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<li><ahref="GOFEE/GOFEE.html#candidate_operations.candidate_generation.CandidateGenerator">CandidateGenerator (class in candidate_operations.candidate_generation)</a>
<li><ahref="GOFEE/GOFEE.html#candidate_operations.basic_mutations.PermutationMutation">PermutationMutation (class in candidate_operations.basic_mutations)</a>
<li><ahref="GOFEE/GOFEE.html#candidate_operations.candidate_generation.StartGenerator">StartGenerator (class in candidate_operations.candidate_generation)</a>
<liclass="toctree-l2"><aclass="reference internal"href="tutorial/tio_clusters/tio_clusters.html">Searching for TiO clusters</a></li>
<liclass="toctree-l2"><aclass="reference internal"href="tutorial/tio2_reconstruction/tio2_reconstruction.html">Searching for the TiO2(001)-(1x4) reconstruction</a></li>
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