Iván Pulido
Iván Pulido
We need to double check if we are using the FireMinimizer from openmmtools in our small molecule pipeline.
We now have a long standing 0.10.x branch that will hold the current stable release of perses. Before we do the big refactor of the API for the 0.11 (or...
## Description More intuitive handling of minimization steps argument `minimisation_steps` ## Motivation and context `minimisation_steps` should work like this instead: * None should be interpreted to run until tolerance is...
## Description This changes the `RelativeFEPSetup` to accept a list of smiles as input. It does it by trying to read the input parameter as smiles using the `openff.toolkit.Molecule` object...
We need to create a legacy branch for 0.10.x and move the `gufe` supporting branch to `main`.
According to the documentation, `RelativeFEPSetup` should be able to handle a list of SMILES strings as input ligands but it makes the interpreter to freeze giving the following warnings: ```...
Pymbar supports bootstrapping since 3.1, we should use it by default in perses.
When working in #1125 it was noted that the `SmallMoleculeSetProposalEngine._constraint_repairs` would benefit from handling `perses.rjmc.atom_mapping.AtomMapping` objects for both input and output. In that way we don't have to rely on...
I'm seeing this error: ``` FAILED openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_partial_charges_are_none - RuntimeError: C=O could not be fully assigned charges. Charges were assigned to atoms set() but the molecule contains {0, 1, 2, 3}....
The openff toolkit allows specifying different methods for assigning partial charges to the molecules via [keyword arguments](https://github.com/openforcefield/openff-toolkit/blob/779565b8e5b676e3a194d15af429a89ca0fbfa5c/openff/toolkit/topology/molecule.py#L2490). Should `openmmforcefields` add support for specifying the backend/wrapper and the method when parameterizing...