0000000000000000000000000000000000000000 4162d53107d001f3db2f0be8159ba4d8092ca0bf uroehrig <ute.roehrig@sib.swiss> 1710246698 +0100	clone: from https://gitlab.sib.swiss/uroehrig/attracting_cavities_charmm_python/
4162d53107d001f3db2f0be8159ba4d8092ca0bf 9447af396db17b1a0e10ec2afbc9c0f839bd51db uroehrig <ute.roehrig@sib.swiss> 1710333447 +0100	pull: Fast-forward
9447af396db17b1a0e10ec2afbc9c0f839bd51db 91510b91bfef7dfe81f610ca3284b0133cca25f5 uroehrig <ute.roehrig@sib.swiss> 1710347504 +0100	pull: Fast-forward
91510b91bfef7dfe81f610ca3284b0133cca25f5 344fbf38b64905ea8a96835c3b88e2f709f65e45 uroehrig <ute.roehrig@sib.swiss> 1710412125 +0100	pull: Fast-forward
344fbf38b64905ea8a96835c3b88e2f709f65e45 e44755eb106f40f747cb193ec40a9468a9fa1f2e uroehrig <ute.roehrig@sib.swiss> 1710418468 +0100	checkout: moving from ac_qmmm_ute_work_5 to master
e44755eb106f40f747cb193ec40a9468a9fa1f2e 33211c1b7f1541156447d03c6a6f998b899387dc uroehrig <ute.roehrig@sib.swiss> 1710418490 +0100	merge ac_qmmm_ute_work_5: Merge made by the 'recursive' strategy.
33211c1b7f1541156447d03c6a6f998b899387dc 33211c1b7f1541156447d03c6a6f998b899387dc uroehrig <ute.roehrig@sib.swiss> 1710425887 +0100	checkout: moving from master to ute_work_6
33211c1b7f1541156447d03c6a6f998b899387dc 33211c1b7f1541156447d03c6a6f998b899387dc uroehrig <ute.roehrig@sib.swiss> 1710427141 +0100	checkout: moving from ute_work_6 to master
33211c1b7f1541156447d03c6a6f998b899387dc a784edfc992fa2cd0225a6d85026f42e179c5e30 uroehrig <ute.roehrig@sib.swiss> 1710428984 +0100	commit: improve input and small fixes
a784edfc992fa2cd0225a6d85026f42e179c5e30 33211c1b7f1541156447d03c6a6f998b899387dc uroehrig <ute.roehrig@sib.swiss> 1710429027 +0100	checkout: moving from master to ute_work_6
33211c1b7f1541156447d03c6a6f998b899387dc a784edfc992fa2cd0225a6d85026f42e179c5e30 uroehrig <ute.roehrig@sib.swiss> 1710429089 +0100	rebase: checkout master
a784edfc992fa2cd0225a6d85026f42e179c5e30 a784edfc992fa2cd0225a6d85026f42e179c5e30 uroehrig <ute.roehrig@sib.swiss> 1710429089 +0100	rebase finished: refs/heads/ute_work_6 onto a784edfc992fa2cd0225a6d85026f42e179c5e30
a784edfc992fa2cd0225a6d85026f42e179c5e30 39c258943c1738cccc84809b64dcad2f54eb2609 uroehrig <ute.roehrig@sib.swiss> 1710515787 +0100	commit: small changes
39c258943c1738cccc84809b64dcad2f54eb2609 513ec8dc0aa89c5a9ff3347fad336953671d7e58 uroehrig <ute.roehrig@sib.swiss> 1710920589 +0100	commit: small changes
513ec8dc0aa89c5a9ff3347fad336953671d7e58 513ec8dc0aa89c5a9ff3347fad336953671d7e58 uroehrig <ute.roehrig@sib.swiss> 1710920726 +0100	checkout: moving from ute_work_6 to ute_work_6
513ec8dc0aa89c5a9ff3347fad336953671d7e58 76e6b4f656b270dec8d4989e02608307fbc9620a uroehrig <ute.roehrig@sib.swiss> 1710920737 +0100	merge remotes/origin/ac_qmmm_ute_work_5: Merge made by the 'recursive' strategy.
76e6b4f656b270dec8d4989e02608307fbc9620a 38e28992bfbaaa84440839ef4dccafe295ba60d4 uroehrig <ute.roehrig@sib.swiss> 1712836270 +0200	merge remotes/origin/ac_qmmm_ute_work_5: Merge made by the 'recursive' strategy.
