Merge pull request #5971 from RosettaCommons/roccomoretti/interactive_fix_tests [Foldit] Test fixes for interactive/develop Right now it's just the library levels test -- the unit test issues aren't showing up on my machine.

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「2」

Merge pull request #5982 from RosettaCommons/joshmiller/fix-textbubbledata [Foldit] Revert GREEN_COLOR rename No release notes

• Summary
• foldit.levels
• foldit.unit.debug 「3」
• foldit.unit.release 「2」

Merge pull request #5958 from RosettaCommons/joshmiller/puzzletimer-namespace [Foldit] Move Puzzle Timer namespace No release notes

• Summary
• foldit.build.debug
• foldit.build.release
• foldit.levels
• foldit.unit.debug
• foldit.unit.release

Merge pull request #5959 from RosettaCommons/joshmiller/v-fixes [Foldit] Minor fixes to level_util and TextBubbleData No release notes

• Summary
• foldit.build.debug
• foldit.build.release
• foldit.levels
• foldit.unit.debug
• foldit.unit.release

Merge pull request #5961 from RosettaCommons/joshmiller/tlc-widgets [Foldit] Fix TLC widget container No release notes

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「2」

Merge pull request #5973 from RosettaCommons/roccomoretti/interactive_rdkit_threading [Foldit] Make RDKit threadsafe.

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「2」

Merge pull request #5969 from RosettaCommons/roccomoretti/interactive_rotlib_fix [Foldit] Hot fix for RareyRotamerLibrary.

• Summary
• foldit.levels
• foldit.unit.debug 「3」
• foldit.unit.release 「2」

Revert "Fix TLC widget container" This reverts commit 63f601c6c6b0406a077d8277bf23ec72cd428571.

• Summary
• foldit.levels
• foldit.unit.debug 「3」
• foldit.unit.release 「2」

Fix TLC widget container

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「2」

Fixing an issue using utility::vector on windows by switching to std::vector

• Summary
• foldit.levels
• foldit.unit.debug 「3」
• foldit.unit.release 「2」

Merge pull request #5953 from RosettaCommons/roccomoretti/interactive_lhf_index_defaults [Foldit] Fix defaults for LigandHydrophobicFilter Small adjustments to the LigandHydrophobicFilter settings to remove an unused parameter, as well as to enable autodetection of designable ligands by default.

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「2」

Merge pull request #5951 from RosettaCommons/koepnick/action_icons [Foldit] Update action icons Release Notes - Updated icons for Wiggle Backbone, Mutate Segment, Delete Segment

• Summary
• foldit.levels
• foldit.unit.debug 「3」
• foldit.unit.release 「2」

Merge pull request #5928 from RosettaCommons/roccomoretti/interactive_rarey_constraints [Foldit] Add Rarey rotamer library based torsions. Coming off of PR #5927 (the content of which is included in this branch), I noticed that it would be really nice to include the ability to minimize against the torsions. By using some of the changes from PR #5926 (which actually was triggered by this effort), I was able to make a SingleResidueRotamerLibrary which bases itself off of the Rarey torsion definitions. Anything "green" has zero energies, but orange and red torsions have harmonic-deviation energetic penalties. (So the energy wells are effectively flat harmonic like.) The current sd parameters were chosen to roughly match the penalty energies seen with fa_dun in a small (two residue) test set. Matching those parameters is good, as the current setup (using the SingleResidueRotamerLibrary mechanism) means that the energies for the Rarey show up in the fa_dun term. The primary goal of this branch was the energy and minimization behavior, but we also can use it for sampling -- rotamer generation proceeds by randomly choosing torsions in the green regions. It's not great (as it misses ring sampling and any torsions which aren't mapped by the Rarey library), but it's much, much faster than the current RDKit-based rotamers. Which torsion library to use for designed ligands can now be selected from the puzzle setup file.

• Summary
• foldit.levels
• foldit.unit.debug 「3」
• foldit.unit.release 「2」

Merge pull request #5927 from RosettaCommons/roccomoretti/interactive_rarey_torsions [Foldit] Add LigandTorsionQuality Objective. One of the issues we saw with the first ligand design puzzle series was the generation of ligand conformations which were unlikely. This PR adds a LigandTorsionQuality Filter/Objective which uses the Rarey 2016 torsional library (https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00522) for the definition of what acceptable ligand torsions are. The Rarey library has a traffic light (red/orange/green) ranking of torsions, and the Objective adds a penalty based on the number of torsions in the orange and red regions. Some changes to GlowBondVizData are needed to allow for custom (orange) colors in the glow.

• Summary
• foldit.levels
• foldit.unit.debug 「1」
• foldit.unit.release 「1」

Merge pull request #5929 from RosettaCommons/roccomoretti/interactive_ligand_tweak [Foldit] Add Ligand Tweak action This PR adds a "Ligand Tweak" action for designable ligands, which, when selected from the action bar, pops up purple tweak arrows on the rotatable bonds of the ligand, and allows you to rotate them back and forth. The concept is that it would be used with the torsion objective to optimize placement/torsions of the ligand. The tool should not be available for residues/puzzles which aren't designable ligands.

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「1」

Merge pull request #5871 from RosettaCommons/phuls/hydrophobicity_filter [Foldit] Hydrophobicity Intersection filter for Small Molecule

• Summary
• foldit.levels
• foldit.unit.debug 「2」
• foldit.unit.release 「1」

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