Cpp mol2db2

[bwhall61]

Adds a c++ version of mol2db2 which speeds up the creation of the db2 files by ~5-10x in my testing on DUDE-Z

Trent did most of the conversion to c++ with claude. I went and changed a few things mostly to get strain working and to have algorithmic parity with some of the functions that we used in mol2db2_py3_strain

[jir322]

awesome! John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu

…

On Tue, Feb 24, 2026 at 1:26 PM bwhall61 ***@***.***> wrote: Adds a c++ version of mol2db2 which speeds up the creation of the db2 files by ~5-10x in my testing on DUDE-Z Trent did most of the conversion to c++ with claude. I went and changed a few things mostly to get strain working and to have algorithmic parity with some of the functions that we used in mol2db2_py3_strain ------------------------------ You can view, comment on, or merge this pull request online at: #5 Commit Summary - 279b554 <279b554> Fix first input tautomer issue - 14ca5d0 <14ca5d0> Fixes to db2tomol2 - 9265027 <9265027> Add mol2db2 cpp version - 91f9f40 <91f9f40> Convert build_ligands to c++ mol2db2 File Changes (57 files <https://github.com/docking-org/zinc22-3d/pull/5/files>) - *M* .gitignore <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-bc37d034bad564583790a46f19d807abfe519c5671395fd494d8cce506c42947> (2) - *M* db22mol2/db2_to_mol2.py <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-b185ca2a75d1abe4e41a2d653ae6ebb9a6b6a648efd9544305b48eeea7fa9d76> (4) - *M* db22mol2/mol2.py <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-08bc8011625d9a8b46ed526442faf36eaeb49a39f1c39ad3d62757c2cfcbe65c> (238) - *M* generate/build_ligands_docker.py <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-5de5978780d0e4ad2268fa6c0c85797297bb1ce29aa37b1219e46cb2c26143ad> (12) - *A* mol2db2_cpp_strain/Makefile <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-10dfd26ebb5ddf6495bd8c257ac81e6c271d549d6acd64e89a152ef466a3ec65> (140) - *A* mol2db2_cpp_strain/README.txt <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-dd81f2d17f1f637a7adb09ef582b91e69edf2f16997b053e4438e39d7311451f> (263) - *A* mol2db2_cpp_strain/bin/mol2db2 <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-e5d185a76e567f52feec776cbea19aefec107ba51b552443b783f94244d82b91> (0) - *A* mol2db2_cpp_strain/build/buckets.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-fb6bec4314f1c4696c3b635fe4cceb241c437b2eb962f533182bef24dc38a0db> (0) - *A* mol2db2_cpp_strain/build/buckets2.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-d47cd7a3c6529f5d488b34351ff81ae78fb4b2bab361253c774cb74d8e4ac539> (0) - *A* mol2db2_cpp_strain/build/clash.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-d9a9fd90158b426814d398e785f04e389cff6251920bc9fcb0dc439737f86d5e> (0) - *A* mol2db2_cpp_strain/build/divisive_clustering.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-cb521fe52e6c0603fc01d469c00b025d34120a35e7507f5cdc1c5d77c280a5d1> (0) - *A* mol2db2_cpp_strain/build/floydwarshall.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-a8d385336c8dc095be01dd3a84f0cbeb728cd4e6551be4ea3470ea0bb9576fe7> (0) - *A* mol2db2_cpp_strain/build/geometry.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-3f5aace8de1b509c0b93472e32f6dfa3cdb425eb3c2edfe247bdf5ed8c809754> (0) - *A* mol2db2_cpp_strain/build/hierarchy.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-5885d723ce4d0fa6ba6c0a115b8b8ac464ad74e33af93c448c5f791a81914f85> (0) - *A* mol2db2_cpp_strain/build/hydrogens.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-3df0edf26a3ed80e06ba2c775d5dc8aabab4f7e5c31a5ed9410985d7a5813ddd> (0) - *A* mol2db2_cpp_strain/build/mol2.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-8d117e2ce0b4c391ff4a1a3c2f4060bd6e09025fb9d85830f6926ccb2ad097f0> (0) - *A* mol2db2_cpp_strain/build/mol2db2.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-4dcd652e3e7ac98bc21fa696175468f680fa92d52c14befec85815665bf537f6> (0) - *A* mol2db2_cpp_strain/build/pca.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-9d9e1c07c8f673f5e1e1660af6e6526c8ee719da8c229d096f3987d603ec7d6c> (0) - *A* mol2db2_cpp_strain/build/shortestpaths.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-160c2142d41c16918d841e83ff91861b9617243d3842ff568a692045b5c762f6> (0) - *A* mol2db2_cpp_strain/build/unionfind.o <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-2f5623736c41d6f4333ee73143942477444fd6fce5620e98c66e7c2d6980e3a5> (0) - *A* mol2db2_cpp_strain/get_eigen_library.sh <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-de8b8efc98f44a4c045edcfc4a293ca5fa910da81b91ed531c992406059598f6> (38) - *A* mol2db2_cpp_strain/mol2.py <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-6e4427f187f37fa8f4d60e112d36f8fa0b94aa9c3c7dd14887f65e3d8c0ba214> (790) - *A* mol2db2_cpp_strain/pdfs/Complete Setup Guide.pdf <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-598d1dcabb0cd9b91de302b10a5f9075c812a9c80f7e256bad396881e5ededa8> (0) - *A* mol2db2_cpp_strain/pdfs/FINAL PACKAGE - Complete File List & Instructions.pdf <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-818b7a0f63a1dadd7b9253ad48ea853bb18821da15875deac3ac5da45a65f7ef> (0) - *A* mol2db2_cpp_strain/pdfs/README.md.pdf <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-825008242e0bce54a09345aadbc6eff952789abe263fd71eeb390d59b24cb6d0> (0) - *A* mol2db2_cpp_strain/quick_setup_script.sh <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-2ae22fc0dd331b508f304530e26d9cc1026ef9d4e3875b8bde1fa7c7845fdc0c> (213) - *A* mol2db2_cpp_strain/src/algorithms/buckets.