38e28992bfbaaa84440839ef4dccafe295ba60d4 e16aa2bb2c9261f0b002ab74299e4a2a7ce70217 uroehrig <ute.roehrig@sib.swiss> 1712846838 +0200	commit: very small changes
e16aa2bb2c9261f0b002ab74299e4a2a7ce70217 e08a9f96931009c6ab255f2e1d40abaecbe147c6 uroehrig <ute.roehrig@sib.swiss> 1712846974 +0200	commit (merge): fix merge
e08a9f96931009c6ab255f2e1d40abaecbe147c6 4098854880aad7aa944b61c30c23b7a6505d4309 uroehrig <ute.roehrig@sib.swiss> 1713185089 +0200	commit: small changes and fix qm-env for testing
4098854880aad7aa944b61c30c23b7a6505d4309 fd21660f95e0bfe9ee92d3696b6bc2eac8dc054c uroehrig <ute.roehrig@sib.swiss> 1713370651 +0200	commit: started implementation of cutting receptor
fd21660f95e0bfe9ee92d3696b6bc2eac8dc054c 0522d8b080d6cfe5b5de29b69de44bb12126cc4e uroehrig <ute.roehrig@sib.swiss> 1713520785 +0200	commit: implemented receptor box
0522d8b080d6cfe5b5de29b69de44bb12126cc4e be02728bf74c690609dae59f9ae41a03e28740a2 uroehrig <ute.roehrig@sib.swiss> 1714573917 +0200	commit: modified receptor cutting
be02728bf74c690609dae59f9ae41a03e28740a2 98c65a0e71d57e7e4454b91622a9a88385407d17 uroehrig <ute.roehrig@sib.swiss> 1714632548 +0200	commit: change path back
98c65a0e71d57e7e4454b91622a9a88385407d17 401648c158532ea66a7ca86e04add26def362d35 uroehrig <ute.roehrig@sib.swiss> 1714744806 +0200	commit: fixed receptor_box file naming
401648c158532ea66a7ca86e04add26def362d35 9cc763f022e0950b44b70cd470601b9d990508b4 uroehrig <ute.roehrig@sib.swiss> 1715790283 +0200	commit: fixed scoring when using receptor_box
9cc763f022e0950b44b70cd470601b9d990508b4 b056e5ac332c93e16c97d20d69d64bd56c6b2514 uroehrig <ute.roehrig@sib.swiss> 1716294089 +0200	commit: small fixes
b056e5ac332c93e16c97d20d69d64bd56c6b2514 c5eed9e7471422700df69d940c1c5c0c248c7596 uroehrig <ute.roehrig@sib.swiss> 1716395701 +0200	commit: check initial coordinates
c5eed9e7471422700df69d940c1c5c0c248c7596 b6ed9a20a39bb9e734f7dfbf2c427411b1b053c0 uroehrig <ute.roehrig@sib.swiss> 1716457181 +0200	commit: small bug fix
b6ed9a20a39bb9e734f7dfbf2c427411b1b053c0 fc58deffec6def50d032cbd386654cdfd3cf8cc5 uroehrig <ute.roehrig@sib.swiss> 1719934851 +0200	commit: implemented possibility to dock heme and other residues from charmm ff
fc58deffec6def50d032cbd386654cdfd3cf8cc5 f389a6b49d8b88cc87a93c7b08cd4de79e3431eb uroehrig <ute.roehrig@sib.swiss> 1720021789 +0200	commit: small fixes
f389a6b49d8b88cc87a93c7b08cd4de79e3431eb 0810f5a260675f068e5b26d71a8650a10fbfdd72 uroehrig <ute.roehrig@sib.swiss> 1722869657 +0200	commit: started implementation of clustering with spyrmsd
0810f5a260675f068e5b26d71a8650a10fbfdd72 7b580e1beb64ca232458e00c945905a93eeeb84f uroehrig <ute.roehrig@sib.swiss> 1722953192 +0200	commit: modified clustering
7b580e1beb64ca232458e00c945905a93eeeb84f dcebbfbeac0cf3289cc2c910232b6099b18a51ef uroehrig <ute.roehrig@sib.swiss> 1722963255 +0200	commit: fixed dock4 pose order
dcebbfbeac0cf3289cc2c910232b6099b18a51ef 72cb920a9ac07bee2d88dffe35f6cd767185d980 uroehrig <ute.roehrig@sib.swiss> 1723025626 +0200	commit: bug fix in clustering
72cb920a9ac07bee2d88dffe35f6cd767185d980 15971f7420489cf4ac80b7a66ef6ae604d32f47c uroehrig <ute.roehrig@sib.swiss> 1723041720 +0200	commit: small bug fix
15971f7420489cf4ac80b7a66ef6ae604d32f47c c5da02e1a0f7ce77a8d1083b1e200ea58ed60054 uroehrig <ute.roehrig@sib.swiss> 1723104327 +0200	commit: small changes for benchmarking
c5da02e1a0f7ce77a8d1083b1e200ea58ed60054 47f0a94dccb427b4c31859027f5ed50e77e1fa20 uroehrig <ute.roehrig@sib.swiss> 1723130144 +0200	commit: test in clustering
47f0a94dccb427b4c31859027f5ed50e77e1fa20 f3e43e541428dd66138836433e8f4ffa0badd19c uroehrig <ute.roehrig@sib.swiss> 1723195149 +0200	commit: fixed bug in clash detection
f3e43e541428dd66138836433e8f4ffa0badd19c 031bb14664fe6c29914682aa010b96b76e52abec uroehrig <ute.roehrig@sib.swiss> 1723212217 +0200	commit: small change in cluster
031bb14664fe6c29914682aa010b96b76e52abec 859e5dfed9525d764b7e2772dab3e7f3800463c9 uroehrig <ute.roehrig@sib.swiss> 1723217038 +0200	commit: small fix in clustering
859e5dfed9525d764b7e2772dab3e7f3800463c9 eed43c777d7991410e5c29aa2022db61e9d850dd uroehrig <ute.roehrig@sib.swiss> 1723455286 +0200	commit: small mods
