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History Graph
Commit | Author | Details | Committed | ||||
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7361b4b17ae7 | puckvg | seems ok | Jan 7 2022 | ||||
90e3ba17ab56 | puckvg | acm ok? | Jan 7 2022 | ||||
1c17dba2d764 | matt | Changed preprocess.py for old qm7 data to have same structure as the new ones. | Jan 6 2022 | ||||
1392955adabe | puckvg | work | Jan 6 2022 | ||||
9d7adea85e44 | puckvg | fix CM | Jan 4 2022 | ||||
16d8a316e929 | puckvg | aCM doesnt work | Dec 21 2021 | ||||
7fdebda55844 | puckvg | merge conflict | Dec 21 2021 | ||||
7459716bca1e | puckvg | aCM seems better but obj value still huge | Dec 21 2021 | ||||
d00e36abbefe | matt | Added modifiable constant for fragmentation penalty | Dec 21 2021 | ||||
fa27a77d2a83 | matt | Support for 3 new vector representations. Model parameters to avoid getting… | Dec 21 2021 | ||||
b3236b2c31ff | puckvg | add lots of new reps to try | Dec 20 2021 | ||||
500a60d21a77 | puckvg | updated database and search is ok | Dec 20 2021 | ||||
8e27e829e380 | puckvg | fix merge | Dec 20 2021 | ||||
d882c03886a3 | puckvg | update database required change to aqml code | Dec 20 2021 | ||||
a3515913792d | matt | Force filling solution pool with best solutions. | Dec 20 2021 | ||||
1b168381f237 | puckvg | Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl | Dec 17 2021 | ||||
351c87156902 | puckvg | fix dims for vit d | Dec 17 2021 | ||||
bcbc7a7b5891 | matt | Added SLATM representation support | Dec 15 2021 | ||||
dea3a35bbba0 | puckvg | update data | Dec 15 2021 | ||||
1f1e3e371fb6 | puckvg | add readme | Dec 15 2021 | ||||
bdb5302eeb90 | puckvg | add vector data for target and amons databases | Dec 15 2021 | ||||
5cc7e9b3d9f7 | puckvg | changed database sizes to 7/8/9 max heavy atom fragments respectively | Dec 14 2021 | ||||
1a514eeaa66c | matt | Added partial molecule penalty | Dec 6 2021 | ||||
a6c6e4a68e80 | matt | fixed objective value | Dec 5 2021 | ||||
3005d8c71b0b | matt | Added back molecule duplication - limited to 3 copies for perfomance | Dec 3 2021 | ||||
2ae2563a46c3 | matt | Switched to ideal databases. Removed duplicate molecules until objective… | Nov 30 2021 | ||||
327fab3e8a81 | puckvg | fixing merge issue | Nov 29 2021 | ||||
83ee1e954e70 | puckvg | add optimal databases for each target | Nov 29 2021 | ||||
3744c8b0cf63 | matt | Removed (commented) the connectivity conditions that were based on adjacency… | Nov 25 2021 | ||||
361d72e931d5 | puckvg | fix sign of constraint in obj | Nov 23 2021 | ||||
74a6c6e3bef1 | puckvg | fix merge | Nov 23 2021 | ||||
c0cc91ff32f3 | puckvg | add output | Nov 23 2021 | ||||
2da90f129e25 | puckvg | update | Nov 23 2021 | ||||
b1b6ccce0c15 | matt | Added preprocessing of the connectivity matrices to improve on runtime; various… | Nov 22 2021 | ||||
23da2886dc0f | matt | Memory improvements; readded taking molecules multiple times. | Nov 20 2021 | ||||
3ae7e7d2c4ca | matt | Added weak connectivity conditions on fragments of molecule taken. Issues… | Nov 19 2021 | ||||
79bcac3b5cb3 | puckvg | :Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl | Nov 16 2021 | ||||
3e70f256a0f5 | puckvg | add adjacency matrices and functional group information | Nov 16 2021 | ||||
3d34d30e4e22 | matt | Removed partial target matching; added parameter for size of molecule fragment | Nov 16 2021 | ||||
1463d851f136 | matt | Improved output runtime; now prints old positions (indices+1) before… | Nov 12 2021 | ||||
cad06c9aec83 | matt | Modifed preprocessing to remove hydrogens; various changes on onepass (i forgot… | Nov 11 2021 | ||||
bd45bf0be154 | matt | Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl | Nov 10 2021 | ||||
51ebee2f6454 | matt | Enhanced output; fixed size constraints. | Nov 10 2021 | ||||
aacc423084e7 | puckvg | adding xyz files for targets and database to look | Nov 10 2021 | ||||
6b022f2e9bb6 | matt | Allow partial molecule with threshold; force portion of target to be assigned… | Nov 9 2021 | ||||
ee3c54d0dd06 | matt | First sketch of preprocessing; allowed taking molecules multiple times | Nov 9 2021 | ||||
a440a7a3f8b0 | matt | Added output for stored solutions; time and gap limits. | Nov 8 2021 | ||||
d457ff7a09fe | matt | Few changes to improve running time | Nov 5 2021 | ||||
d3cf1ed4215f | matt | Code refactoring | Nov 4 2021 | ||||
ec9dddbcc754 | matt | few fixes | Nov 3 2021 | ||||
2870d9c1d762 | matt | New file aiming for one-pass algorithm based on gurobi.py. | Nov 3 2021 | ||||
b06fc17d9898 | matt | Actually added size penalty this time | Nov 2 2021 | ||||
67a64e4986a7 | matt | Revert last commit | Nov 2 2021 | ||||
e2bd4b3dbe78 | matt | Added penalty on size of molecule (needs later tuning) | Nov 2 2021 | ||||
7d7c6bfa4252 | matt | Added timer on definition of each model; need to fix high running time leading… | Nov 2 2021 | ||||
a1f2b52fe731 | matt | Added loop on candidate molecules M to find best objective value | Nov 2 2021 | ||||
3cc0e97f8a12 | puckvg | revert last commit | Sep 16 2021 | ||||
7b98704f5055 | puckvg | try to allow partial molecule match | Sep 13 2021 | ||||
be18e6f69234 | eisen | Update gurobi.py | Jul 1 2021 | ||||
1b45bca55357 | puckvg | added comments and now it doesn't seem to be working | Jun 30 2021 | ||||
620d11b77c77 | eisen | Update gurobi.py | Jun 29 2021 | ||||
8001508755b3 | puckvg | update readme | Jun 25 2021 | ||||
30edc66e0e5c | puckvg | add ncharges | Jun 25 2021 | ||||
932496916e1a | puckvg | change to return indices of match | Jun 25 2021 | ||||
e34a2155c356 | puckvg | Updated project.tex | Jun 25 2021 | ||||
17187692f7a6 | eisen | Update gurobi.py | Jun 24 2021 | ||||
7a56525d8735 | eisen | update | Jun 22 2021 | ||||
fd5f9ead7415 | eisen | Continuing to understand Gurobi for our problem | Jun 22 2021 | ||||
c3a4ad5d93eb | eisen | starting ILP | Jun 21 2021 | ||||
e9ac2bb02e20 | eisen | Create Untitled.ipynb | Jun 1 2021 | ||||
b94aad4e00c2 | puckvg | data and README | Apr 22 2021 | ||||
6821c4d7fe05 | eisen | Create utf8math.sty | Apr 21 2021 | ||||
e98cae21cc4e | eisen | Create Project.tex | Apr 21 2021 |
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