├── .clang-format ├── .gitignore ├── .gitlab-ci.yml ├── .gitlab ├── issue_templates │ ├── bug-report.md │ ├── feature-request.md │ └── task.md └── merge_request_templates │ └── default.md ├── .locate-site-packages.py ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE ├── Makefile ├── README.md ├── benchmark ├── conftest.py ├── cuda │ └── time_resizable_array.py ├── graph │ └── time_graph.py └── kernel │ ├── marginalized │ └── time_kernel.py │ └── molecular │ └── time_molecular.py ├── docs ├── Makefile ├── api.rst ├── conf.py ├── contribute.rst ├── example.rst ├── example │ ├── molecular-2d.rst │ ├── molecular-3d.rst │ ├── unweighted-nodelabeled.rst │ ├── unweighted-unlabeled.rst │ ├── variable-length-features.rst │ ├── weighted-labeled.rst │ └── weighted-nodelabeled.rst ├── index.rst ├── installation.rst ├── make.bat ├── marginalized.rst ├── pycuda │ └── __init__.py ├── quickstart.rst └── rdkit │ └── __init__.py ├── example ├── active-learning.py ├── labeled-weighted.py ├── mcts.py ├── metric-maximin.py ├── molecular-2d.py ├── molecular-3d.py ├── nodelabeled-unweighted.py ├── nodelabeled-weighted.py ├── nystrom.py ├── perfbench │ ├── Makefile │ ├── molecule-cookie-cutter.py │ ├── pdb-3kDa-1324.json │ └── protein-time-to-solution.py ├── unlabeled-unweighted.py ├── variable-length-features.py └── vector-feature-dot-product.py ├── graphdot ├── __init__.py ├── codegen │ ├── __init__.py │ ├── cpptool.py │ ├── sympy_printer.py │ ├── template.py │ └── typetool.py ├── cpp │ ├── __init__.py │ ├── array.h │ ├── basekernel.h │ ├── basekernel │ │ ├── convolution.h │ │ ├── dotproduct.h │ │ └── normalize.h │ ├── fmath.h │ ├── frozen_array.h │ ├── graph.h │ ├── marginalized_kernel.h │ ├── metadbg.h │ ├── numpy_type.h │ ├── tensor_view.h │ └── util_cuda.h ├── cuda │ ├── __init__.py │ ├── array.py │ └── resizable_array.py ├── dataset │ ├── __init__.py │ ├── _get.py │ ├── qm7.py │ └── qm9.py ├── experimental │ ├── __init__.py │ ├── alterantive_mgk │ │ ├── __init__.py │ │ ├── _backend_cuda.py │ │ ├── _kernel.py │ │ └── template.cu │ └── metric │ │ ├── __init__.py │ │ └── m3.py ├── graph │ ├── __init__.py │ ├── _from_ase.py │ ├── _from_networkx.py │ ├── _from_pymatgen.py │ ├── _from_rdkit.py │ ├── _to_networkx.py │ ├── adjacency │ │ ├── __init__.py │ │ ├── atomic.py │ │ └── euclidean.py │ └── reorder │ │ ├── __init__.py │ │ ├── pbr │ │ ├── __init__.py │ │ ├── colnet_hypergraph.py │ │ ├── config.py │ │ ├── hypergraph.py │ │ └── mnom.py │ │ └── rcm.py ├── kernel │ ├── __init__.py │ ├── _kernel_over_metric.py │ ├── basekernel.py │ ├── fix.py │ ├── marginalized │ │ ├── __init__.py │ │ ├── _backend.py │ │ ├── _backend_cuda.py │ │ ├── _backend_factory.py │ │ ├── _kernel.py │ │ ├── _octilegraph.py │ │ ├── _scratch.py │ │ ├── basekernel.py │ │ ├── starting_probability.py │ │ └── template.cu │ ├── molecular.py │ └── rbf.py ├── linalg │ ├── __init__.py │ ├── block.py │ ├── cg.py │ ├── cholesky.py │ ├── low_rank.py │ └── spectral.py ├── metric │ ├── __init__.py │ ├── _kernel_induced.py │ └── maximin │ │ ├── __init__.py │ │ ├── _backend.cu │ │ ├── _backend_cuda.py │ │ └── _maximin.py ├── microkernel │ ├── __init__.py │ ├── _base.py │ ├── additive.py │ ├── composite.py │ ├── convolution.py │ ├── dotproduct.py │ ├── kronecker_delta.py │ ├── product.py │ ├── rational_quadratic.py │ ├── square_exponential.py │ └── tensor_product.py ├── minipandas │ ├── __init__.py │ ├── dataframe.py │ └── series.py ├── model │ ├── __init__.py │ ├── active_learning │ │ ├── __init__.py │ │ ├── determinant_maximizer.py │ │ ├── hierarchical_drafter.py │ │ └── variance_minimizer.py │ ├── gaussian_field │ │ ├── __init__.py │ │ ├── gfr.py │ │ └── weight.py │ ├── gaussian_process │ │ ├── __init__.py │ │ ├── base.py │ │ ├── gpr.py │ │ ├── nystrom.py │ │ └── outlier_detector.py │ └── tree_search │ │ ├── __init__.py │ │ ├── _rewriter.py │ │ ├── _tree.py │ │ └── graph_transformer.py └── util │ ├── __init__.py │ ├── cookie.py │ ├── iterable.py │ ├── pretty_tuple.py │ └── printer.py ├── requirements ├── common.txt ├── docs.txt ├── install-rdkit.md └── tests.txt ├── setup.py ├── test ├── codegen │ ├── test_cpptool.py │ ├── test_template.py │ ├── test_template.tpl │ └── test_typetool.py ├── cpp │ ├── Makefile │ ├── catch.cpp │ ├── catch.hpp │ └── marginalized │ │ └── catch_basekernel.cpp ├── cuda │ └── test_resizable_array.py ├── dataset │ ├── test_builtins.py │ ├── test_get.py │ ├── test_qm7.py │ └── test_qm9.py ├── experimental │ └── metric │ │ └── test_m3.py ├── graph │ ├── adjacency │ │ ├── test_atomic.py │ │ └── test_euclidean.py │ ├── reorder │ │ ├── test_pbr.py │ │ └── test_rcm.py │ ├── test_from_ase.py │ ├── test_from_rdkit.py │ ├── test_from_smiles.py │ ├── test_graph.py │ └── test_to_networkx.py ├── kernel │ ├── marginalized │ │ ├── test_backend_cuda.py │ │ ├── test_kernel.py │ │ ├── test_octilegraph.py │ │ └── test_scratch.py │ ├── test_decorator.py │ ├── test_kernel_over_metric.py │ ├── test_molecular.py │ └── test_rbf.py ├── linalg │ ├── test_block.py │ ├── test_low_rank.py │ └── test_spectral.py ├── metric │ ├── maximin │ │ └── test_maximin.py │ └── test_kernel_induced.py ├── microkernel │ └── test_microkernel.py ├── minipandas │ ├── test_dataframe.py │ └── test_series.py ├── model │ ├── active_learning │ │ ├── test_determinant_maximizer.py │ │ └── test_variance_minimizer.py │ ├── gaussian_field │ │ ├── test_gfr.py │ │ └── test_weight.py │ ├── gaussian_process │ │ ├── test_base.py │ │ ├── test_gpr.py │ │ ├── test_nystrom.py │ │ └── test_outlier_detector.py │ └── tree_search │ │ └── test_rewriter.py └── util │ ├── test_cookie.py │ ├── test_iterable.py │ ├── test_printer.py │ └── test_util.py └── tox.ini /.clang-format: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yhtang/GraphDot/HEAD/.clang-format -------------------------------------------------------------------------------- /.gitignore: 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