eed43c777d7991410e5c29aa2022db61e9d850dd b5c7238b8ee6cf00df771ce62a82f6ac3b5aca0c uroehrig <ute.roehrig@sib.swiss> 1723652630 +0200	commit: started to change facts+scoring logic - not yet working for cov
b5c7238b8ee6cf00df771ce62a82f6ac3b5aca0c ae634d89beb988230a32907dfd6de8c2043d4f34 uroehrig <ute.roehrig@sib.swiss> 1723735555 +0200	commit: fixed many remaining issues
ae634d89beb988230a32907dfd6de8c2043d4f34 5bc2646797e14b98cd6ff5380419a0dc6d7e944b uroehrig <ute.roehrig@sib.swiss> 1723814942 +0200	commit: finished implementing changes in code structure
5bc2646797e14b98cd6ff5380419a0dc6d7e944b 940d5ff5c2ee5cbad9cc7d800f05e9e49d84cddc uroehrig <ute.roehrig@sib.swiss> 1724832519 +0200	commit: fixes for rescoring+flex
940d5ff5c2ee5cbad9cc7d800f05e9e49d84cddc f4e9149f1a1dbc5aa9fdeebfc4f25203e435e56f uroehrig <ute.roehrig@sib.swiss> 1724852109 +0200	commit: fix flex rescoring
f4e9149f1a1dbc5aa9fdeebfc4f25203e435e56f 0ef155c6f31370ec032d15c7e2feb731e764a76e uroehrig <ute.roehrig@sib.swiss> 1724929426 +0200	commit: readme
0ef155c6f31370ec032d15c7e2feb731e764a76e 471c68cba97298b3d6c74d6344655e00036cbe3c uroehrig <ute.roehrig@sib.swiss> 1725548739 +0200	commit: continue implementation of docking ligands with more than 4-letter name
471c68cba97298b3d6c74d6344655e00036cbe3c e5cf5d1ee87097f3501e303f6284b5346dafd61d uroehrig <ute.roehrig@sib.swiss> 1725634577 +0200	commit: trying to solve offset issues, not yet finished
e5cf5d1ee87097f3501e303f6284b5346dafd61d 18e2c5508fc7a8c8902ec7c985ae6d5411030bda uroehrig <ute.roehrig@sib.swiss> 1725891082 +0200	commit: fix resno/resid of ligand when reading from pdb/crd
18e2c5508fc7a8c8902ec7c985ae6d5411030bda 839df28645bdeeb0bd1883852f4e2d9d3944c78f uroehrig <ute.roehrig@sib.swiss> 1725949689 +0200	commit: some cleaning
839df28645bdeeb0bd1883852f4e2d9d3944c78f 38329c4bc2f70bd3adc9e6b026c99fffad260cbe uroehrig <ute.roehrig@sib.swiss> 1726054478 +0200	pull: Fast-forward
38329c4bc2f70bd3adc9e6b026c99fffad260cbe f8c5936f81b016fc7b6b6174b10836c94e7297e8 uroehrig <ute.roehrig@sib.swiss> 1726154157 +0200	commit: small fixes
f8c5936f81b016fc7b6b6174b10836c94e7297e8 b73fd7a4433e02f3eea594092aa5f9dabf871768 uroehrig <ute.roehrig@sib.swiss> 1727282881 +0200	commit: started implementing i/o of dcd files
b73fd7a4433e02f3eea594092aa5f9dabf871768 2f5b22538d70dcf1b3b9d59100817a52c19818f1 uroehrig <ute.roehrig@sib.swiss> 1727364081 +0200	commit: develop dcd i/o
2f5b22538d70dcf1b3b9d59100817a52c19818f1 2aff7c63e0ddb99ab28843460bd3c66fec23b1ee uroehrig <ute.roehrig@sib.swiss> 1727448517 +0200	commit: further dcd development
2aff7c63e0ddb99ab28843460bd3c66fec23b1ee 54face96b358b748467cab5796c3c6b6de7fcd96 uroehrig <ute.roehrig@sib.swiss> 1727704169 +0200	commit: cont dcd implementation
54face96b358b748467cab5796c3c6b6de7fcd96 befc4560105113c30b23619f070871d4565119a7 uroehrig <ute.roehrig@sib.swiss> 1728578304 +0200	commit: cont dcd implementation
befc4560105113c30b23619f070871d4565119a7 e64acbca44b3c8fd25f68fc993d1e442e80a1f43 uroehrig <ute.roehrig@sib.swiss> 1728656839 +0200	commit: dcd working for simple case
e64acbca44b3c8fd25f68fc993d1e442e80a1f43 f4502fcfd2e0ce518d1b0ecb3c6ee468670cc2b1 uroehrig <ute.roehrig@sib.swiss> 1729610998 +0200	commit: working on dcd files
f4502fcfd2e0ce518d1b0ecb3c6ee468670cc2b1 acd16a8da477c6a90001df8cc339a664beb323a9 uroehrig <ute.roehrig@sib.swiss> 1729782886 +0200	commit: working on file ordering in dcd output
acd16a8da477c6a90001df8cc339a664beb323a9 3b95f48c7013bc76057db5a5404b488b52785fb2 uroehrig <ute.roehrig@sib.swiss> 1729870353 +0200	commit: adapted start and relax0 to dcd
3b95f48c7013bc76057db5a5404b488b52785fb2 2dffdde86f1928ad673b5d1444a674f3ccbbd8ea uroehrig <ute.roehrig@sib.swiss> 1730218021 +0100	commit: fixing dcd for rescoring and receptor_box
2dffdde86f1928ad673b5d1444a674f3ccbbd8ea 40bfe7edbc1c0f3beb86a34df1844c0d6b659f08 uroehrig <ute.roehrig@sib.swiss> 1730285119 +0100	commit: fixing cov/dcd
40bfe7edbc1c0f3beb86a34df1844c0d6b659f08 b8fc3edbc80302642eaf9a117bf3f4ea818e683e uroehrig <ute.roehrig@sib.swiss> 1730310659 +0100	commit: working on dcd/cov
b8fc3edbc80302642eaf9a117bf3f4ea818e683e 89d29e78cbee34403a13b6dcdeee3e5e244ffe2b uroehrig <ute.roehrig@sib.swiss> 1730390882 +0100	commit: change from dcd to mult-pdb files
