (not a great name) when building rotamers for disallowed block types as will happen when a block has all of its block-types disallowed.
…mp_jflat_sparse_disp_torch28
This includes a bug in neighbor detection that was allowing the first rotamer from pose i+1 to get checked as a neighbor with rotamers of the last residue of pose i!
* Update modern GPU to CUDA13 compatibility (See moderngpu/moderngpu#56) * Add conda/mamba-installed nvtx to search path * Update NVidia conda channel to torch 2.8.0 for CUDA 13 compatibility * Add nvtx to conda packages * Fix broken unit test enable_tensor_view that lead to a "Illegal Operation" error * Change error-propogation command location in "linting" script until after conda activation
…w rotamer-pair scoring scheme
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Disulfide term implemented in sparse-dispatch compatible version.
This one is rather interesting as we have left open the idea that the disulfide term could be used by things besides the CYS/CYD residue type, including residue types that may have more than one disulfide-forming sulfur. The dispatching code makes it relatively easy to make sure that all of the pair interactions are scored without double counting. For each rotamer, we look at its inter-block connections and see if any of them qualify as disulfide-forming, and then we look to see if they are forming a connection to a higher-indexed residue. The dispatch indices keep track of the conn_index of both residues i and j, using separate dispatch indices for different disulfide-forming sulfurs. In the monstrous event of residue i forming two disulfides bonds to residue j, we avoid counting their interactions twice by scoring each disulfide in a separate thread (with a separate dispatch index) and will rely on the fact that we can have multiple entries for a single rotamer pair in a torch sparse matrix.