Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / openforcefield/openff-toolkit issues and pull requests

#1691 - 0.14.3 postrelease

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1690 - Avoid circular import attempting to display "no cheminf toolkits installed" warning

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1689 - Do not assume "method" keyword argument specified in `vdWHandler` 0.3

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1688 - vdWHandler 0.4 does not assume a default value of `method` in up-conversion

Issue - State: closed - Opened by mattwthompson over 1 year ago - 2 comments
Labels: bug, reliability

#1687 - Fix docs builds

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 5 comments

#1686 - 0.14.2 releasenotes

Pull Request - State: closed - Opened by j-wags over 1 year ago - 3 comments

#1685 - Use Pydantic v1 in tests

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1684 - Allow Pydantic v2 in test environments

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#1683 - Do not require OpenMM for tests

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#1681 - 0.14.1 postrelease

Pull Request - State: closed - Opened by j-wags over 1 year ago

#1680 - `ParameterAttribute` does not implement `__delete__`

Issue - State: open - Opened by mattwthompson over 1 year ago
Labels: bug

#1679 - Support version 0.4 of SMIRNOFF vdW section

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 4 comments

#1678 - Support version 0.4 of SMIRNOFF vdW section

Issue - State: closed - Opened by mattwthompson over 1 year ago
Labels: enhancement, smirnoff spec change

#1677 - 0.14.1 release prep

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1676 - [DNM] Remove 0.10.x automation

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#1675 - Improve InChI parsing failure reporting

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1674 - Poor error messages on InChI parsing failures

Issue - State: closed - Opened by mattwthompson over 1 year ago - 1 comment
Labels: error handling

#1673 - Update README

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1672 - ForceField round trip changes Angle parameterize field

Issue - State: open - Opened by ntBre over 1 year ago - 4 comments
Labels: bug, effort:low, priority:medium

#1671 - Render examples without an OpenEye license

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1670 - Wrong atom types while generating gromacs topology

Issue - State: open - Opened by aniketsh over 1 year ago - 7 comments

#1669 - fixed oe wrapper typo

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#1667 - Raise exception when `Topology.from_openmm` is given virtual sites

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1666 - Unhelpful error message when `Topology.from_pdb` fails

Issue - State: open - Opened by mattwthompson over 1 year ago
Labels: error handling

#1665 - 0.14.0 releasenotes

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1664 - Remove `openff.toolkit.typing.chemistry`, attempt 2

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1663 - Revert "Remove `openff.toolkit.typing.chemistry`"

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1662 - Forbid registration of `HierarchyScheme`s with attribute name conflicts

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1661 - Add hierarchy scheme iterators to `Topology`

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#1659 - `HierarchyElement` does not implement equality checks

Issue - State: open - Opened by mattwthompson over 1 year ago - 3 comments

#1658 - Ensure `pytest` finds `conftest.py`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 5 comments

#1657 - Error loading a valid PDB file

Issue - State: open - Opened by peastman over 1 year ago - 3 comments

#1656 - Central examples

Pull Request - State: closed - Opened by Yoshanuikabundi over 1 year ago - 6 comments

#1655 - Remove warnings for undefined stereo

Issue - State: open - Opened by peastman over 1 year ago

#1654 - Fix #1653

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1652 - AmberTools wrapper thread safety

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1651 - Fix broken links in examples

Pull Request - State: closed - Opened by Yoshanuikabundi over 1 year ago - 3 comments

#1650 - Flaky `from_qcschema` tests since QCArchive migration

Issue - State: open - Opened by j-wags over 1 year ago - 4 comments

#1649 - Make tests private(-ish)

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1648 - Refresh examples

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 3 comments

#1647 - Validating the conversion to GROMACS

Issue - State: closed - Opened by 8marmar8 over 1 year ago - 9 comments

#1646 - Standardize typing and 0.13.2 releasenotes

Pull Request - State: closed - Opened by j-wags over 1 year ago - 10 comments

#1645 - Explicitly support well-defined periodic box vectors

Issue - State: open - Opened by mattwthompson over 1 year ago - 1 comment
Labels: interoperability, reliability

#1644 - Update examples to use `Interchange.to_openmm_simulation`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1643 - Make molecule.from_qcschema docstring test also pull a safe set of molecules

Pull Request - State: closed - Opened by j-wags over 1 year ago - 1 comment

#1642 - Assigning partial charges is not thread safe

Issue - State: closed - Opened by peastman over 1 year ago - 17 comments

#1641 - VirtualSiteType.inPlaneAngle and outOfPlaneAngle._unit is None

Issue - State: open - Opened by lilyminium over 1 year ago - 2 comments

#1640 - Fix force field parsing with Pint 0.22 or of OpenFF 2.1.0

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1638 - How to get canonical order transformation