89d29e78cbee34403a13b6dcdeee3e5e244ffe2b 6c9be369e30ace736eb400af334847319d73449b uroehrig <ute.roehrig@sib.swiss> 1730477131 +0100	commit: fix cov dock with mult pdb files
6c9be369e30ace736eb400af334847319d73449b 828d1505e351f056ecff61a5b18f5010e953db4d uroehrig <ute.roehrig@sib.swiss> 1730736942 +0100	commit: work on rescoring
828d1505e351f056ecff61a5b18f5010e953db4d 9ff03bf45b07e1322f4749d76e5ca1beb94cb1a2 uroehrig <ute.roehrig@sib.swiss> 1730824125 +0100	commit: fixed trj for cov/rescoring/flex/receptor_box
9ff03bf45b07e1322f4749d76e5ca1beb94cb1a2 fca746e7d3f9b8fda7ad06e2d79573259cd2fa1d uroehrig <ute.roehrig@sib.swiss> 1730912649 +0100	commit: parallel/trj working now
fca746e7d3f9b8fda7ad06e2d79573259cd2fa1d 0c1a40193d139f378b3dc7be82c3c6d9849dbf52 uroehrig <ute.roehrig@sib.swiss> 1730978027 +0100	commit: fixed rescoring/trj
0c1a40193d139f378b3dc7be82c3c6d9849dbf52 ff4b317a86ea65ad0e3aebf8bdcacc7c7352f882 uroehrig <ute.roehrig@sib.swiss> 1731514169 +0100	commit: small changes
ff4b317a86ea65ad0e3aebf8bdcacc7c7352f882 af87f0072aee3f3ad26d5344e51bdf0b0390d975 uroehrig <ute.roehrig@sib.swiss> 1731595699 +0100	commit: implement rescoring of sdf file
af87f0072aee3f3ad26d5344e51bdf0b0390d975 e8eced55d0702a94dcea800b391610e337eca601 uroehrig <ute.roehrig@sib.swiss> 1731672929 +0100	commit: small modif
e8eced55d0702a94dcea800b391610e337eca601 3c82a6d29768f29f0e645cbdce6a73de3c261fc2 uroehrig <ute.roehrig@sib.swiss> 1731677648 +0100	commit: bug fixed
3c82a6d29768f29f0e645cbdce6a73de3c261fc2 a61e0405fe1d4c82ec0496e00038a530888d361b uroehrig <ute.roehrig@sib.swiss> 1731934516 +0100	commit: correcting pose order after facts
a61e0405fe1d4c82ec0496e00038a530888d361b e7d91717d7da18cbe6d2c7851f485c267cb429a0 uroehrig <ute.roehrig@sib.swiss> 1731937773 +0100	commit: pose printing after clustering changed
e7d91717d7da18cbe6d2c7851f485c267cb429a0 278217023a4bbe19fdbcebb4e6a9bec8ea70b9d7 uroehrig <ute.roehrig@sib.swiss> 1731945854 +0100	commit: consolidate subdirectories
278217023a4bbe19fdbcebb4e6a9bec8ea70b9d7 ec5875b75c85b6804c6dc2f375c541799e7fc0ca uroehrig <ute.roehrig@sib.swiss> 1732118236 +0100	commit: bug fixes
ec5875b75c85b6804c6dc2f375c541799e7fc0ca 6bd4e6265e3eba1d321b605a610f569aac025523 uroehrig <ute.roehrig@sib.swiss> 1732541757 +0100	commit: allow 5-letter ligand names
6bd4e6265e3eba1d321b605a610f569aac025523 5e64a563d6c941f5860659bb8c71d38e895bab99 uroehrig <ute.roehrig@sib.swiss> 1732729460 +0100	commit: working on using names not indices to identify poses
5e64a563d6c941f5860659bb8c71d38e895bab99 03219dbccc72c86da85693a527a62b953cd863f4 uroehrig <ute.roehrig@sib.swiss> 1732796897 +0100	pull: Fast-forward
03219dbccc72c86da85693a527a62b953cd863f4 4ec6cc4118265cee44f4f6bdfc79331b1e329ab8 uroehrig <ute.roehrig@sib.swiss> 1732890387 +0100	commit: allow for heme c binding
4ec6cc4118265cee44f4f6bdfc79331b1e329ab8 7853c4a68bcfd65f865d49d4fc858212ad4b0037 uroehrig <ute.roehrig@sib.swiss> 1733137521 +0100	commit: try to do first facts with reduced receptor only
7853c4a68bcfd65f865d49d4fc858212ad4b0037 6e6945945bca26c5499ab4dada31f9d651c45f33 uroehrig <ute.roehrig@sib.swiss> 1733142988 +0100	commit: make sasa calculation optional
6e6945945bca26c5499ab4dada31f9d651c45f33 b9d23fdeea07843d05f825cf20907c7fead31549 uroehrig <ute.roehrig@sib.swiss> 1733238992 +0100	commit: add clash detection run after relax3
b9d23fdeea07843d05f825cf20907c7fead31549 d651e29c83b673963eea79d6b4ff3894d4fd3718 uroehrig <ute.roehrig@sib.swiss> 1733306039 +0100	commit: new removal of receptor box clashes
d651e29c83b673963eea79d6b4ff3894d4fd3718 a8cbb8b48293367892c769054521bc5878eba20a uroehrig <ute.roehrig@sib.swiss> 1733398886 +0100	commit: clash filtering and cleaning
a8cbb8b48293367892c769054521bc5878eba20a ba6cf76d7afee0b362117053ceddaf42bdead829 uroehrig <ute.roehrig@sib.swiss> 1733753929 +0100	commit: changed readme
ba6cf76d7afee0b362117053ceddaf42bdead829 a784edfc992fa2cd0225a6d85026f42e179c5e30 uroehrig <ute.roehrig@sib.swiss> 1733754061 +0100	checkout: moving from ute_work_6 to master
a784edfc992fa2cd0225a6d85026f42e179c5e30 91fc67b31b3ace807569eebed74f074997fefbec uroehrig <ute.roehrig@sib.swiss> 1733754190 +0100	merge ute_work_6: Merge made by the 'ort' strategy.
