Brownbp1/pharmmap fld - #3

Open

brownbp1 wants to merge 34 commits into

brownbp1/pharmmap_fld

Commits on Jul 5, 2022

Fleshed out ScoreFunctionGeneric a bit.
brownbp1
committed
6906a08
In the middle of replacing the hard-coded mutates with serializable mutates
brownbp1
committed
d789fec

Commits on Jul 6, 2022

Merged workstation branch into local.
brownbp1
committed
6ab9aa3

Commits on Jul 7, 2022

First version of the FLD refactor complete. Compiles, but not tested yet. Major changes include making the mutates serializable, removing most of the member data from the thread manager, adding fin…
brownbp1
committed
189dee9
Accidentally kept the same alias for the new FragmentMutateInterface classes.
brownbp1
committed
f268d65
Changed default in ScoreFunctionGeneric from Mean to Index.
brownbp1
committed
1231df0
Similarly changed constructor defaults in ScoreFunctionGeneric. Changed FLD to take a CheminfoProperty instead of a ScoreFunctionGeneric. I still construct the ScoreFunctionGeneric from the Cheminf…
brownbp1
committed
a8e2c7f
Fixed a null pointer issue that I made during initialization of the MutateDecisionNode. There was a second one with the MutateRepeater, but for now I just commented out the repeater code, effective…
brownbp1
committed
bbf49a1
Swapping to get best instead of get last. Also added final metrics to another location.
brownbp1
committed
1b46094
Working on a long overdue refactor of the druglikeness filter in FragmentMutateInterface. Before it was just a string that was parsed in MapConformer as a CheminfoProperty, but we really should ser…
brownbp1
committed
8474369
Forgot a few classes where MapConformer was instantiated.
brownbp1
committed
55ebc62
Missed some
brownbp1
committed
bebf798
Deprecated app, but whatever
brownbp1
committed
b84a940
Changed default in FragmentMutateInterface
brownbp1
committed
4c05c3e
Trying something in Alchemy serialization
brownbp1
committed
de3d388
Nope
brownbp1
committed
81296a4
hmm
brownbp1
committed
64a4c70
nevermind
brownbp1
committed
66a9b08
Adding another FragmentSplitInterface-derived class to make it easier to prepare molecules for input to FLD or Mutate.
brownbp1
committed
18743b7
Headers and other stuff
brownbp1
committed
5125ebe
Added back a function that is pure virtual. Oops. Ran cleaner.
brownbp1
committed
f39e75d
added empty default
brownbp1
committed
3456b2b
fixed atom index parsing
brownbp1
committed
82e6175
typo in RISH
brownbp1
committed
8e5d1ce
Include bonded hydrogen atoms (if desired) in new split
brownbp1
committed
548b5eb
minor
brownbp1
committed
3ac2ff9
make indices mutable
brownbp1
committed
32d27dd
bug fix; minor feature add
brownbp1
committed
8bc6b87

Commits on Jul 9, 2022

Commits on Jul 10, 2022

Fixed bug in MoleculeFit during MolAlign RMSDX assignment. Minor feature enhancement to Mutate to allow output of only final structure.
brownbp1
committed
ac15244

Commits on Jul 11, 2022

Moving some functionality to the base class of FragmentMutateInterface so that users have control over molecule standardization independent of the mutate used. Will also allow some more complex com…
brownbp1
committed
8d53f8e

Commits on Jul 15, 2022

Finished updating the FragmentMutateInterface-derived class options. Basically just expanding a the moveable indices during 3D conformer generation outside of RingSwap.
brownbp1
committed
ec30422

Commits on Jul 21, 2022

Noted a bug in FragmentAlchemy and applied a small patch. Should be revisited later, though. May be deeper issues related to the PossibleAtomTypes class that need addressed. Updated options.
brownbp1
committed
8b83f9d