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-7288cd4ac9f1014eebf1207f3118af625d637f7d9767098b957823164e6cf448> (176) - *A* mol2db2_cpp_strain/src/algorithms/buckets.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-de966e43434b3ed9038fdb3c98f97bdd4cf487f09b9b3c4494edb2349fb12fbc> (53) - *A* mol2db2_cpp_strain/src/algorithms/buckets2.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-790717fd31de9e0ae31390a9d90b955b3e55d4a4d9d050d7dbd66c130e0aae93> (90) - *A* mol2db2_cpp_strain/src/algorithms/buckets2.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-ba62f76d6ac26323e0f78141ca64bc6653e82a782d1e425f357b0aba5218962c> (72) - *A* mol2db2_cpp_strain/src/algorithms/divisive_clustering.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-b459aab237080ea53ac9156d1479a23fdc447f3138b28466b8b7a5c07614e12d> (141) - *A* mol2db2_cpp_strain/src/algorithms/divisive_clustering.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-16795fe898c067ef8e9969c70074d26110722621cfbaf6c0b77959fe7c166c13> (61) - *A* mol2db2_cpp_strain/src/algorithms/floydwarshall.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-6cc918c1894ac58db97698055478071a811da6520cb866aa5950f32c5b46ce55> (65) - *A* mol2db2_cpp_strain/src/algorithms/floydwarshall.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-b6ac168ed1c5260894469894d71ed25245ac1c6e594cf6d0c5c50ecab5f1dc65> (24) - *A* mol2db2_cpp_strain/src/algorithms/pca.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-ada59500141cd5daa22456b9bf1d6a15b5ece0773a79e5c2a4df2d63ac1c97ba> (372) - *A* mol2db2_cpp_strain/src/algorithms/pca.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-6107c62dc613072b8b20b67ea63ef7b30d88d052df798074d8e391056b11478d> (63) - *A* mol2db2_cpp_strain/src/algorithms/shortestpaths.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-ab3d3417505ae5e7571c644b4f2adb3310f84e797fab397e003b2902e5d173ae> (54) - *A* mol2db2_cpp_strain/src/algorithms/shortestpaths.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-d0ac76d855fdde9d97b030b13faadfba942bcc8cd95a99be1240067ebfa484e9> (30) - *A* mol2db2_cpp_strain/src/core/combinatorics.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-ac055de86320a7eb4614ebe834306c6abf25d11910d2b3b614efa0818ec60522> (45) - *A* mol2db2_cpp_strain/src/core/geometry.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-4b1f8fbab9c93802e0018ca192974134792038a3b941e373fefe595b399f173e> (628) - *A* mol2db2_cpp_strain/src/core/geometry.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-c4c31790cd9731a9cf48c9d40594f4b804206223b569476b6ea9a7b8121944e1> (127) - *A* mol2db2_cpp_strain/src/core/priodict.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-528e3663b7e5bd6b56a01e21f109da81f8704331b2b5bbb3b1a6f78bf74e7635> (196) - *A* mol2db2_cpp_strain/src/core/unionfind.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-97029e7af0ee8236d4aee862d0d8ed45b10cb0c3e4924dfb29df5b1ef8083667> (182) - *A* mol2db2_cpp_strain/src/core/unionfind.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-acd415f4897e939443cb2db480ce658649bf056218d904ff050110f7e573937a> (74) - *A* mol2db2_cpp_strain/src/hierarchy/hierarchy.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-01f32e90b1e1bec994776adb2993bf91cee7ba2e146e48a34c425e47b26175bb> (615) - 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*A* mol2db2_cpp_strain/src/molecular/mol2.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-af800bfdfb9e4bd1f065634847c3fdc4f642f17b120181c20a9eadce75b80576> (1418) - *A* mol2db2_cpp_strain/src/molecular/mol2.h <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-7028ec3fbff51a6274b3e9ca75ae7f1db31e8fcbdc37b10a43e11f2e8832be0e> (229) - *A* mol2db2_cpp_strain/tests/test_geometry.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-9476d1133706303d8ff2b38495da47556928fe5558afb354a43c23d57260fe3e> (117) - *A* mol2db2_cpp_strain/tests/test_mol2.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-8a1b87ecd801a093a52d2c26e93e56a687838c57379adeb6bf5bc2de566a886e> (227) - *A* mol2db2_cpp_strain/tests/test_unionfind.cpp <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-d8f5b2ec724931b95b9689fc7c2f92a163fbcb210febd6bd6961c06d553e40b2> (186) - *M* protonate/tautprot_cxcalc.sh <https://github.com/docking-org/zinc22-3d/pull/5/files#diff-db9a6e5c12d87817e7517c1bc0da625b5eaddb102653a19e3ffe6d1c0941e6e0> (31) Patch Links: - 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