Issue - State: closed - Opened by peastman over 1 year ago - 2 comments

#1637 - Convert ParameterAttribute based on units

Pull Request - State: open - Opened by lilyminium over 1 year ago - 2 comments

#1636 - Fix #1634

Pull Request - State: closed - Opened by j-wags over 1 year ago - 4 comments

#1635 - Not being able to load the 2.1.0 forcefield file

Issue - State: closed - Opened by ijpulidos over 1 year ago - 12 comments

#1633 - Substituting units for "id" attribute

Issue - State: closed - Opened by lilyminium over 1 year ago - 4 comments

#1632 - Our old friend pint has failed us again

Issue - State: closed - Opened by xiki-tempula over 1 year ago - 3 comments

#1631 - Test on Python 3.11

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 4 comments

#1630 - Switch to `setup-micromamba`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1629 - 0.13.1 post release updates

Pull Request - State: closed - Opened by j-wags over 1 year ago

#1628 - 0.13.1 releasenotes

Pull Request - State: closed - Opened by j-wags over 1 year ago

#1627 - [WIP] General polymer implementation

Pull Request - State: closed - Opened by connordavel over 1 year ago - 5 comments

#1626 - Implement improper enumeration on `_SimpleMolecule`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1625 - Solving env

Issue - State: closed - Opened by xperrylinn over 1 year ago - 4 comments

#1624 - Do not rely on wrapped toolkits for improper enumeration

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1623 - Visualization overhaul

Pull Request - State: open - Opened by Yoshanuikabundi over 1 year ago - 1 comment

#1622 - Improve `pathlib` handling

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1621 - `Topology.from_pdb` does not accept `pathlib.Path`

Issue - State: closed - Opened by mattwthompson over 1 year ago

#1619 - Update partial_charges.setter to convert type and give errors

Pull Request - State: closed - Opened by lilyminium over 1 year ago - 3 comments

#1617 - Type charges to float in nagl and when converting to_openeye

Pull Request - State: closed - Opened by lilyminium over 1 year ago - 4 comments

#1616 - non-float partial_charges make to_openeye throw an error

Issue - State: closed - Opened by lilyminium over 1 year ago - 2 comments

#1615 - Niche openeye edge case causing errors in OpenEye generate_conformers

Issue - State: closed - Opened by hmacdope over 1 year ago - 7 comments

#1614 - Remove binder

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1613 - Finish #1606

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1611 - Toolkit is sluggish

Issue - State: open - Opened by Yoshanuikabundi over 1 year ago - 2 comments

#1610 - Passing keyword arguments to underlying toolkits

Issue - State: open - Opened by tlfobe over 1 year ago - 1 comment

#1609 - Return atom map if requested with identical inputs

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1609 - Return atom map if requested with identical inputs

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1607 - isIsomorphic function behaves oddly

Issue - State: closed - Opened by steinbt2 over 1 year ago - 2 comments

#1606 - Fix CI, update examples

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 7 comments

#1605 - Allow version locked licenses of OpenEye Toolkits

Issue - State: open - Opened by joeyulbrichOE over 1 year ago - 1 comment

#1605 - Allow version locked licenses of OpenEye Toolkits

Issue - State: closed - Opened by joeyulbrichOE over 1 year ago - 2 comments

#1604 - Add `Topology.visualize`

Issue - State: open - Opened by mattwthompson over 1 year ago - 3 comments
Labels: enhancement

#1604 - Add `Topology.visualize`

Issue - State: open - Opened by mattwthompson over 1 year ago - 2 comments
Labels: enhancement

#1603 - Remove `Topology._to_openeye`/`Topology._from_openeye`

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 1 comment

#1603 - Remove `Topology._to_openeye`/`Topology._from_openeye`

Pull Request - State: open - Opened by mattwthompson over 1 year ago - 1 comment

#1602 - Remove `Topology._to_openeye`/`Topology._from_openeye`

Issue - State: closed - Opened by mattwthompson over 1 year ago
Labels: code cleanup

#1602 - Remove `Topology._to_openeye`/`Topology._from_openeye`

Issue - State: open - Opened by mattwthompson over 1 year ago
Labels: code cleanup

#1602 - Remove `Topology._to_openeye`/`Topology._from_openeye`

Issue - State: open - Opened by mattwthompson over 1 year ago
Labels: code cleanup

#1601 - Add hierarchy iterators as attributes of `Topology`

Issue - State: open - Opened by mattwthompson over 1 year ago - 2 comments
Labels: enhancement, effort:medium

#1601 - Add hierarchy iterators as attributes of `Topology`

Issue - State: open - Opened by mattwthompson over 1 year ago
Labels: enhancement, effort:medium

#1600 - General polymer implementation with existing from_pdb and rdkit wrapper

Pull Request - State: open - Opened by connordavel over 1 year ago - 3 comments

#1600 - General polymer implementation with existing from_pdb and rdkit wrapper

Pull Request - State: closed - Opened by connordavel over 1 year ago - 5 comments

#1599 - Test against AmberTools 23RC6

Pull Request - State: closed - Opened by mattwthompson over 1 year ago - 2 comments

#1598 - `Topology.from_openmm` chokes on virtual sites

Issue - State: closed - Opened by mattwthompson over 1 year ago
Labels: reliability

#1598 - `Topology.from_openmm` chokes on virtual sites

Issue - State: open - Opened by mattwthompson over 1 year ago
Labels: reliability