[DO NOT MERGE] Pre-generate residue templates#492

Closed

zhang-ivy wants to merge 41 commits intomasterfrom residue_templates

+1,687-740

Commits on Sep 26, 2018

polymer engine works, point mutation engineminor changes
zhang-ivy
committed

Commits on Oct 3, 2018

fix point mutation engine, still have oemol res warnings
zhang-ivy
committed
Merge remote-tracking branch 'origin/master' into protein_mutations_ivy
zhang-ivy
committed

Commits on Oct 4, 2018

fix chain id problem, compute state key base class problem, and construct atom map problem
zhang-ivy
committed

Commits on Oct 9, 2018

finish PointMutationEngine, started stereochem
zhang-ivy
committed

Commits on Oct 18, 2018

update stereochem, getting NaNs for logP_work and logP_energy
zhang-ivy
committed

Commits on Oct 22, 2018

Commits on Oct 23, 2018

Commits on Oct 24, 2018

Commits on Oct 25, 2018

Commits on Oct 30, 2018

Commits on Oct 31, 2018

update generateOEMolFromResidue, replace openmoltools calls with call to it in FFAllAngleGeometryEngine
zhang-ivy
committed

Commits on Nov 6, 2018

fix atom.stereo missing in determine_extra_torsions
zhang-ivy
committed

Commits on Nov 7, 2018

handle atom and bond stereochemistry in determine extra torsions
zhang-ivy
committed

Commits on Nov 9, 2018

add atom and bond stereo to determine_extra_torsions, changed test system to use generateForcefieldFromMolecules
zhang-ivy
committed

Commits on Nov 12, 2018

Commits on Nov 21, 2018