91fc67b31b3ace807569eebed74f074997fefbec 91fc67b31b3ace807569eebed74f074997fefbec uroehrig <ute.roehrig@sib.swiss> 1733754731 +0100	checkout: moving from master to ute_work_7
91fc67b31b3ace807569eebed74f074997fefbec d442728cf6dadf6ee813b9d16003778d600fd286 uroehrig <ute.roehrig@sib.swiss> 1733814420 +0100	commit: working on qmmm
d442728cf6dadf6ee813b9d16003778d600fd286 80fa27470c19c7c92139706f97818d61f8857947 uroehrig <ute.roehrig@sib.swiss> 1733846855 +0100	commit: improved qmmm and fixed bug in flex_rec
80fa27470c19c7c92139706f97818d61f8857947 1bc550e8c3f0949e4a4c21b2ae91e6c35f2cfc98 uroehrig <ute.roehrig@sib.swiss> 1733934604 +0100	commit: updated qmmm part
1bc550e8c3f0949e4a4c21b2ae91e6c35f2cfc98 e0b5d5563151974b5a2a498e504e94ba37664320 uroehrig <ute.roehrig@sib.swiss> 1734013276 +0100	commit: qmmm bug fixes
e0b5d5563151974b5a2a498e504e94ba37664320 1331fb63fdf80ab4a2c5f6b24048db8dd7a12f80 uroehrig <ute.roehrig@sib.swiss> 1734085807 +0100	commit: small bug fix
1331fb63fdf80ab4a2c5f6b24048db8dd7a12f80 123140accb53ccc24f98db8e9b544476771f70b2 uroehrig <ute.roehrig@sib.swiss> 1734112347 +0100	commit: started merging with qmmm version including also bb atoms
123140accb53ccc24f98db8e9b544476771f70b2 878b8aa28fe3763556152eaa4d2ab60562d64a6e uroehrig <ute.roehrig@sib.swiss> 1734347262 +0100	commit: fixes for including bb in qm
878b8aa28fe3763556152eaa4d2ab60562d64a6e d636021b56d8f308f042f945dd575e4a29afbd44 uroehrig <ute.roehrig@sib.swiss> 1734362953 +0100	commit: small fixes
d636021b56d8f308f042f945dd575e4a29afbd44 faf3d95e8a9a4bc46e4a68f03dbac2243177b9c1 uroehrig <ute.roehrig@sib.swiss> 1734452215 +0100	commit: working on qmmm
faf3d95e8a9a4bc46e4a68f03dbac2243177b9c1 58f7e78aa3f7452972f8f798dee748541771e745 uroehrig <ute.roehrig@sib.swiss> 1734597934 +0100	commit: fixed heme: small vdw radii only used when heme is ligand not receptor
58f7e78aa3f7452972f8f798dee748541771e745 b8b76d7212f23a1c588b3fae2186b90ef6c32683 uroehrig <ute.roehrig@sib.swiss> 1734604520 +0100	commit: use only box center as pp
b8b76d7212f23a1c588b3fae2186b90ef6c32683 5b4d5c89641555622b32da756bf477957791b75a uroehrig <ute.roehrig@sib.swiss> 1734705819 +0100	commit: small fixes
5b4d5c89641555622b32da756bf477957791b75a af8d993b6e69fe02279563f7633d8f29af58d092 uroehrig <ute.roehrig@sib.swiss> 1734708110 +0100	commit: add keyword to include bb in qm
af8d993b6e69fe02279563f7633d8f29af58d092 c137f3f9a972290b77a65266aacc60233e30e67b uroehrig <ute.roehrig@sib.swiss> 1734971445 +0100	commit: small fixes for qmmm, not finished for disulfides
c137f3f9a972290b77a65266aacc60233e30e67b 1100141dd06ce70a2e72267d89d0659e42c94237 uroehrig <ute.roehrig@sib.swiss> 1735922774 +0100	commit: bug fix qmmm disulfide bridges
1100141dd06ce70a2e72267d89d0659e42c94237 99a2adc2136d784499e2ca1260a8d0f9e258b6a2 uroehrig <ute.roehrig@sib.swiss> 1736169166 +0100	commit: qmmm fixed and charge division
99a2adc2136d784499e2ca1260a8d0f9e258b6a2 0955e0f62569a23e8458a24153a7ccbd021286c2 uroehrig <ute.roehrig@sib.swiss> 1736266626 +0100	commit: work on qm charges
0955e0f62569a23e8458a24153a7ccbd021286c2 1c033a0bcda3c8054e9db3246e448ad53635ad7b uroehrig <ute.roehrig@sib.swiss> 1736357647 +0100	commit: started implementing use of Mullikan charges for QMMM/FACTS
1c033a0bcda3c8054e9db3246e448ad53635ad7b 3807fcf98e95122071c57015710792b71c41ac44 uroehrig <ute.roehrig@sib.swiss> 1736430210 +0100	commit: automatic mmbp for heme docking
3807fcf98e95122071c57015710792b71c41ac44 6caeb33903567f519728458e096889fcb69ce58c uroehrig <ute.roehrig@sib.swiss> 1736434545 +0100	commit: test qmmm mullikan charges
6caeb33903567f519728458e096889fcb69ce58c 84debfb8e2b1780c0d0891db918790e6648fa457 uroehrig <ute.roehrig@sib.swiss> 1736521829 +0100	commit: bug fixes
84debfb8e2b1780c0d0891db918790e6648fa457 59f58dbdbc521d70f104d572eeed6a387b82c54a uroehrig <ute.roehrig@sib.swiss> 1736777171 +0100	commit: fix qmmm refine
59f58dbdbc521d70f104d572eeed6a387b82c54a 856fdb8e821e00223e527f8bb2bd36fe2278bb46 uroehrig <ute.roehrig@sib.swiss> 1737365626 +0100	commit: bug fix in qmmm/cov
856fdb8e821e00223e527f8bb2bd36fe2278bb46 e2a470935a441c69f84b0955b3f51d1f27b33665 uroehrig <ute.roehrig@sib.swiss> 1738070188 +0100	commit: fixed qmmm charge/facts calculations
e2a470935a441c69f84b0955b3f51d1f27b33665 0387cc48d9d6e91f97d769042f7d0c6862bcddf8 uroehrig <ute.roehrig@sib.swiss> 1738662407 +0100	commit: very small fixes
