Diffusion MOLEKUEHL (master) History

History
master932081c4a349e0341aa0e8a…

Jan 10 2022

Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl
932081c4a349
·matt on Jan 10 2022, 11:56.
Added support for vector representations of qm7 database.
93eb3e78a418
·matt on Jan 10 2022, 01:34.

Jan 7 2022

seems ok
7361b4b17ae7
·puckvg on Jan 7 2022, 14:31.
acm ok?
90e3ba17ab56
·puckvg on Jan 7 2022, 14:30.

Jan 6 2022

Changed preprocess.py for old qm7 data to have same structure as the new ones.
1c17dba2d764
·matt on Jan 6 2022, 23:05.
work
1392955adabe
·puckvg on Jan 6 2022, 15:18.

Jan 4 2022

fix CM
9d7adea85e44
·puckvg on Jan 4 2022, 16:31.

Dec 21 2021

aCM doesnt work
16d8a316e929
·puckvg on Dec 21 2021, 17:54.
merge conflict
7fdebda55844
·puckvg on Dec 21 2021, 17:40.
aCM seems better but obj value still huge
7459716bca1e
·puckvg on Dec 21 2021, 17:39.
Added modifiable constant for fragmentation penalty
d00e36abbefe
·matt on Dec 21 2021, 15:03.
Support for 3 new vector representations. Model parameters to avoid getting…
fa27a77d2a83
·matt on Dec 21 2021, 14:20.

Dec 20 2021

add lots of new reps to try
b3236b2c31ff
·puckvg on Dec 20 2021, 16:47.
updated database and search is ok
500a60d21a77
·puckvg on Dec 20 2021, 16:02.
fix merge
8e27e829e380
·puckvg on Dec 20 2021, 15:49.
update database required change to aqml code
d882c03886a3
·puckvg on Dec 20 2021, 15:48.
Force filling solution pool with best solutions.
a3515913792d
·matt on Dec 20 2021, 15:27.

Dec 17 2021

Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl
1b168381f237
·puckvg on Dec 17 2021, 12:01.
fix dims for vit d
351c87156902
·puckvg on Dec 17 2021, 12:01.

Dec 15 2021

Added SLATM representation support
bcbc7a7b5891
·matt on Dec 15 2021, 21:12.
update data
dea3a35bbba0
·puckvg on Dec 15 2021, 12:03.
add readme
1f1e3e371fb6
·puckvg on Dec 15 2021, 12:03.
add vector data for target and amons databases
bdb5302eeb90
·puckvg on Dec 15 2021, 11:57.

Dec 14 2021

changed database sizes to 7/8/9 max heavy atom fragments respectively
5cc7e9b3d9f7
·puckvg on Dec 14 2021, 17:16.

Dec 6 2021

Added partial molecule penalty
1a514eeaa66c
·matt on Dec 6 2021, 15:55.

Dec 5 2021

fixed objective value
a6c6e4a68e80
·matt on Dec 5 2021, 01:43.

Dec 3 2021

Added back molecule duplication - limited to 3 copies for perfomance
3005d8c71b0b
·matt on Dec 3 2021, 14:57.

Nov 30 2021

Switched to ideal databases. Removed duplicate molecules until objective…
2ae2563a46c3
·matt on Nov 30 2021, 01:36.

Nov 29 2021

fixing merge issue
327fab3e8a81
·puckvg on Nov 29 2021, 11:13.
add optimal databases for each target
83ee1e954e70
·puckvg on Nov 29 2021, 11:12.

Nov 25 2021

Removed (commented) the connectivity conditions that were based on adjacency…
3744c8b0cf63
·matt on Nov 25 2021, 16:38.

Nov 23 2021

fix sign of constraint in obj
361d72e931d5
·puckvg on Nov 23 2021, 13:57.
fix merge
74a6c6e3bef1
·puckvg on Nov 23 2021, 13:56.
add output
c0cc91ff32f3
·puckvg on Nov 23 2021, 13:54.
update
2da90f129e25
·puckvg on Nov 23 2021, 13:49.

Nov 22 2021

Added preprocessing of the connectivity matrices to improve on runtime; various…
b1b6ccce0c15
·matt on Nov 22 2021, 15:25.

Nov 20 2021

Memory improvements; readded taking molecules multiple times.
23da2886dc0f
·matt on Nov 20 2021, 18:49.

Nov 19 2021

Added weak connectivity conditions on fragments of molecule taken. Issues…
3ae7e7d2c4ca
·matt on Nov 19 2021, 19:41.

