0000000000000000000000000000000000000000 33211c1b7f1541156447d03c6a6f998b899387dc uroehrig <ute.roehrig@sib.swiss> 1710425887 +0100	branch: Created from HEAD
33211c1b7f1541156447d03c6a6f998b899387dc 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 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