0387cc48d9d6e91f97d769042f7d0c6862bcddf8 28bcf7066c11a64736f08b9a4f27cde45253221d uroehrig <ute.roehrig@sib.swiss> 1738920532 +0100	commit: small qmmm fixes
28bcf7066c11a64736f08b9a4f27cde45253221d 2c1e16ae6d810ba1f87fad57bc8b0854650ab49b uroehrig <ute.roehrig@sib.swiss> 1739531152 +0100	commit: qmmm fixes
2c1e16ae6d810ba1f87fad57bc8b0854650ab49b 686eb6b4b7de4469c0c93437eb41f29a6b5df82e uroehrig <ute.roehrig@sib.swiss> 1739784275 +0100	commit: fixed qmmm/facts bug using old coordinates
686eb6b4b7de4469c0c93437eb41f29a6b5df82e 482f1af7bb5926bd66b4a4d0c9178f786543944e uroehrig <ute.roehrig@sib.swiss> 1739795746 +0100	commit: several bug fixes
482f1af7bb5926bd66b4a4d0c9178f786543944e d533b2f583278e21a8db06235b9f5e51d62b41c6 uroehrig <ute.roehrig@sib.swiss> 1739892880 +0100	commit: qmmm bug fix and dock_heme
d533b2f583278e21a8db06235b9f5e51d62b41c6 045c60139e7c2717a01289892c083b6b4a6cbc20 uroehrig <ute.roehrig@sib.swiss> 1739977941 +0100	commit: small modifs for webserver
045c60139e7c2717a01289892c083b6b4a6cbc20 2c1e16ae6d810ba1f87fad57bc8b0854650ab49b uroehrig <ute.roehrig@sib.swiss> 1740391888 +0100	checkout: moving from ute_work_7 to old-state
2c1e16ae6d810ba1f87fad57bc8b0854650ab49b 045c60139e7c2717a01289892c083b6b4a6cbc20 uroehrig <ute.roehrig@sib.swiss> 1741943351 +0100	checkout: moving from old-state to ute_work_7
045c60139e7c2717a01289892c083b6b4a6cbc20 28fd585a124ab1d2a7df5ad0a88f7493f12a5eb2 uroehrig <ute.roehrig@sib.swiss> 1741943358 +0100	pull: Fast-forward
28fd585a124ab1d2a7df5ad0a88f7493f12a5eb2 adf4afabb90bffdc212296efc4e35a5b6275893c uroehrig <ute.roehrig@sib.swiss> 1743171775 +0100	commit: Check for duplicate residues and atom names
adf4afabb90bffdc212296efc4e35a5b6275893c bd09fe892c0b83501d2d7f03675f174239f3c3ad uroehrig <ute.roehrig@sib.swiss> 1743432247 +0200	commit: fixed issue in initial conformers
bd09fe892c0b83501d2d7f03675f174239f3c3ad 9c7ae13b3113e78b002084e08ad7a38829922855 uroehrig <ute.roehrig@sib.swiss> 1743516405 +0200	commit: changes to conf generation
9c7ae13b3113e78b002084e08ad7a38829922855 2520e00ea2d911b08ee4aa4715169e33caa196e8 uroehrig <ute.roehrig@sib.swiss> 1743583717 +0200	commit: bug fix for rdkit conformers
2520e00ea2d911b08ee4aa4715169e33caa196e8 518c9b532bc750ad518756dac8ee4ecc179521f0 uroehrig <ute.roehrig@sib.swiss> 1743584651 +0200	commit: small fix
518c9b532bc750ad518756dac8ee4ecc179521f0 dbb6fe0f6752c3574e042f3be63ab98a911dbce1 uroehrig <ute.roehrig@sib.swiss> 1743687065 +0200	commit: adapt number of pp
dbb6fe0f6752c3574e042f3be63ab98a911dbce1 3ed9b7fae48b6f481febdbfb8e24298fa8bdb4b6 uroehrig <ute.roehrig@sib.swiss> 1743761523 +0200	commit: always keep box center as pp
3ed9b7fae48b6f481febdbfb8e24298fa8bdb4b6 6470b11b77478dcc0f729f0be5557319251bed0a uroehrig <ute.roehrig@sib.swiss> 1744020479 +0200	commit: fixed pp bug
6470b11b77478dcc0f729f0be5557319251bed0a bca8d0ae8a9787abd1b92d77666688a157ac54a3 uroehrig <ute.roehrig@sib.swiss> 1744301027 +0200	commit: removed use of box center as pp
bca8d0ae8a9787abd1b92d77666688a157ac54a3 a61f8e0b5bba7172aa77dd8aefd0e9049185dc40 uroehrig <ute.roehrig@sib.swiss> 1744380224 +0200	commit: changed reduction of number of pp
a61f8e0b5bba7172aa77dd8aefd0e9049185dc40 f356a1c1468d848b57f87f8ffcfaf8c070ca959a uroehrig <ute.roehrig@sib.swiss> 1746192249 +0200	commit: changed relax0 parallellization
f356a1c1468d848b57f87f8ffcfaf8c070ca959a 0569fb796e07e781d7d854b56f6afed4ec37088e uroehrig <ute.roehrig@sib.swiss> 1747730231 +0200	commit: small fix for heme and qmmm tests
0569fb796e07e781d7d854b56f6afed4ec37088e c64212f8d4e7aa8308cfaed6f4141375fb2e37f0 uroehrig <ute.roehrig@sib.swiss> 1747833879 +0200	commit: small change for qmmm/refine
c64212f8d4e7aa8308cfaed6f4141375fb2e37f0 29109e9f5776f6792cda4df223ee8fb8570b3b2f uroehrig <ute.roehrig@sib.swiss> 1748954793 +0200	commit: QMMM: activated DIV keyword
29109e9f5776f6792cda4df223ee8fb8570b3b2f 2ddf63d5de56171d48d76d9f01fc38230f81cbed uroehrig <ute.roehrig@sib.swiss> 1749654096 +0200	commit: small fixes for new master
2ddf63d5de56171d48d76d9f01fc38230f81cbed 376d9716703981a9d8428667e506bba08544e2d6 uroehrig <ute.roehrig@sib.swiss> 1749654469 +0200	commit: delete an extra file
376d9716703981a9d8428667e506bba08544e2d6 91fc67b31b3ace807569eebed74f074997fefbec uroehrig <ute.roehrig@sib.swiss> 1749654563 +0200	checkout: moving from ute_work_7 to master
91fc67b31b3ace807569eebed74f074997fefbec da191c35d3f2de191127542213af99406c911c85 uroehrig <ute.roehrig@sib.swiss> 1749654580 +0200	merge ute_work_7: Merge made by the 'ort' strategy.