Nov 16 2021

:Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl
79bcac3b5cb3
·puckvg on Nov 16 2021, 16:11.
add adjacency matrices and functional group information
3e70f256a0f5
·puckvg on Nov 16 2021, 16:11.
Removed partial target matching; added parameter for size of molecule fragment
3d34d30e4e22
·matt on Nov 16 2021, 13:44.

Nov 12 2021

Improved output runtime; now prints old positions (indices+1) before…
1463d851f136
·matt on Nov 12 2021, 13:37.

Nov 11 2021

Modifed preprocessing to remove hydrogens; various changes on onepass (i forgot…
cad06c9aec83
·matt on Nov 11 2021, 16:28.

Nov 10 2021

Merge branch 'master' of https://c4science.ch/diffusion/11301/molekuehl
bd45bf0be154
·matt on Nov 10 2021, 14:48.
Enhanced output; fixed size constraints.
51ebee2f6454
·matt on Nov 10 2021, 14:42.
adding xyz files for targets and database to look
aacc423084e7
·puckvg on Nov 10 2021, 12:08.

Nov 9 2021

Allow partial molecule with threshold; force portion of target to be assigned…
6b022f2e9bb6
·matt on Nov 9 2021, 16:22.
First sketch of preprocessing; allowed taking molecules multiple times
ee3c54d0dd06
·matt on Nov 9 2021, 14:45.

Nov 8 2021

Added output for stored solutions; time and gap limits.
a440a7a3f8b0
·matt on Nov 8 2021, 16:51.

Nov 5 2021

Few changes to improve running time
d457ff7a09fe
·matt on Nov 5 2021, 19:19.

Nov 4 2021

Code refactoring
d3cf1ed4215f
·matt on Nov 4 2021, 14:12.

Nov 3 2021

few fixes
ec9dddbcc754
·matt on Nov 3 2021, 17:47.
New file aiming for one-pass algorithm based on gurobi.py.
2870d9c1d762
·matt on Nov 3 2021, 17:43.

Nov 2 2021

Actually added size penalty this time
b06fc17d9898
·matt on Nov 2 2021, 16:07.
Revert last commit
67a64e4986a7
·matt on Nov 2 2021, 16:03.
Added penalty on size of molecule (needs later tuning)
e2bd4b3dbe78
·matt on Nov 2 2021, 13:04.
Added timer on definition of each model; need to fix high running time leading…
7d7c6bfa4252
·matt on Nov 2 2021, 12:43.
Added loop on candidate molecules M to find best objective value
a1f2b52fe731
·matt on Nov 2 2021, 12:35.

Sep 16 2021

revert last commit
3cc0e97f8a12
·puckvg on Sep 16 2021, 16:35.

Sep 13 2021

try to allow partial molecule match
7b98704f5055
·puckvg on Sep 13 2021, 11:08.

Jul 1 2021

Update gurobi.py
be18e6f69234
·eisen on Jul 1 2021, 13:44.

Jun 30 2021

added comments and now it doesn't seem to be working
1b45bca55357
·puckvg on Jun 30 2021, 16:26.

Jun 29 2021

Update gurobi.py
620d11b77c77
·eisen on Jun 29 2021, 17:31.

Jun 25 2021

update readme
8001508755b3
·puckvg on Jun 25 2021, 13:50.
add ncharges
30edc66e0e5c
·puckvg on Jun 25 2021, 13:49.
change to return indices of match
932496916e1a
·puckvg on Jun 25 2021, 12:06.
Updated project.tex
e34a2155c356
·puckvg on Jun 25 2021, 11:39.

Jun 24 2021

Update gurobi.py
17187692f7a6
·eisen on Jun 24 2021, 12:57.

Jun 22 2021

update
7a56525d8735
·eisen on Jun 22 2021, 15:41.
Continuing to understand Gurobi for our problem
fd5f9ead7415
·eisen on Jun 22 2021, 15:07.

Jun 21 2021

starting ILP
c3a4ad5d93eb
·eisen on Jun 21 2021, 15:05.

Jun 1 2021

Create Untitled.ipynb
e9ac2bb02e20
·eisen on Jun 1 2021, 16:16.

Apr 22 2021

data and README
b94aad4e00c2
·puckvg on Apr 22 2021, 16:34.

Apr 21 2021

Create utf8math.sty
6821c4d7fe05
·eisen on Apr 21 2021, 11:52.
Create Project.tex
e98cae21cc4e
·eisen on Apr 21 2021, 11:51.