Add structural metrics #245
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a-r-j
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* Add tensor parsing util * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add missing arg comma * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add backbone check util * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * linting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add chain tensor * add test for io utils * fix loguru import * add torchtyping dependency * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix import message import * add tests for angle utils * add tests for angle utils * add tests for tensor parsing * add tests for tensor parsing * add sidechain atom groups * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add io tests * add geometry tests * add geom ad sequence mnodules * add test for inferring sequence from coordinates * add einops as an optional dependecy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add sequence inference utils * add data testing utils * add nan util * add angle computation utils * add test for distmat reconstruction * wrap torch imports * wrap imports * wrap imports * add representation utils * wrap torch-dependent tests * add edge tensor type * update changelog * add build params * add updated angles script * add graphein package test * wrap imports * add plotting utils * push tensor utils * update centering default args * add reconstruction utils * add data objects * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add PyG dep * add pnerf * update nx to numpy array to support 3.0 * fix kabsch test * fix centering masking * remove nx.info - deprecated in nx 3.0 * rm gpickle reference - deprecated in nx 3.0 * rm gpickle reference - deprecated in nx 3.0 * fix nx 3.0 adjacency issues * fix for nx 3.0 * ignore tensor tests for minimal build * ignore tensor tests for minimal build * add additional docs * add additional testin utils * add docstrings to plot * finish sequence docstrings * add notimplemented errors and todos * finalise io * add tensor submodule to docs * add edges * update license year * add documented code * add documented code and edge funcs * add updated tests * update doc config * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add additional constants * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix test * update changelog * update readme * update docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update docstrings * update docstrings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * bump license year * fix angle dims * add noising and plotting * add node id to plots * add esmfold util * add noise util * Add structural metrics (#245) * Add gdt metric * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add TMScore * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add init * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update readme Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * add dataloader * add folding utils * update readme * add docs * add tutorial notebooks * add fasta parsing util * add data updates * fix df output * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove DL-dependent notebooks from minimal install test * add watermark * rm dataloaders from test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix typo in inc_dict attr * add doc dep install to build * fix typo * remove wildcard pyyaml version * add try/except for atomic peptide bonds * update tensor tutorial --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Pull Request Checklist
./CHANGELOG.mdfile (if applicable)./graphein/tests/*directories (if applicable)./notebooks/(if applicable)python -m py.test tests/and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,python -m py.test tests/protein/test_graphs.py)black .andisort .