Diffusion MOLEKUEHL (master) History

History
master3d34d30e4e22a0e109967d3…

Nov 16 2021

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.