da191c35d3f2de191127542213af99406c911c85 da191c35d3f2de191127542213af99406c911c85 uroehrig <ute.roehrig@sib.swiss> 1749654880 +0200	checkout: moving from master to ute_work_8
da191c35d3f2de191127542213af99406c911c85 b6bdfaf8c11fa06d9aabdbaf455318d7a915f3cb uroehrig <ute.roehrig@sib.swiss> 1749656899 +0200	commit: clean up files
b6bdfaf8c11fa06d9aabdbaf455318d7a915f3cb fd5bea4a188b14d079329fb4217e76d4d8d4ab66 uroehrig <ute.roehrig@sib.swiss> 1749733858 +0200	commit: small change in pp clustering
fd5bea4a188b14d079329fb4217e76d4d8d4ab66 9f7935807c34c965939cb7d32c683f240ebbba65 uroehrig <ute.roehrig@sib.swiss> 1750692153 +0200	commit: modifying grid functions
9f7935807c34c965939cb7d32c683f240ebbba65 ee7b40fdf0968e6efd1142bf664c8484d9821033 uroehrig <ute.roehrig@sib.swiss> 1750758415 +0200	commit: still working on grid
ee7b40fdf0968e6efd1142bf664c8484d9821033 55f80a5f35830dbb7098f1cd05f4a5b7617924ce uroehrig <ute.roehrig@sib.swiss> 1750863894 +0200	commit: changed pp algorithm anf nthr determination
55f80a5f35830dbb7098f1cd05f4a5b7617924ce c3491a6dfcbc4ac677224bced5804ce8ed9689a5 uroehrig <ute.roehrig@sib.swiss> 1750924116 +0200	commit: small bug fix in grid
c3491a6dfcbc4ac677224bced5804ce8ed9689a5 4e0de8c46f41bec541f73fbf2e76701ee54c0fae uroehrig <ute.roehrig@sib.swiss> 1750951036 +0200	commit: small fix for conf generation
4e0de8c46f41bec541f73fbf2e76701ee54c0fae eeb014209d75b5f70c28394c701066c1fff75b00 uroehrig <ute.roehrig@sib.swiss> 1751379364 +0200	commit: changed npoints < no_heavy_atoms instead of npoints < 2*no_heavy_atoms
eeb014209d75b5f70c28394c701066c1fff75b00 60651750bdb0f57c26d8c1d4a0f4a22ed6bdc1ec uroehrig <ute.roehrig@sib.swiss> 1751899542 +0200	commit: implemented nconf auto
60651750bdb0f57c26d8c1d4a0f4a22ed6bdc1ec 445d88ca0b9409a8059d2db7a6adc02bf7e7a332 uroehrig <ute.roehrig@sib.swiss> 1751974568 +0200	commit: changed auto conf
445d88ca0b9409a8059d2db7a6adc02bf7e7a332 7ce9854341fcfc1003354e867737992eb5ad726f uroehrig <ute.roehrig@sib.swiss> 1751982757 +0200	commit: fixed conf generation
7ce9854341fcfc1003354e867737992eb5ad726f 7e1cee2e9eacd7a9567fea076ae71882c940dd8c uroehrig <ute.roehrig@sib.swiss> 1752825164 +0200	commit: small bug fix for nconf
7e1cee2e9eacd7a9567fea076ae71882c940dd8c b6608d1968bb3ae485ca511dc10956ca68068395 uroehrig <ute.roehrig@sib.swiss> 1753110753 +0200	commit: run time estimation with 180 deg; shorten mol2 ligid to 4 letters
b6608d1968bb3ae485ca511dc10956ca68068395 5f8b732a818fc3b450b56da23fd09a7dbd8ed30e uroehrig <ute.roehrig@sib.swiss> 1753372478 +0200	commit: small fix for mmbp
5f8b732a818fc3b450b56da23fd09a7dbd8ed30e 720caa018a42f9ababd5ee4f2dcef8d4fc852f75 uroehrig <ute.roehrig@sib.swiss> 1755260815 +0200	pull: Fast-forward
720caa018a42f9ababd5ee4f2dcef8d4fc852f75 1abaa7841b0ac4fc2f9fadad9e5b4056fd99ae27 uroehrig <ute.roehrig@sib.swiss> 1755874322 +0200	commit: changed pp clustering, fixed bugs, fixed nonstd aa
1abaa7841b0ac4fc2f9fadad9e5b4056fd99ae27 4ecb1685984c673012116663446664898e399cd6 uroehrig <ute.roehrig@sib.swiss> 1756192528 +0200	commit: fixed bug in determine_opt_attr_grid and improved pp clustering
4ecb1685984c673012116663446664898e399cd6 c69c9d8d0c216b46f85cfdb9fec9b1c82fa96a23 uroehrig <ute.roehrig@sib.swiss> 1756458309 +0200	pull: Fast-forward
c69c9d8d0c216b46f85cfdb9fec9b1c82fa96a23 432b591066085cc2789dc2bc93b4740b33bc8c96 uroehrig <ute.roehrig@sib.swiss> 1756715681 +0200	commit: suggest number of pp
432b591066085cc2789dc2bc93b4740b33bc8c96 f6a36ee979890482f9486b715f13920ab1f54249 uroehrig <ute.roehrig@sib.swiss> 1758174170 +0200	commit: small changes in pp auto
f6a36ee979890482f9486b715f13920ab1f54249 c5ad9825ad96b68793a05010fda5f55a76e2ad38 uroehrig <ute.roehrig@sib.swiss> 1758789070 +0200	commit: fixed bug in relax2+hbuild and added use of rseed for conformersRdkit
c5ad9825ad96b68793a05010fda5f55a76e2ad38 e33211fbddff2d84808095f0cee57d25db11a06a uroehrig <ute.roehrig@sib.swiss> 1759479117 +0200	commit: bug fixes for cov and qmmm
