Software Open Access
David L. Mobley; Jeff Wagner; John Chodera; Caitlin Bannan; Andrea Rizzi; Camila; Christopher Bayly; SimonBoothroyd; Nathan M. Lim; Victoria Lim; Yutong Zhao; Lee-Ping
This update fixes several toolkit bugs that have been reported by the community. Details of these bugfixes are provided below.
It also refactors how
ParameterHandler store their attributes, by introducing
IndexedParameterAttribute. These new attribute-handling classes provide a consistent backend which should simplify manipulation of parameters and implementation of new handlers.
A richer version of these release notes with live links to API documentation is available on our ReadTheDocs page
See our installation instructions.
Please report bugs, request features, or ask questions through our issue tracker.
Please note that there may still be some changes to the API prior to a stable 1.0.0 release.Bug fixes
lengthwere treated as indexed attributes. (per the SMIRNOFF spec,
lengthvalues that correspond to specific bond orders will be indexed under
k_bondorder2, etc when implemented in the future)
ImproperTorsionHandlerexposed non-functional indexed parameters.
FrozenMoleculeconstructor and several other Molecule-construction functions ignored or did not expose the
ForceField(now instructs users to specify
RDKitToolkitWrapper.from_smilesto make implicit hydrogens explicit before molecule creation. These functions also now raise an error if the optional keyword
hydrogens_are_explicit=Truebut the SMILES are interpreted by the backend cheminformatics toolkit as having implicit hydrogens.
SMIRFFtag is present only in legacy files. Since developing a formal specification, the only acceptable top-level tag value in a SMIRNOFF data structure is
ParameterTypewas refactored to improve its extensibility. It is now possible to create new parameter types by using the new descriptors
test_forcefields/smirnoff99frosst_experimental.offxmlto address hierarchy problems, redundancies, SMIRKS pattern typos etc., as documented in issue #367. Will ultimately be propagated to an updated forcefield in the
test_forcefields/smirff99Frosst_reference_0_1_spec.offxml, a SMIRNOFF 0.1 spec file enclosed by the legacy
SMIRFFtag. This file is used in backwards-compatibility testing.