openforcefield/openff-toolkit
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
PythonMIT
Pinned issues
Issues
- 2
- 20
Infer bond orders and formal charges
#1828 opened by peastman - 5
- 0
Confusing `HierarchyElement.__str__()`
#1924 opened by mattwthompson - 2
`Topology.identical_molecule_groups` is slow and order-dependent with some `_SimpleMoleucles`
#1917 opened by mattwthompson - 1
`Topology.add_molecule` returns 1-indexed indices, toolkit elsewhere uses 0-index
#1922 opened by mattwthompson - 1
`Topology.add_molecule` is slow when adding many molecules to a topology
#1916 opened by mattwthompson - 1
- 23
Partial charge methods fail in clean environment
#1911 opened by slochower - 3
Unable to load some SDFs with RDKit backend
#1909 opened by j-wags - 2
to_inchi() returns empty string on failure
#1897 opened by lilyminium - 0
Improve citation guidelines
#1905 opened by mattwthompson - 6
Openeye license check
#1896 opened by insukjoung - 1
Partial Charges for Rare Atoms
#1903 opened by maciejwisniewski-drugdiscovery - 4
Assign Partial Charges for many conformers of Small Molecule
#1901 opened by maciejwisniewski-drugdiscovery - 4
Error calling ambertools
#1900 opened by velocirraptor23 - 2
OpenEye license check in OpenEyeToolkitWrapper
#1895 opened by isty2e - 1
- 1
- 0
Generating conformers with some single ions in OpenEye results in additional ghost atoms
#1892 opened by lilyminium - 6
how to describe a terminal atom type with openff
#1876 opened by Lili-Cao - 4
Is it possible to use the same parameters in `openmm.app.Forcefield.createSystem` for openff Forcefield objects
#1877 opened by WillGPoole - 1
Broken link for PR checklist regarding changelog
#1879 opened by ethanholz - 1
- 4
openff.toolkit.Molecule unable to parse molecule in .sdf file, but is ok with parsing from rdkit
#1872 opened by David-Araripe - 3
- 2
- 1
Virtual site parameter lookups should return multiple (or no?) parameters if multiple have the same SMIRKS
#1857 opened by mattwthompson - 0
`Topology.set_positions` chokes when setting positions on `_SimpleMolecule`s which lacked conformers
#1867 opened by mattwthompson - 2
- 4
Add method for deleting conformer(s)
#1841 opened by mattwthompson - 0
- 2
openff.toolkit.topology.Molecule.from_openeye would add atoms to the molecule where it shouldn't
#1860 opened by xiki-tempula - 3
The toolkit showcase stochastically fails with OMP_NUM_THREADS=1 and AmberToolsToolkitWrapper
#1842 opened by Yoshanuikabundi - 4
oemol.GetConfs() consuming large amount of memory even when no conformers are present
#1855 opened by lilyminium - 9
- 2
- 0
- 0
Update FAQ
#1848 opened by mattwthompson - 0
Unused, undocumented argument `assume_missing_is_default` in `check_handler_compatibility`
#1843 opened by mattwthompson - 0
- 3
Allow `Topology.set_positions(None)`
#1820 opened by mattwthompson - 0
Change defaults and allow configuration of Antechamber charge assignment threads
#1831 opened by Yoshanuikabundi - 2
`Topology.from_pdb(_additional_substructures=...` can use a LOT of memory
#1829 opened by Yoshanuikabundi - 6
- 0
Preserve hierarchy metadata in `_SimpleMolecule`
#1810 opened by mattwthompson - 2
- 2
Error for molecular contains boron element.
#1806 opened by Aunity - 1
ForceField.parse_sources fails when given a string
#1803 opened by ntBre - 3