├── .editorconfig ├── .github └── ISSUE_TEMPLATE.md ├── .gitignore ├── .readthedocs.yml ├── .travis.yml ├── .worms_pytest_cache └── bblock │ ├── 0cdd70886d879ae8.pickle │ ├── 1050c3a0f82999c9.pickle │ ├── 1a4fd31ebf43a9a1.pickle │ ├── 1c059f43f25be586.pickle │ ├── 2fbb0c36e7330200.pickle │ ├── 3160fab08da5dfbe.pickle │ ├── 328ea93f7f721b49.pickle │ ├── 3415393d6862349b.pickle │ ├── 4c1926923fd82489.pickle │ ├── 5a1c14fceddeed73.pickle │ ├── 5cdcd30714d7995d.pickle │ ├── 60bb1bc102bd61cf.pickle │ ├── 66bb319d37dd8dc8.pickle │ └── 6e3355b62f3a8667.pickle ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── docs ├── Makefile ├── conf.py ├── contributing.rst ├── history.rst ├── img │ └── worms_triangle_600.png ├── index.rst ├── installation.rst ├── make.bat ├── modules.rst ├── readme.rst ├── usage.rst ├── worms.criteria.rst ├── worms.data.rst ├── worms.khash.rst └── worms.rst ├── environment.yml ├── examples ├── C3_2comp.config ├── C4_2comp.config ├── C5_1comp_het.config ├── build_worms_database.py ├── dihedral_layers │ ├── test_p3d3c3.flags │ ├── test_p4d2c4.flags │ ├── test_p4d4c2.flags │ ├── test_p4d4c4.flags │ ├── test_p6d2c3.flags │ ├── test_p6d2c6.flags │ ├── test_p6d3c2.flags │ └── test_p6d3c6.flags ├── filter_audit.py ├── flags │ ├── build_database.flags │ ├── database_2018_09.flags │ ├── database_will_laptop.flags │ ├── db_test.config │ ├── db_test.flags │ ├── test_Crystal_P213_C3_C3.flags │ ├── test_c3_NNN.flags │ ├── test_c3_c3_stack.flags │ ├── test_c3_small.flags │ ├── test_c3_tiny_CCN.flags │ ├── test_c3_tiny_CNC.flags │ ├── test_c5_N_CCC_NN_CCC.flags │ ├── test_c5_N_CN_CCC_NN_CCC.flags │ ├── test_cyclic_c5.flags │ ├── test_cyclic_c5_single.flags │ ├── test_d3.flags │ ├── test_donut.flags │ ├── test_sheet_p321.flags │ ├── test_sheet_p4212.flags │ ├── test_sheet_p6.flags │ └── test_sheet_p6m.flags ├── glumpy_points.py ├── glumpy_side_by_side.py ├── glumpy_trackball.py ├── mandelbrot.py ├── p213-test.py ├── peacemaker.py ├── plot3d.py ├── prefilter_test.py ├── pymol_cage.py ├── worms_cyclic_threechain.py ├── worms_example.py ├── worms_huge_test.py ├── worms_memory_test.py └── worms_peace_sign.py ├── requirements_dev.txt ├── requirements_rtd.txt ├── setup.cfg ├── setup.py ├── test_cases ├── clash_score0 │ ├── test.json │ └── test_wheel_c5_N_CCY_NNN_CCY_NNN.flags ├── dan_ellis │ ├── test.flags │ └── trihead_worms_setup.txt ├── pose_memory_leak.py ├── rubul_dups │ └── notes.txt └── yang_crown │ ├── C5_1comp_het.config │ ├── cache │ ├── bblock │ │ └── 7ba6d5d735ccbcfe.pickle │ ├── poses │ │ └── test_cases__yang_crown__Sh29_3_Sh29_3_DHR64_AB_C_0001_0006_Sh29_3_DHR71_BA_A_0001_0015.pdb.pickle │ └── splices │ │ └── 5ca73d84c6eb0f3e │ │ ├── 7ba6d5d735ccbcfe.pickle │ │ └── 7ba6d5d735ccbcfe_list.pickle │ ├── yang_crown.json │ ├── yang_crown_REORDER.json │ ├── yang_crown_goodcase.json │ └── yang_crown_goodcase_reversed.json ├── tox.ini ├── travis_pypi_setup.py ├── util ├── add_db_names.py ├── copy_baker_databases.sh ├── make_db_file.py ├── make_sphere_asym.py ├── rsync_worms_database.py ├── runtests.py ├── runtests_old.py └── tmp.py ├── worms.sublime-project └── worms ├── __init__.py ├── __main__.py ├── app ├── ._plug_from_oligomer.py ├── __init__.py ├── main.py └── plug_from_oligomer.py ├── bblock.py ├── clashgrid.py ├── cli.py ├── criteria ├── __init__.py ├── base.py ├── bounded.py ├── bridge.py ├── cyclic.py ├── dihedral_lattice.py ├── f222.py ├── fiber.py ├── hash_util.py ├── null.py ├── stack.py └── unbounded.py ├── data ├── 1coi.pdb ├── 1coi_A.pdb ├── 1coi_B.pdb ├── 1coi_C.pdb ├── 3uc7A.pdb ├── 3uc7A_clean.pdb ├── HBRP_Cx_database.json ├── HFuse_Cx_database.20180219.json ├── HFuse_het_2chain_2arm_database.ZCON-103_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-112_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-127_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-13_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-15_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-34_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-37_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-39_2.20180406.json ├── HFuse_het_2chain_2arm_database.ZCON-9_2.20180406.json ├── HFuse_het_3chain_2arm_database.Sh13_3.20180406.json ├── HFuse_het_3chain_2arm_database.Sh13_3.20180416.json ├── HFuse_het_3chain_2arm_database.Sh29_3.20180406.json ├── HFuse_het_3chain_2arm_database.Sh29_3.20180416.json ├── HFuse_het_3chain_2arm_database.Sh34_3.20180416.json ├── HFuse_het_3chain_2arm_database.Sh3e_3.20180406.json ├── HFuse_het_3chain_3arm_database.Sh13_3.20180406.json ├── HFuse_het_3chain_3arm_database.Sh13_3.20180416.json ├── HFuse_het_3chain_3arm_database.Sh29_3.20180406.json ├── HFuse_het_3chain_3arm_database.Sh29_3.20180416.json ├── HFuse_het_3chain_3arm_database.Sh34_3.20180416.json ├── HFuse_het_3chain_3arm_database.Sh3e_3.20180406.json ├── __init__.py ├── buildingblock_list_dihedrals2.txt ├── c1.pdb ├── c2.pdb ├── c3.pdb ├── c3_splay.pdb ├── c3het.pdb ├── c4.pdb ├── c5.pdb ├── c6.pdb ├── c6_database.json ├── curved_helix.pdb ├── db_asu.pdb ├── default.sc ├── fullsize1.pdb ├── fullsize2.pdb ├── hetC2A.pdb ├── hetC2B.pdb ├── loop.pdb ├── master_database_generation2.json ├── repeat_1_2.json ├── repeat_helix_1_2.json ├── small.pdb ├── sphere.py ├── sphere │ ├── sphere_0.966_17282.pickle │ ├── sphere_ics_asu.pickle │ ├── sphere_oct_asu.pickle │ └── sphere_tet_asu.pickle ├── strand.pdb ├── test_db_file.json ├── test_fullsize_prots.json └── wheel │ ├── 1BH_69.pdb │ ├── 3L6HC2-4_2_asu_DHR64_BA_0001_0002.pdb │ ├── 6H2LD-8_6_asu_DHR64_BA_0001_0001.pdb │ ├── Sh13_3_Sh13_3_DHR04_BA_C_0001_Sh13_3_DHR10_BA_A_0001_0001.pdb │ ├── Sh13_3_Sh13_3_DHR04_BA_C_0001_Sh13_3_DHR10_BA_A_0001_0002.pdb │ ├── Sh13_3_Sh13_3_DHR04_BA_C_0001_Sh13_3_DHR49_BA_A_0001_0003.pdb │ ├── Sh13_h1BH09A_h1BH23C.pdb │ ├── Sh13_h1BH24A_h1BH23C.pdb │ ├── Sh13_pqk06B_h1BH23C.pdb │ ├── h1BH09_pqk06_h1BH16_Sh13ABC.pdb │ ├── manual_test.sh │ ├── manual_test_setup.sh │ ├── test_c2.flags │ ├── test_c3.flags │ ├── test_c6.flags │ ├── wheel_c2.json │ ├── wheel_c3.json │ └── wheel_c6.json ├── database.py ├── edge.py ├── edge_batch.py ├── filters ├── ._clash.py ├── alignment_validator.py ├── clash.py ├── contact_analyzer.py ├── db_filters.py ├── geometry.py ├── interface_contacts.py └── pack_filters.py ├── khash ├── __init__.py ├── khash.h ├── khash_cffi.py └── khash_int2int.h ├── merge ├── concat.py └── wye.py ├── output.py ├── pose_contortions.py ├── rosetta_symdef ├── C10.sym ├── C11.sym ├── C12.sym ├── C13.sym ├── C14.sym ├── C15.sym ├── C16.sym ├── C17.sym ├── C18.sym ├── C19.sym ├── C2.sym ├── C20.sym ├── C21.sym ├── C22.sym ├── C23.sym ├── C24.sym ├── C25.sym ├── C26.sym ├── C27.sym ├── C28.sym ├── C29.sym ├── C3.sym ├── C30.sym ├── C31.sym ├── C32.sym ├── C33.sym ├── C34.sym ├── C35.sym ├── C36.sym ├── C37.sym ├── C38.sym ├── C39.sym ├── C4.sym ├── C40.sym ├── C41.sym ├── C42.sym ├── C43.sym ├── C44.sym ├── C45.sym ├── C46.sym ├── C47.sym ├── C48.sym ├── C49.sym ├── C5.sym ├── C50.sym ├── C51.sym ├── C52.sym ├── C53.sym ├── C54.sym ├── C55.sym ├── C56.sym ├── C57.sym ├── C58.sym ├── C59.sym ├── C6.sym ├── C60.sym ├── C61.sym ├── C62.sym ├── C63.sym ├── C64.sym ├── C65.sym ├── C66.sym ├── C67.sym ├── C68.sym ├── C69.sym ├── C7.sym ├── C70.sym ├── C71.sym ├── C72.sym ├── C73.sym ├── C74.sym ├── C75.sym ├── C76.sym ├── C77.sym ├── C78.sym ├── C79.sym ├── C8.sym ├── C80.sym ├── C81.sym ├── C82.sym ├── C83.sym ├── C84.sym ├── C85.sym ├── C86.sym ├── C87.sym ├── C88.sym ├── C89.sym ├── C9.sym ├── C90.sym ├── C91.sym ├── C92.sym ├── C93.sym ├── C94.sym ├── C95.sym ├── C96.sym ├── C97.sym ├── C98.sym ├── C99.sym ├── Crystal_P213_C3_C3_depth2_1comp.sym ├── Crystal_P213_C3_C3_depth3_1comp.sym ├── Crystal_P213_C3_C3_depth3_2comp.sym ├── Crystal_P213_C3_C3_depth8_1comp.sym ├── Crystal_P213_C3_C3_depth8_2comp.sym ├── D2.sym ├── D3.sym ├── D4.sym ├── D5.sym ├── D6.sym ├── D7.sym ├── D8.sym ├── F222_D2_D2_3.sym ├── F23_T_C2_depth2_1comp.sym ├── F23_T_C3_depth2_1comp.sym ├── F23_T_T_depth2_1comp.sym ├── I.sym ├── O.sym ├── P2m_D2_C2_4.sym ├── P3m_D3_C3_3.sym ├── P432_D4_C3_2.sym ├── P4m_D2_C4_4.sym ├── P4m_D4_C2_3.sym ├── P4m_D4_C4_3.sym ├── P6m_D2_C3_4.sym ├── P6m_D2_C6_3.sym ├── P6m_D3_C2_4.sym ├── P6m_D3_C6_3.sym ├── Sheet_P321_C3_C2_depth3_1comp.sym ├── Sheet_P321_C3_C2_depth3_2comp.sym ├── Sheet_P321_C3_C2_depth6_1comp.sym ├── Sheet_P321_C3_C2_depth6_2comp.sym ├── Sheet_P331_C3_C3_depth4_1comp.sym ├── Sheet_P331_C3_C3_depth4_2comp.sym ├── Sheet_P4212_C4_C2_depth3_1comp.sym ├── Sheet_P4212_C4_C2_depth3_2comp.sym ├── Sheet_P6_C6_C2_depth3_1comp.sym ├── Sheet_P6_C6_C2_depth3_2comp.sym └── T.sym ├── search ├── ._result.py ├── __init__.py ├── linear.py ├── old_search.py └── result.py ├── segments.py ├── ssdag.py ├── ssdag_pose.py ├── tests ├── __init__.py ├── conftest.py ├── criteria │ ├── __init__.py │ ├── test_base.py │ ├── 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