openforcefield/openff-fragmenter

Issues

• Fragmentation failed

  #177 opened 5 months ago by okbckim
  2

• Use xtb for the WBO

  #160 opened a year ago by jthorton
  2

• Skip OpenEye functions if license not found, even if installed

  #163 opened a year ago by mattwthompson
  0

• Fragmentation issue because of stereochem when the bond involves Sulfur

  #127 opened 3 years ago by rvkrishnan30
  3

• Provide a way to map from `WBOFragmenter` input molecule to parent molecule

  #129 opened 3 years ago by j-wags
  1

• Expand states generates different SMILES

  #33 opened 3 years ago by ChayaSt
  0

• Add API docs pages for all modules

  #48 opened 3 years ago by jchodera
  0

• Fragments have missing stereochemistry

  #62 opened 3 years ago by jthorton
  2

• `find_rotatable_bonds` fails unless an atom map is present

  #128 opened 3 years ago by j-wags
  1

• fragmented molecule atom mapping rearrangement

  #126 opened 3 years ago by ldamore
  3

• Return parent fragment mapping

  #59 opened 4 years ago by jthorton
  2

• Grow fragments when stereochemistry can not be fixed

  #118 opened 3 years ago by jthorton
  0

• Refactor into an OpenFF namespace

  #97 opened 3 years ago by SimonBoothroyd
  0

• Omega returned error code 0

  #66 opened 3 years ago by ewu20
  1

• Fragmentation API

  #49 opened 4 years ago by jchodera
  18

• Make fragmenters stateless

  #98 opened 4 years ago by SimonBoothroyd
  0

• How to handle multiple starting conformation for coupled torsions

  #29 opened 4 years ago by ChayaSt
  1

• Flag torsions in linear molecules

  #21 opened 4 years ago by ChayaSt
  1

• Multiple torsions found for the same central bond

  #23 opened 4 years ago by ChayaSt
  1

• Support openforcefield.topology.Molecule?

  #50 opened 4 years ago by jchodera
  2

• Charging molecules while only returning the original coordinates returns a wonky molecule

  #55 opened 4 years ago by ChayaSt
  1

• Ideas for future refactor

  #60 opened 4 years ago by mattwthompson
  1

• Fragmentation fails with new openeye toolkit.

  #61 opened 4 years ago by jthorton
  2

• Functional groups on rings do not come along with ring

  #51 opened 4 years ago by ChayaSt
  1

• Wiberg Order Not Found

  #65 opened 4 years ago by ewu20
  2

• Segmentation Fault

  #64 opened 4 years ago by ewu20
  5

• Handle different charging failures appropriately

  #52 opened 5 years ago by ChayaSt
  0

• Cutting a release

  #37 opened 5 years ago by jchodera
  7

• Update openeye license

  #45 opened 5 years ago by jchodera
  0

• What happened to fragment.expand_states()?

  #44 opened 5 years ago by jchodera
  1

• Move openeye imports inside functions that need them

  #40 opened 5 years ago by jchodera
  1

• Write documentation

  #41 opened 5 years ago by jchodera
  1

• Tautomers and protonation state

  #6 opened 5 years ago by ChayaSt
  2

• Atom map from substructure match flips indices for symmetrical atoms

  #27 opened 5 years ago by ChayaSt
  4

• chirality of fragments sometimes flip

  #34 opened 5 years ago by ChayaSt
  0

• Add tests for QCPortal

  #20 opened 5 years ago by ChayaSt
  0

• Canonical SMILES generation

  #9 opened 6 years ago by ChayaSt
  1

• Fragment JSON

  #16 opened 6 years ago by dgasmith
  4

• Stereochemistry

  #5 opened 6 years ago by ChayaSt
  6