e33211fbddff2d84808095f0cee57d25db11a06a c961d3d1186a1df8d7953b3fff28b7ede06c9743 uroehrig <ute.roehrig@sib.swiss> 1761743831 +0100	commit: small fixes
c961d3d1186a1df8d7953b3fff28b7ede06c9743 0275e2f6b21a100024eaa0e4d3ebd8ad6bce78a6 uroehrig <ute.roehrig@sib.swiss> 1766062695 +0100	commit: added stereochemistry checks
0275e2f6b21a100024eaa0e4d3ebd8ad6bce78a6 d095492e2c420fe088fce38a73aada5916555a65 uroehrig <ute.roehrig@sib.swiss> 1766074261 +0100	commit: fixed issue when non-unique atom names
d095492e2c420fe088fce38a73aada5916555a65 9fef9a9b386918eeb05c0ea64d8bc71fab066461 uroehrig <ute.roehrig@sib.swiss> 1766161908 +0100	commit: working on stereo filtering
9fef9a9b386918eeb05c0ea64d8bc71fab066461 1871a9c06e9a4e3a76dd74e5bb4b1314315d98e8 uroehrig <ute.roehrig@sib.swiss> 1766484397 +0100	commit: bug fix for match
1871a9c06e9a4e3a76dd74e5bb4b1314315d98e8 6e4460f84a7342410cd325b5c59aae168684e21e uroehrig <ute.roehrig@sib.swiss> 1766503596 +0100	commit: use sdf file as reference for stereocheck
6e4460f84a7342410cd325b5c59aae168684e21e 07c1a85859d613eef6bfa970d6ba31df26d9a4cb uroehrig <ute.roehrig@sib.swiss> 1767716289 +0100	commit: bug fixes for stereo
07c1a85859d613eef6bfa970d6ba31df26d9a4cb 930518cf74508c304ac8045ccc28459a27b18fdc uroehrig <ute.roehrig@sib.swiss> 1767890243 +0100	commit: improving stereochemistry
930518cf74508c304ac8045ccc28459a27b18fdc c6553267726eec5b8526b6093c9b951da23b9278 uroehrig <ute.roehrig@sib.swiss> 1768553570 +0100	commit: added atom names to printing of stereo elements
c6553267726eec5b8526b6093c9b951da23b9278 97808ec641fbbde69ba7d3aca24597f4107f394a uroehrig <ute.roehrig@sib.swiss> 1770044904 +0100	commit: Improved strain calculation, pp clustering
97808ec641fbbde69ba7d3aca24597f4107f394a a060602bc117c7bffc41d99f9ca7238a1e189ca7 uroehrig <ute.roehrig@sib.swiss> 1772026850 +0100	commit: started implementation of exhaustivity keyword
a060602bc117c7bffc41d99f9ca7238a1e189ca7 02182503a38a96a2abe59a0a2089734bb52fdaa1 uroehrig <ute.roehrig@sib.swiss> 1772028597 +0100	commit: small bug fix
02182503a38a96a2abe59a0a2089734bb52fdaa1 e5ea5cfaabbafa6d77b0b3eaa5164cb6e8ece82a uroehrig <ute.roehrig@sib.swiss> 1772444274 +0100	commit: change exhaustivity; bug fix for conformer generation
e5ea5cfaabbafa6d77b0b3eaa5164cb6e8ece82a 94aa02d5ed4cecb2bedb9b80160ef2eea77851aa uroehrig <ute.roehrig@sib.swiss> 1772553564 +0100	commit: changed conformer generation
94aa02d5ed4cecb2bedb9b80160ef2eea77851aa 10e92be43028bb7cef08b2dfe9bdaa853e0c6b3f uroehrig <ute.roehrig@sib.swiss> 1772721660 +0100	commit: bug fix fot cov/flex
10e92be43028bb7cef08b2dfe9bdaa853e0c6b3f 67ec7c73d949ccb60a73bbadd2b9cc7ab4cff670 uroehrig <ute.roehrig@sib.swiss> 1773734186 +0100	commit: allow flex+receptor_box
67ec7c73d949ccb60a73bbadd2b9cc7ab4cff670 a47ec4f369ea6b119210ac7570ebe8666e4386cb uroehrig <ute.roehrig@sib.swiss> 1774010995 +0100	commit: less debugging info printed
a47ec4f369ea6b119210ac7570ebe8666e4386cb 9599ebf3126dc4e1b0cd91df65099a986d8e43a8 uroehrig <ute.roehrig@sib.swiss> 1774019448 +0100	commit: added energy_range for output poses
9599ebf3126dc4e1b0cd91df65099a986d8e43a8 d294fd7550586371c900e83c724f5ac104bc6798 uroehrig <ute.roehrig@sib.swiss> 1774348741 +0100	commit: small changes in input and log printing
d294fd7550586371c900e83c724f5ac104bc6798 6eb42b49f246ee63fb32e0799cd23ce147ca4c8b uroehrig <ute.roehrig@sib.swiss> 1779793704 +0200	commit: some fixes and exhaustivity implementation
6eb42b49f246ee63fb32e0799cd23ce147ca4c8b da191c35d3f2de191127542213af99406c911c85 uroehrig <ute.roehrig@sib.swiss> 1779793824 +0200	checkout: moving from ute_work_8 to master
da191c35d3f2de191127542213af99406c911c85 97795923047683bc1b4c91e32c17dd908e1f1fa9 uroehrig <ute.roehrig@sib.swiss> 1779793839 +0200	merge ute_work_8: Merge made by the 'ort' strategy.
97795923047683bc1b4c91e32c17dd908e1f1fa9 97795923047683bc1b4c91e32c17dd908e1f1fa9 uroehrig <ute.roehrig@sib.swiss> 1779794084 +0200	checkout: moving from master to ute_work_9
